Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008504.1 Hibiscus syriacus cultivar Beakdansim tig00111356_pilon, 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: 2056749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 10
Found at i:2486 original size:14 final size:15
Alignment explanation
Indices: 2459--2487 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2449 CCACGGTGCT
2459 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
2474 CCCGGAA-CCTGCGC
1 CCCGGAATCCTGCGC
2488 GATTGTGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.48, G:0.28, T:0.10
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:12140 original size:15 final size:15
Alignment explanation
Indices: 12122--12151 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12112 CCACGGTGCT
12122 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
12137 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
12152 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:16996 original size:15 final size:15
Alignment explanation
Indices: 16978--17007 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
16968 CCACGGTGCT
16978 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
16993 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
17008 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:21301 original size:22 final size:22
Alignment explanation
Indices: 21276--21327 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
21266 AAAGAACCGA
*
21276 AAAACATGCCA-AAAAGCATAAG
1 AAAACAT-CCATAAAAGCAGAAG
* *
21298 AAAACATCCATAAAGGCAGATG
1 AAAACATCCATAAAAGCAGAAG
21320 AAAACATC
1 AAAACATC
21328 TAATAGAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.56, C:0.19, G:0.13, T:0.12
Consensus pattern (22 bp):
AAAACATCCATAAAAGCAGAAG
Found at i:28720 original size:20 final size:21
Alignment explanation
Indices: 28684--28723 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
28674 TGGGATGAGA
28684 TTTATATAAATAAATATAATT
1 TTTATATAAATAAATATAATT
*
28705 TTTATATTAA-AAATATAAT
1 TTTATATAAATAAATATAAT
28724 AAATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTATATAAATAAATATAATT
Found at i:30918 original size:81 final size:81
Alignment explanation
Indices: 30804--31098 Score: 484
Period size: 81 Copynumber: 3.6 Consensus size: 81
30794 ATTTTTAACT
* *
30804 GTTCATCTAACTGTCATAATTGGTACTTTTCTACCAATTGCACAATTAGGCCATTATTCCTTTAC
1 GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAATTAGGCCATTATTCCTTTAC
30869 TCAACGGTATTAAACTC
66 TCAACGGTATTAAAC-C
* *
30886 -TTTATCTAACTGGCATAATTGGTACCTTTCTACTAATTGCACAATTAGGCCATTATTCCTTTAC
1 GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAATTAGGCCATTATTCCTTTAC
30950 TCAACGGTATTAAACC
66 TCAACGGTATTAAACC
* *
30966 GTTCATCTAACTGGCATAATTGATACCTTTTTACCAATTGCACAATTAGGCCATTATTCCTTTAC
1 GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAATTAGGCCATTATTCCTTTAC
31031 TCAACGGTATTAAACC
66 TCAACGGTATTAAACC
* * * *
31047 GTTCATGTAATTGGCATAATTGGTATCTTTCTACCAATTGCACAGTTAGGCC
1 GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAATTAGGCC
31099 TCAAAGGCAC
Statistics
Matches: 198, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
80 1 0.01
81 197 0.99
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (81 bp):
GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAATTAGGCCATTATTCCTTTAC
TCAACGGTATTAAACC
Found at i:31165 original size:68 final size:68
Alignment explanation
Indices: 31086--31436 Score: 587
Period size: 68 Copynumber: 5.2 Consensus size: 68
31076 TCTACCAATT
** *
31086 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTTTTCTAACTTGCTTATATGACACCTTTCTGTCA
1 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCA
31151 TAA
66 TAA
*
31154 GCACAGTTAGGCCTCAGAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCA
1 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCA
*
31219 TGA
66 TAA
* ** *
31222 GTACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATAAAACTGGCTTATATGATACCTTTCTGTCA
1 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCA
31287 TAA
66 TAA
*
31290 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGTTTATATGACACCTTTCTGTCA
1 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCA
31355 TAA
66 TAA
*
31358 GCACAGTT-GGCCTCAAAGGCACTTAACCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCA
1 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCA
31422 TAA
66 TAA
*
31425 TCACAGTTAGGC
1 GCACAGTTAGGC
31437 ATATTAATCT
Statistics
Matches: 263, Mismatches: 19, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
67 64 0.24
68 199 0.76
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (68 bp):
GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCA
TAA
Found at i:31783 original size:59 final size:56
Alignment explanation
Indices: 31690--31818 Score: 159
Period size: 58 Copynumber: 2.2 Consensus size: 56
31680 TCTTATTTCA
* * * * * *
31690 CACACATAGTGCCCATACAGAATTTCATACACTTAGTGTGTATTTCTTAATATTTTAG
1 CACACATAGTGCCAATACAGAAATTCATACACTTAGTATG-AATTATTAACATTTT-G
*
31748 CACACATAGTGCTCAATACTGAAATTCATACACTTAGTATGAATTATTAACATTTTG
1 CACACATAGTGC-CAATACAGAAATTCATACACTTAGTATGAATTATTAACATTTTG
*
31805 CACACTTAGTGCCA
1 CACACATAGTGCCA
31819 TTTGGTAATA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
56 2 0.03
57 12 0.19
58 24 0.39
59 24 0.39
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (56 bp):
CACACATAGTGCCAATACAGAAATTCATACACTTAGTATGAATTATTAACATTTTG
Found at i:38561 original size:20 final size:21
Alignment explanation
Indices: 38536--38576 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
38526 TTGTTTGGCT
38536 CTAAATG-GAACCATTCAACG
1 CTAAATGCGAACCATTCAACG
*
38556 CTAAATGCTGAACCGTTCAAC
1 CTAAATGC-GAACCATTCAAC
38577 ATTCAGACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.22
Consensus pattern (21 bp):
CTAAATGCGAACCATTCAACG
Found at i:50654 original size:15 final size:15
Alignment explanation
Indices: 50636--50667 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
50626 GCAAATGTGA
*
50636 GTGCATGTTTAATTT
1 GTGCATATTTAATTT
50651 GTGCATATTTAATTT
1 GTGCATATTTAATTT
50666 GT
1 GT
50668 ACTTATGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.06, G:0.19, T:0.53
Consensus pattern (15 bp):
GTGCATATTTAATTT
Found at i:54974 original size:34 final size:35
Alignment explanation
Indices: 54906--54989 Score: 127
Period size: 34 Copynumber: 2.4 Consensus size: 35
54896 GGTTAAGATT
*
54906 AAATCCTACCTAACACCAAATCCCTTAAATCAAGG
1 AAATCCCACCTAACACCAAATCCCTTAAATCAAGG
*
54941 AATTCCCACCTAACACC-AATCTCC-TAAATCAAGG
1 AAATCCCACCTAACACCAAATC-CCTTAAATCAAGG
54975 AAATCCCACCTAACA
1 AAATCCCACCTAACA
54990 TTAACCTTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.62
35 17 0.38
ACGTcount: A:0.42, C:0.35, G:0.05, T:0.19
Consensus pattern (35 bp):
AAATCCCACCTAACACCAAATCCCTTAAATCAAGG
Found at i:59928 original size:15 final size:15
Alignment explanation
Indices: 59904--59936 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
59894 TATATTGTCA
59904 TTAGTTA-TTTCTAT
1 TTAGTTATTTTCTAT
59918 TTAGCTTATTTTCTAT
1 TTAG-TTATTTTCTAT
59934 TTA
1 TTA
59937 ATATGCAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 3 0.18
16 10 0.59
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.64
Consensus pattern (15 bp):
TTAGTTATTTTCTAT
Found at i:61433 original size:37 final size:37
Alignment explanation
Indices: 61357--61433 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
61347 TTTTTATATT
*
61357 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* *
61394 TTTAATGTTT-TAAAGAAAA-TATATAAATATTTTACAA
1 TTTAAT-TTTGTAAAAAAAATTATATAAATATTAT-CAA
61431 TTT
1 TTT
61434 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 19 0.54
38 3 0.09
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.45
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:61613 original size:20 final size:20
Alignment explanation
Indices: 61577--61614 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
61567 ATCCTATTCC
*
61577 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTCATTCCCA
61597 CTGGTAAT-TTTACATTCC
1 CTGGTAATCTTT-CATTCC
61615 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTTCATTCCCA
Found at i:69501 original size:3 final size:3
Alignment explanation
Indices: 69493--69518 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
69483 ATTAACATTG
69493 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
69519 ACTACTTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:77229 original size:21 final size:21
Alignment explanation
Indices: 77199--77238 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
77189 ATATAAAATT
77199 TGTCCAGAAGGACCTCATATA
1 TGTCCAGAAGGACCTCATATA
*
77220 TGTCCCGAAGGACCTCATA
1 TGTCCAGAAGGACCTCATA
77239 GAACCCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (21 bp):
TGTCCAGAAGGACCTCATATA
Found at i:79527 original size:17 final size:17
Alignment explanation
Indices: 79505--79606 Score: 78
Period size: 17 Copynumber: 5.9 Consensus size: 17
79495 GCATCTTAAA
*
79505 TCATTCATTAAACTACT
1 TCATTCATTAAACTAGT
** *
79522 TCATTCATGCAATTAGT
1 TCATTCATTAAACTAGT
* * *
79539 TAAATTCAATAAAGTTAGT
1 T-CATTCATTAAA-CTAGT
* *
79558 TCTTTAATTAAACTAGT
1 TCATTCATTAAACTAGT
* *
79575 TCATTTATTTAACTAGT
1 TCATTCATTAAACTAGT
*
79592 TCATTAATTAAACTA
1 TCATTCATTAAACTA
79607 AGCCTTTAAT
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
17 45 0.69
18 14 0.22
19 6 0.09
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (17 bp):
TCATTCATTAAACTAGT
Found at i:82993 original size:45 final size:42
Alignment explanation
Indices: 82901--83008 Score: 117
Period size: 44 Copynumber: 2.5 Consensus size: 42
82891 ATACGTATAC
* *
82901 TATATATATATTTTAAAAGCAATATTTTTTCAAAAACTATAAAA
1 TATATATATATTTTAAAA--ACTATGTTTTCAAAAACTATAAAA
* **
82945 TATATATCATATTTTCAAAAACTATGTTTTCAAAAACTGTATGTA
1 TATATAT-ATATTTT-AAAAACTATGTTTTCAAAAACTATA-AAA
*
82990 TATATATATACTTTAAAAA
1 TATATATATATTTTAAAAA
83009 AACTATATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
43 5 0.09
44 31 0.56
45 15 0.27
46 4 0.07
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (42 bp):
TATATATATATTTTAAAAACTATGTTTTCAAAAACTATAAAA
Found at i:83009 original size:44 final size:43
Alignment explanation
Indices: 82901--83014 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 43
82891 ATACGTATAC
*
82901 TATATATATATTTTAAAAGCAA-TATTTTTTCAAAAACTATAAAA
1 TATATATATATTTTAAAA--AACTATGTTTTCAAAAACTATAAAA
* * **
82945 TATATATCATATTTTCAAAAACTATGTTTTCAAAAACTGTATGTA
1 TATATAT-ATATTTTAAAAAACTATGTTTTCAAAAACTATA-AAA
*
82990 TATATATATACTTTAAAAAAACTAT
1 TATATATATA-TTTTAAAAAACTAT
83015 ATATATATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
43 2 0.03
44 27 0.46
45 30 0.51
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (43 bp):
TATATATATATTTTAAAAAACTATGTTTTCAAAAACTATAAAA
Found at i:83071 original size:26 final size:24
Alignment explanation
Indices: 82988--83071 Score: 64
Period size: 24 Copynumber: 3.5 Consensus size: 24
82978 AAACTGTATG
* **
82988 TATA-TATATATACTTTAAAAAAA
1 TATACTATATATATTTTAAAATTA
83011 CTATA-TATATATATTTTAAAATTA
1 -TATACTATATATATTTTAAAATTA
* * * *
83035 TATAGTTTATATTTTTTGAAATTA
1 TATACTATATATATTTTAAAATTA
83059 TACATACTATATA
1 T--ATACTATATA
83072 ATATAAATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
23 4 0.08
24 37 0.76
26 8 0.16
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (24 bp):
TATACTATATATATTTTAAAATTA
Found at i:86253 original size:25 final size:24
Alignment explanation
Indices: 86215--86262 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
86205 TGAAAATAAA
*
86215 ATAAAAATTGCATAACATACATAC
1 ATAAAAATTACATAACATACATAC
*
86239 ATAAAAATGTACATACCATACATA
1 ATAAAAAT-TACATAACATACATA
86263 AAATAGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.54, C:0.17, G:0.04, T:0.25
Consensus pattern (24 bp):
ATAAAAATTACATAACATACATAC
Found at i:87872 original size:15 final size:15
Alignment explanation
Indices: 87852--87886 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
87842 CCGTAGGACC
87852 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
87867 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
87882 ACTAC
1 ACTAC
87887 AGAACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:94726 original size:15 final size:15
Alignment explanation
Indices: 94706--94740 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
94696 CCGTAGGACC
94706 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
94721 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
94736 ACTAC
1 ACTAC
94741 AGAACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:97363 original size:55 final size:55
Alignment explanation
Indices: 97307--97665 Score: 482
Period size: 53 Copynumber: 6.6 Consensus size: 55
97297 CGGGTTCGCT
* * * * * * *
97307 CCCTCTTTCTTTAGAGAGTAT-AGAACTCGGATAATCTTCAATAATCATGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGTGTCTGCC
* *
97362 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCC
*
97415 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAATCGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCC
* * *
97468 CCCTATTTCTTCAGAGAGTATAAAACTCGAACAATCTTCAACAATCGCGTCTGTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCC
* *
97523 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCC
* * *
97578 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATA-AATCGCGTATGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCA-ACAATCGTGTCTGCC
97631 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
97666 TCCATCAAAC
Statistics
Matches: 278, Mismatches: 20, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
53 144 0.52
54 5 0.02
55 127 0.46
56 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (55 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCC
Found at i:97424 original size:108 final size:108
Alignment explanation
Indices: 97307--97665 Score: 517
Period size: 108 Copynumber: 3.3 Consensus size: 108
97297 CGGGTTCGCT
* * * * * * *
97307 CCCTCTTTCTTTAGAGAGTAT-AGAACTCGGATAATCTTCAATAATCATGTCTGCTCCCTATTTC
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTC
*
97371 TTCAGAGAGTATAAGACCCACAATCTTCATCAATCGTGTCTGCC
65 TTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
*
97415 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
* * * *
97478 TCAGAGAGTATAAAACTCGAACAATCTTCAACAATCGCGTCTGTC
66 TCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
* *
97523 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
* *
97588 TCAGAGAGTATAAGACCCACAATCTTCATAAATCGCGTATGCC
66 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
97631 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
97666 TCCATCAAAC
Statistics
Matches: 225, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
106 46 0.20
107 2 0.01
108 125 0.56
109 4 0.02
110 48 0.21
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (108 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
Found at i:98738 original size:33 final size:33
Alignment explanation
Indices: 98676--98740 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
98666 AACCCTCATT
* *
98676 TTTTCATTCATTTTTTATTTTTTTATTTTTTCA
1 TTTTCACTCATTTTTTATTTTCTTATTTTTTCA
*
98709 TTTTCACTCATTTTTT-TTCTTCTTCTTTTTTC
1 TTTTCACTCATTTTTTATT-TTCTTATTTTTTC
98741 TTCAAGCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (33 bp):
TTTTCACTCATTTTTTATTTTCTTATTTTTTCA
Found at i:108716 original size:16 final size:16
Alignment explanation
Indices: 108695--108732 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
108685 AACCTTATTC
108695 ACATGATATCTACCCA
1 ACATGATATCTACCCA
108711 ACATGATATCTACCCA
1 ACATGATATCTACCCA
108727 ATCATG
1 A-CATG
108733 CTTTAGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (16 bp):
ACATGATATCTACCCA
Found at i:110536 original size:25 final size:24
Alignment explanation
Indices: 110498--110545 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
110488 TGAAAATAAA
*
110498 ATAAAAATTGCATAACATACATAC
1 ATAAAAATTACATAACATACATAC
*
110522 ATAAAAATGTACATACCATACATA
1 ATAAAAAT-TACATAACATACATA
110546 AAATAGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.54, C:0.17, G:0.04, T:0.25
Consensus pattern (24 bp):
ATAAAAATTACATAACATACATAC
Found at i:112651 original size:11 final size:11
Alignment explanation
Indices: 112632--112663 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
112622 CCTAAGCATT
112632 AAAAGAAAAAA
1 AAAAGAAAAAA
*
112643 AAGAGAAAAAA
1 AAAAGAAAAAA
112654 AAAAGAAAAA
1 AAAAGAAAAA
112664 TAATGTAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:114065 original size:2 final size:2
Alignment explanation
Indices: 114058--114113 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
114048 TAAGCGAATT
114058 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
114100 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
114114 AAAGAGAGAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:124167 original size:20 final size:20
Alignment explanation
Indices: 124144--124193 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
124134 GCAAAAGTTG
124144 ATTTTGAAAATCAAAATAAA
1 ATTTTGAAAATCAAAATAAA
*
124164 ATTTTGAAAATCAAAATGAA
1 ATTTTGAAAATCAAAATAAA
124184 ATTTTGAAAA
1 ATTTTGAAAA
124194 ATGACTTAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (20 bp):
ATTTTGAAAATCAAAATAAA
Found at i:127171 original size:61 final size:60
Alignment explanation
Indices: 127106--127305 Score: 163
Period size: 61 Copynumber: 3.1 Consensus size: 60
127096 TTATTGGAAA
127106 TTTAAGAATTAAAAAATATATTTAATTCATAATCTTGTTATTTAAAATTTATTAATATATT
1 TTTAAGAATTAAAAAATATATTTAATTCATAATCTTGTTATTTAAAATTTATTAATATA-T
* * ** *
127167 TTTAAGAAAATATAAAATATAAAACCTAAAGATTC-TAAT-TTGAATTATTAAAAAGATATGTAT
1 TTTAAG--AAT-TAAAAAAT-ATA--TTTA-ATTCATAATCTTG--TTATT-TAAA-AT-T-TAT
127230 TAATA-AT
53 TAATATAT
* * * *
127237 TTTAAGAAATCAAAAATATATTTAATTCATAATCATGTTATTTCAAATTTATTAATATAAT
1 TTTAAGAATTAAAAAATATATTTAATTCATAATCTTGTTATTTAAAATTTATTAATAT-AT
127298 TTTAAGAA
1 TTTAAGAA
127306 AATATATTAA
Statistics
Matches: 108, Mismatches: 14, Indels: 34
0.69 0.09 0.22
Matches are distributed among these distances:
59 8 0.07
60 1 0.01
61 18 0.17
62 2 0.02
63 12 0.11
64 13 0.12
65 4 0.04
66 5 0.05
67 12 0.11
68 11 0.10
69 3 0.03
70 9 0.08
71 2 0.02
72 8 0.07
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (60 bp):
TTTAAGAATTAAAAAATATATTTAATTCATAATCTTGTTATTTAAAATTTATTAATATAT
Found at i:127445 original size:18 final size:18
Alignment explanation
Indices: 127411--127445 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
127401 TCCATTTCTT
*
127411 AATATTAAAAAATAAATA
1 AATATTAAAAAACAAATA
*
127429 AATATTAATAAACAAAT
1 AATATTAAAAAACAAAT
127446 TCTATAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AATATTAAAAAACAAATA
Found at i:127689 original size:3 final size:3
Alignment explanation
Indices: 127681--127716 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
127671 TATATGACTA
*
127681 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
127717 TAAACATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:129652 original size:124 final size:126
Alignment explanation
Indices: 129398--129734 Score: 424
Period size: 124 Copynumber: 2.7 Consensus size: 126
129388 GAATTAAGGC
* * * * *
129398 AAGGTTGAGCAAGTTATTCTTATTATGAACTTCTT-TTCATTCTTCATATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATGAGTTCTTCTCATTA
* **
129462 TGAAC-ACT-TCTGG--AAATGTTGATGCTGATATATCTCCTTCTGTGATAGAGTCATGCAA
65 TGAACTATTCTCTGGAAAAATGTTGATGCTGATATATCTCCTTCTACGATAGAGTCATGCAA
* * *
129520 AAGATTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCGTTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * *
129585 GAACTATTCTCTGGAAAAATG-T-ATGTTGATCTATCTCCTTCTACGATAGAGTCATGTAA
66 GAACTATTCTCTGGAAAAATGTTGATGCTGATATATCTCCTTCTACGATAGAGTCATGCAA
* * * * *
129644 AAGGTTGAACAAGTTCTTCTCATAATGAACTTCTTCTTCCTCTTTAGATAAGTTATTCTTATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
129709 GAACT-TTCTCTGG-AAAA-GTTGATGCT
66 GAACTATTCTCTGGAAAAATGTTGATGCT
129735 AATCTAGTGA
Statistics
Matches: 185, Mismatches: 23, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
121 1 0.01
122 62 0.34
123 17 0.09
124 99 0.54
125 1 0.01
126 5 0.03
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (126 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTATTCTCTGGAAAAATGTTGATGCTGATATATCTCCTTCTACGATAGAGTCATGCAA
Found at i:129774 original size:114 final size:122
Alignment explanation
Indices: 129398--129789 Score: 346
Period size: 124 Copynumber: 3.3 Consensus size: 122
129388 GAATTAAGGC
* * * * * * *
129398 AAGGTTGAGCAAGTTATTCTTATTATGAACTTCTT-TTCATTCTTCATATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATAAGTTATTCTCATTA
* * * * *
129462 TGAAC-ACT-TCTGG--AAATGTTGATGCTGA-TATATCTCCTTCTGTGATAGAGTCATGCAA
65 TGAACTATTCTCTGGAAAAATG-T-ATGATGACTATA--TCCTACT-AGATAGAGTCAAGCAA
* * * * *
129520 AAGATTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCGTTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTATTCTCATTAT
* * * * *
129585 GAACTATTCTCTGGAAAAATGTATGTTGATCTATCTCCTTCTACGATAGAGTCATGTAA
66 GAACTATTCTCTGGAAAAATGTATGATGA-CTATATCCTACTA-GATAGAGTCAAGCAA
* * *
129644 AAGGTTGAACAAGTTCTTCTCATAATGAACTTCTTCTTCCTCTTTAGATAAGTTATTCTTATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTATTCTCATTAT
* *
129709 GAACT-TTCTCTGG-AAAA-GT-TGATG-CTA-AT-CTAGT-GAT-GAATTCAAGCAA
66 GAACTATTCTCTGGAAAAATGTATGATGACTATATCCTACTAGATAG-AGTCAAGCAA
*
129758 AAGGTTGAATAAGTTCTTCTCATTATGAACTT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTT
129790 TCTCTGGAAA
Statistics
Matches: 231, Mismatches: 30, Indels: 26
0.80 0.10 0.09
Matches are distributed among these distances:
113 1 0.00
114 40 0.17
116 3 0.01
117 1 0.00
118 3 0.01
120 4 0.02
121 2 0.01
122 61 0.26
123 13 0.06
124 94 0.41
125 1 0.00
126 8 0.03
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (122 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTATTCTCATTAT
GAACTATTCTCTGGAAAAATGTATGATGACTATATCCTACTAGATAGAGTCAAGCAA
Found at i:129846 original size:73 final size:75
Alignment explanation
Indices: 129691--129862 Score: 276
Period size: 73 Copynumber: 2.3 Consensus size: 75
129681 TCCTCTTTAG
* * * *
129691 ATAAGTTATTCTTATTATGAACTTTCTCTGGAAAAGTTGATGCTAATCTAGTGATGAATTCAAGC
1 ATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTAACCGAGTGATGAATTCAAGC
129756 AAAAGGTTGA
66 AAAAGGTTGA
* *
129766 ATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGAT-C-CACCGAGTGATGAATTCAAGC
1 ATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTAACCGAGTGATGAATTCAAGC
129829 AAAAGGTTGA
66 AAAAGGTTGA
129839 ATAAGTTCTTCTCATTATGAACTT
1 ATAAGTTCTTCTCATTATGAACTT
129863 CTTTTTCCTT
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
73 52 0.57
74 1 0.01
75 38 0.42
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (75 bp):
ATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTAACCGAGTGATGAATTCAAGC
AAAAGGTTGA
Found at i:129898 original size:113 final size:113
Alignment explanation
Indices: 129769--130164 Score: 616
Period size: 113 Copynumber: 3.5 Consensus size: 113
129759 AGGTTGAATA
* * *
129769 AGTTCTTCTCATTATGAACT-TTCTCTGGAAAGGTTGATCCACCGAGTGATGAATTCAAGCAAAA
1 AGTTCTTCTCATTATGAACTCTAC-CTGGAAATGTTGATCCATCGAGTGATGAATTCAAGCAAAA
*
129833 GGTTGAATAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATG
65 GGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * *
129882 AGTTCTTCTCATTATGAACTCTACCTGGCAATGATGATCCATCAAGTGATGAATTCAAGCAAAAG
1 AGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCGAGTGATGAATTCAAGCAAAAG
*
129947 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * * *
129995 AGTTCTTCTCATTATGAACTCGACCTGGCAATGTTAATCCATCGAGTGATGAATTAAAGCAAAAG
1 AGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCGAGTGATGAATTCAAGCAAAAG
*
130060 GTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATG
66 GTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * * *
130108 AGTTCTTCTCATTATGAACTCT-TCTGGAAATGCTGATCCATCGAGTAATGGATTCAA
1 AGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCGAGTGATGAATTCAA
130165 ATCTTTGCTA
Statistics
Matches: 259, Mismatches: 23, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
112 28 0.11
113 229 0.88
114 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.36
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCGAGTGATGAATTCAAGCAAAAG
GTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:131230 original size:29 final size:30
Alignment explanation
Indices: 131184--131264 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
131174 CCGAAGGACA
* *
131184 TATCCAGAGATCACAAAG-ACCCCGGTAAC
1 TATCCAGAGGTCACAAAGAACCCCGGCAAC
* *
131213 TATCCAGAGGTCATAAAGAACCTCGGCAAC
1 TATCCAGAGGTCACAAAGAACCCCGGCAAC
* * *
131243 TGTCCATAGGTCCCAAAGAACC
1 TATCCAGAGGTCACAAAGAACC
131265 TAGGTAAACT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 16 0.37
30 27 0.63
ACGTcount: A:0.36, C:0.30, G:0.19, T:0.16
Consensus pattern (30 bp):
TATCCAGAGGTCACAAAGAACCCCGGCAAC
Found at i:131254 original size:30 final size:31
Alignment explanation
Indices: 131194--131281 Score: 83
Period size: 30 Copynumber: 2.9 Consensus size: 31
131184 TATCCAGAGA
** * *
131194 TCACAAAG-ACCCCGGT-AACTATCCAGAGG
1 TCACAAAGAACCTAGGTAAACTGTCCATAGG
* * *
131223 TCATAAAGAACCTCGG-CAACTGTCCATAGG
1 TCACAAAGAACCTAGGTAAACTGTCCATAGG
*
131253 TCCCAAAGAACCTAGGTAAACTGTCCATA
1 TCACAAAGAACCTAGGTAAACTGTCCATA
131282 TGTTTCTTAG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 7 0.15
30 30 0.62
31 11 0.23
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.18
Consensus pattern (31 bp):
TCACAAAGAACCTAGGTAAACTGTCCATAGG
Found at i:131954 original size:2 final size:2
Alignment explanation
Indices: 131947--131981 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
131937 TACAAATTCC
131947 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
131982 CTAACTCATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:132605 original size:64 final size:63
Alignment explanation
Indices: 132466--132632 Score: 174
Period size: 64 Copynumber: 2.6 Consensus size: 63
132456 ATCTTTTAAT
* * *
132466 AAAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTA
1 AAAGGAATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCAATGTTTGTATTTA
** * *
132531 ATGGGGATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCAATGTTT-TCTTTTA
1 AAAGGAATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCAATGTTTGT-ATTTA
** * * *
132595 AAATTAATGCATCGATGAACTGCATGTGCATCGATGCA
1 AAAGGAATGCATCGATGCACT-CCTATGCATCGATGCA
132633 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
63 2 0.02
64 64 0.75
65 19 0.22
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (63 bp):
AAAGGAATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCAATGTTTGTATTTA
Found at i:136710 original size:2 final size:2
Alignment explanation
Indices: 136703--136729 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
136693 TACAAATTCC
136703 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
136730 CTAACTCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:137352 original size:64 final size:62
Alignment explanation
Indices: 137219--137379 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 62
137209 TAATAAAGGT
* * * *
137219 ATGCATCGATGCACTACACCATGCATCGATGTATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* *
137284 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
137348 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
137380 CTTTAAACAA
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.68
65 23 0.27
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:143039 original size:16 final size:17
Alignment explanation
Indices: 143015--143049 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
143005 TCCATCTTGA
143015 TTCAATTTTTTC-CTTT
1 TTCAATTTTTTCACTTT
*
143031 TTCACTTTTTTCACTTT
1 TTCAATTTTTTCACTTT
143048 TT
1 TT
143050 TTTTTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (17 bp):
TTCAATTTTTTCACTTT
Found at i:146630 original size:285 final size:284
Alignment explanation
Indices: 146121--146690 Score: 1122
Period size: 285 Copynumber: 2.0 Consensus size: 284
146111 CTAAAATTGA
146121 ACAGTCGTTCAGACAAAGGCGACGTAACCAACGAGCTAGAGAGTATATGAACCAACTACAGTTCA
1 ACAGTCGTTCAGACAAAGGCGACGTAACCAACGAGCTAGAGAGTATATGAACCAACTACAGTTCA
146186 ATGTAACAACACATGGGAGATCAAGAAAATCTTGATGTAGCAACAAATAATTTTCCTAGAGAAGT
66 ATGTAACAACACATGGGAGATCAAGAAAATCTTGATGTAGCAACAAATAATTTTCCTAGAGAAGT
146251 TGCAAGACCACGAGAAATACGAGACCACTTGAATCCAATTCTTGATGATCTCAATTCAGTCATCG
131 TGCAAGACCACGAGAAATACGAGACCACTTGAATCCAATTCTTGATGATCTCAATTCAGTCATCG
146316 TGGCACCTGAAATACAGGCAACCTATTTTGAACTTAAACCGGTGATGTTTAACATGCTAAACTCC
196 TGGCACCTGAAATACAGGCAACCTATTTTGAACTTAAACCGGTGATGTTTAACATGCTAAACTCC
146381 ATGGGTCAATTTGGTGGCTCGCCT
261 ATGGGTCAATTTGGTGGCTCGCCT
146405 ACAGTCGTTCAGACAAAGGCGACGTAACCAACGAGCTAGAGAGTATATGAACCAACTACAGTTCA
1 ACAGTCGTTCAGACAAAGGCGACGTAACCAACGAGCTAGAGAGTATATGAACCAACTACAGTTCA
*
146470 ATGTAACAACATCATGGGAGATCAAGCAAATCTTGATGTAGCAACAAATAATTTTCCTAGAGAAG
66 ATGTAACAACA-CATGGGAGATCAAGAAAATCTTGATGTAGCAACAAATAATTTTCCTAGAGAAG
146535 TTGCAAGACCACGAGAAATACGAGACCACTTGAATCCAATTCTTGATGATCTCAATTCAGTCATC
130 TTGCAAGACCACGAGAAATACGAGACCACTTGAATCCAATTCTTGATGATCTCAATTCAGTCATC
146600 GTGGCACCTGAAATACAGGCAACCTATTTTGAACTTAAACCGGTGATGTTTAACATGCTAAACTC
195 GTGGCACCTGAAATACAGGCAACCTATTTTGAACTTAAACCGGTGATGTTTAACATGCTAAACTC
146665 CATGGGTCAATTTGGTGGCTCGCCT
260 CATGGGTCAATTTGGTGGCTCGCCT
146690 A
1 A
146691 ATAAGGATGT
Statistics
Matches: 284, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
284 76 0.27
285 208 0.73
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (284 bp):
ACAGTCGTTCAGACAAAGGCGACGTAACCAACGAGCTAGAGAGTATATGAACCAACTACAGTTCA
ATGTAACAACACATGGGAGATCAAGAAAATCTTGATGTAGCAACAAATAATTTTCCTAGAGAAGT
TGCAAGACCACGAGAAATACGAGACCACTTGAATCCAATTCTTGATGATCTCAATTCAGTCATCG
TGGCACCTGAAATACAGGCAACCTATTTTGAACTTAAACCGGTGATGTTTAACATGCTAAACTCC
ATGGGTCAATTTGGTGGCTCGCCT
Found at i:151853 original size:81 final size:80
Alignment explanation
Indices: 151766--152016 Score: 351
Period size: 81 Copynumber: 3.1 Consensus size: 80
151756 CGCATTTAGG
* * * * * * *
151766 CTTTTACTTAAAGGCATATATCCTTTCATCTAACTTGCATGATTGACA-CTTTCCTGTCAAATGC
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTT-CTGCCAAATGC
*
151830 ACAGCTAGTCAATTAAT
65 ACAGCTAG-CCATTAAT
* * *
151847 ATTTTACTCAAATGTATTTAACCTATCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA
*
151912 AAGCTAAGCCATTAAT
66 CAGCT-AGCCATTAAT
151928 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA
151993 CAGCTAGGCCATTAAT
66 CAGCTA-GCCATTAAT
152009 CTTTTACT
1 CTTTTACT
152017 TTGGAATAGT
Statistics
Matches: 151, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
80 1 0.01
81 144 0.95
82 6 0.04
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (80 bp):
CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA
CAGCTAGCCATTAAT
Found at i:152285 original size:56 final size:56
Alignment explanation
Indices: 152169--152424 Score: 401
Period size: 56 Copynumber: 4.6 Consensus size: 56
152159 ACCAATACCA
* * *
152169 AAATTCATAAACTTATTATGAATTTCTT-ATTTTTTCACCCAAAGTGCCCATATGG
1 AAATTCATAAACTTATTATGAATTTCTTAACTTTTTCACACAAAGTGCCCATAAGG
*
152224 AAATTCATAAACTTATTATGAATTTCTTAACTTTTTCACACAAAGTGCTCATAAGG
1 AAATTCATAAACTTATTATGAATTTCTTAACTTTTTCACACAAAGTGCCCATAAGG
* * *
152280 AAATTCATAAATTTATTATGAATTTATT-A-TTTTTGCACACAAAGTGGCCATAAGG
1 AAATTCATAAACTTATTATGAATTTCTTAACTTTTT-CACACAAAGTGCCCATAAGG
* *
152335 AAATTCATAAACTTATTATGAATTTCTTAACTTTTGCACACAAAGAGCCCATAAGG
1 AAATTCATAAACTTATTATGAATTTCTTAACTTTTTCACACAAAGTGCCCATAAGG
152391 AAATTCATAAACTTATTATGAATTTCTTAACTTT
1 AAATTCATAAACTTATTATGAATTTCTTAACTTT
152425 GCACGCATCG
Statistics
Matches: 184, Mismatches: 13, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
54 5 0.03
55 73 0.40
56 102 0.55
57 4 0.02
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.38
Consensus pattern (56 bp):
AAATTCATAAACTTATTATGAATTTCTTAACTTTTTCACACAAAGTGCCCATAAGG
Found at i:152285 original size:111 final size:111
Alignment explanation
Indices: 152169--152428 Score: 421
Period size: 111 Copynumber: 2.3 Consensus size: 111
152159 ACCAATACCA
* * *
152169 AAATTCATAAACTTATTATGAATTTCTTATTTTTTCACCCAAAGTGCCCATATGGAAATTCATAA
1 AAATTCATAAACTTATTATGAATTTCTTATTTTTGCACACAAAGTGCCCATAAGGAAATTCATAA
* * *
152234 ACTTATTATGAATTTCTTAACTTTTTCACACAAAGTGCTCATAAGG
66 ACTTATTATGAATTTCTTAACTTTTGCACACAAAGAGCCCATAAGG
* * *
152280 AAATTCATAAATTTATTATGAATTTATTATTTTTGCACACAAAGTGGCCATAAGGAAATTCATAA
1 AAATTCATAAACTTATTATGAATTTCTTATTTTTGCACACAAAGTGCCCATAAGGAAATTCATAA
152345 ACTTATTATGAATTTCTTAACTTTTGCACACAAAGAGCCCATAAGG
66 ACTTATTATGAATTTCTTAACTTTTGCACACAAAGAGCCCATAAGG
**
152391 AAATTCATAAACTTATTATGAATTTCTTAACTTTGCAC
1 AAATTCATAAACTTATTATGAATTTCTTATTTTTGCAC
152429 GCATCGTGCA
Statistics
Matches: 136, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 136 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (111 bp):
AAATTCATAAACTTATTATGAATTTCTTATTTTTGCACACAAAGTGCCCATAAGGAAATTCATAA
ACTTATTATGAATTTCTTAACTTTTGCACACAAAGAGCCCATAAGG
Found at i:157698 original size:81 final size:79
Alignment explanation
Indices: 157473--157724 Score: 279
Period size: 81 Copynumber: 3.1 Consensus size: 79
157463 AAGCATTTAG
* * * * * * * *
157473 TCTTTGACTCAAAGGCATATAGCCTTTTATCTAACTTGCATGATTGACACTTTCCTTTCAAATGA
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAAC-TGCATAATTGACACTTT-CTTCCAAATGC
*
157538 ACAACTAGGCCATTAA
64 ACAGCTAGGCCATTAA
* * * * *
157554 TATTTTACTCAAATGTATTTAACATTTCATCTAACTGTCATAATTGACACCTTTCTGCGAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTG-CATAATTGACA-CTTTCTTCCAAATGC
*
157619 ATAGCTAGGCCATTAA
64 ACAGCTAGGCCATTAA
157635 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACATCTTTCTTCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTG-CATAATTGACA-CTTTCTTCCAAATGC
* ** *
157700 ACAGTTAAACCATTAT
64 ACAGCTAGGCCATTAA
157716 TCTTTTACT
1 TCTTTTACT
157725 TTGGAATAGT
Statistics
Matches: 142, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
80 2 0.01
81 136 0.96
82 4 0.03
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (79 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGCATAATTGACACTTTCTTCCAAATGCAC
AGCTAGGCCATTAA
Found at i:157997 original size:55 final size:56
Alignment explanation
Indices: 157876--158081 Score: 281
Period size: 56 Copynumber: 3.7 Consensus size: 56
157866 TACCAATACC
* * * * *
157876 GAAATTCATAAACTTATTATGAATTTTTTAAATTTTACACACAAAGTTCTCACAAG
1 GAAATTCATAAACTTATTATGAATTTATTAAATTTTGCACACAAAGTGCCCATAAG
* * *
157932 GAAATTCATAAATTTATTATGAATTTATT-ATTTTTGCACACAAAGTGGCCATAAG
1 GAAATTCATAAACTTATTATGAATTTATTAAATTTTGCACACAAAGTGCCCATAAG
* *
157987 GAAATTCATAAACTTATTATGAATTTCTTAAGTTTTGCACACAAAGTGCCCATAAG
1 GAAATTCATAAACTTATTATGAATTTATTAAATTTTGCACACAAAGTGCCCATAAG
* * *
158043 GAAATTCAAAAACTTATTATGAATTTCTT-AACTTTGCAC
1 GAAATTCATAAACTTATTATGAATTTATTAAATTTTGCAC
158082 GCATCGTGCA
Statistics
Matches: 134, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
55 55 0.41
56 79 0.59
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (56 bp):
GAAATTCATAAACTTATTATGAATTTATTAAATTTTGCACACAAAGTGCCCATAAG
Found at i:158079 original size:111 final size:111
Alignment explanation
Indices: 157876--158081 Score: 313
Period size: 111 Copynumber: 1.9 Consensus size: 111
157866 TACCAATACC
* * * *
157876 GAAATTCATAAACTTATTATGAATTTTTTAAATTTTACACACAAAGTTCTCACAAGGAAATTCAT
1 GAAATTCATAAACTTATTATGAATTTCTTAAATTTTACACACAAAGTGCCCACAAGGAAATTCAA
* **
157941 AAATTTATTATGAATTTATTATTTTTGCACACAAAGTGGCCATAAG
66 AAACTTATTATGAATTTATTAACTTTGCACACAAAGTGGCCATAAG
* * *
157987 GAAATTCATAAACTTATTATGAATTTCTTAAGTTTTGCACACAAAGTGCCCATAAGGAAATTCAA
1 GAAATTCATAAACTTATTATGAATTTCTTAAATTTTACACACAAAGTGCCCACAAGGAAATTCAA
*
158052 AAACTTATTATGAATTTCTTAACTTTGCAC
66 AAACTTATTATGAATTTATTAACTTTGCAC
158082 GCATCGTGCA
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
111 84 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (111 bp):
GAAATTCATAAACTTATTATGAATTTCTTAAATTTTACACACAAAGTGCCCACAAGGAAATTCAA
AAACTTATTATGAATTTATTAACTTTGCACACAAAGTGGCCATAAG
Found at i:158462 original size:22 final size:21
Alignment explanation
Indices: 158426--158483 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
158416 TCGATACATG
* *
158426 TACCATTGTATCGATACTACTA
1 TACCATGGTACCGATACT-CTA
158448 TACCATGGTACCGATACTCTA
1 TACCATGGTACCGATACTCTA
*
158469 TA--ACGGTACCGATAC
1 TACCATGGTACCGATAC
158484 CATTTATGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 12 0.36
21 5 0.15
22 16 0.48
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (21 bp):
TACCATGGTACCGATACTCTA
Found at i:160608 original size:26 final size:26
Alignment explanation
Indices: 160578--160645 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
160568 AAACATGTAT
*
160578 GATAAAAATTTATAGTAAATAAATTA
1 GATAAAATTTTATAGTAAATAAATTA
* *
160604 GATAAAATTTTATAATAAATAGATTA
1 GATAAAATTTTATAGTAAATAAATTA
*
160630 AATAAAATTTTATAGT
1 GATAAAATTTTATAGT
160646 TTCATAGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.38
Consensus pattern (26 bp):
GATAAAATTTTATAGTAAATAAATTA
Found at i:162630 original size:2 final size:2
Alignment explanation
Indices: 162623--162667 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
162613 GAGGATGGGA
162623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
162665 AT A
1 AT A
162668 GTTCTGTTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:164575 original size:9 final size:11
Alignment explanation
Indices: 164543--164576 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
164533 TTATAGTATT
164543 ATATTATTAAAA
1 ATATTA-TAAAA
164555 ATATTATAAAA
1 ATATTATAAAA
164566 AT-TTATAAAA
1 ATATTATAAAA
164576 A
1 A
164577 AAAAAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.41
11 7 0.32
12 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATTATAAAA
Found at i:164974 original size:14 final size:14
Alignment explanation
Indices: 164952--164981 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
164942 ATATATTTAT
*
164952 TTTACAATTTATTA
1 TTTAAAATTTATTA
164966 TTTAAAATTTATTA
1 TTTAAAATTTATTA
164980 TT
1 TT
164982 ATTTCTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTAAAATTTATTA
Found at i:165867 original size:16 final size:16
Alignment explanation
Indices: 165837--165866 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
165827 AAAAAGTGGG
165837 AAAATAAAGATAAAAC
1 AAAATAAAGATAAAAC
165853 AAAATAAA-ATAAAA
1 AAAATAAAGATAAAA
165867 AGGGGAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAATAAAGATAAAAC
Found at i:165950 original size:18 final size:18
Alignment explanation
Indices: 165929--165971 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
165919 GTTGTTTTTA
*
165929 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
165947 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
165965 AAATAAA
1 AAATAAA
165972 TAATCTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:172401 original size:2 final size:2
Alignment explanation
Indices: 172394--172425 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
172384 GCTTCATTTA
172394 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
172426 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:172755 original size:11 final size:11
Alignment explanation
Indices: 172739--172763 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
172729 TTTTAAGAGA
172739 TTTATTATTAT
1 TTTATTATTAT
172750 TTTATTATTAT
1 TTTATTATTAT
172761 TTT
1 TTT
172764 GGGGCAATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTATTAT
Found at i:173509 original size:245 final size:248
Alignment explanation
Indices: 173039--173532 Score: 967
Period size: 245 Copynumber: 2.0 Consensus size: 248
173029 TCACAAACCA
173039 AGCACCCTGGTTCCTTCAAGTGCAGCCAACATCGCCGTTCCAACCACCCACCCGCACTCGTGCCC
1 AGCACCCTGGTTCCTTCAAGTGCAGCCAACATCGCCGTTCCAACCACCCACCCGCACTCGTGCCC
173104 GCCCGTCGAGCCACGGCGGTGCGAGCATGGTTGAATTACAGAGAAATAGTTTTGATTGCTGGAGC
66 GCCCGTCGAGCCACGGCGGTGCGAGCATGGTTGAATTACAGAGAAATAGTTTTGATTGCTGGAGC
173169 AAATCCCCACAAGGCGTTTCTGCATCAAGGCGTGAAGCCGTCGAGATCGACCGCTATTAGCATGC
131 AAATCCCCACAAGGCGTTTCTGCATCAAGGCGTGAAGCCGTCGAGATCGACCGCTATTAGCATGC
173234 AAAGGAGAAGGAATTTCCAACCTAAACCTTATAGGTTCTATTTATTGAACGGC
196 AAAGGAGAAGGAATTTCCAACCTAAACCTTATAGGTTCTATTTATTGAACGGC
173287 AGCACCCTGGTTCCTTCAAGTGCAGCCAACATCGCCGTTCCAACCACCCACCCGCACTCGTGCCC
1 AGCACCCTGGTTCCTTCAAGTGCAGCCAACATCGCCGTTCCAACCACCCACCCGCACTCGTGCCC
173352 GCCCGTCGAGCCACGGCGGTGCGAGCATGGTTGAATTACAGAG-AA-A-TTTTGATTGCTGGAGC
66 GCCCGTCGAGCCACGGCGGTGCGAGCATGGTTGAATTACAGAGAAATAGTTTTGATTGCTGGAGC
173414 AAATCCCCACAAGGCGTTTCTGCATCAAGGCGTGAAGCCGTCGAGATCGACCGCTATTAGCATGC
131 AAATCCCCACAAGGCGTTTCTGCATCAAGGCGTGAAGCCGTCGAGATCGACCGCTATTAGCATGC
173479 AAAGGAGAAGGAATTTCCAACCTAAACCTTATAGGTTCTATTTATTGAACGGC
196 AAAGGAGAAGGAATTTCCAACCTAAACCTTATAGGTTCTATTTATTGAACGGC
173532 A
1 A
173533 ATAGGTTTCG
Statistics
Matches: 246, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
245 135 0.55
246 1 0.00
247 2 0.01
248 108 0.44
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.22
Consensus pattern (248 bp):
AGCACCCTGGTTCCTTCAAGTGCAGCCAACATCGCCGTTCCAACCACCCACCCGCACTCGTGCCC
GCCCGTCGAGCCACGGCGGTGCGAGCATGGTTGAATTACAGAGAAATAGTTTTGATTGCTGGAGC
AAATCCCCACAAGGCGTTTCTGCATCAAGGCGTGAAGCCGTCGAGATCGACCGCTATTAGCATGC
AAAGGAGAAGGAATTTCCAACCTAAACCTTATAGGTTCTATTTATTGAACGGC
Found at i:176685 original size:18 final size:17
Alignment explanation
Indices: 176662--176701 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
176652 TAAATTTCTC
*
176662 TAAAAACCATTTTTCCTT
1 TAAAAACCA-ATTTCCTT
176680 TAAAAACCAATTTCCTT
1 TAAAAACCAATTTCCTT
176697 TAAAA
1 TAAAA
176702 TAATATAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAACCAATTTCCTT
Found at i:176936 original size:3 final size:3
Alignment explanation
Indices: 176928--176994 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
176918 ATCTTCTGAA
176928 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
176975 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
176995 AAGTATAATC
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 61 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:177129 original size:14 final size:13
Alignment explanation
Indices: 177087--177132 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
177077 TTAATTATTA
177087 ATAAAAAT-G-AT
1 ATAAAAATCGTAT
*
177098 AAAAAAATCGTAT
1 ATAAAAATCGTAT
*
177111 ATAAAATTCGTAT
1 ATAAAAATCGTAT
177124 ATTAAAAAT
1 A-TAAAAAT
177133 AACTTTTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
11 7 0.25
12 1 0.04
13 14 0.50
14 6 0.21
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (13 bp):
ATAAAAATCGTAT
Found at i:177407 original size:18 final size:17
Alignment explanation
Indices: 177384--177423 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
177374 TAAATTTCTC
*
177384 TAAAAACCAGTTTTCCTT
1 TAAAAACCA-ATTTCCTT
177402 TAAAAACCAATTTCCTT
1 TAAAAACCAATTTCCTT
177419 TAAAA
1 TAAAA
177424 TAATATAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.35
Consensus pattern (17 bp):
TAAAAACCAATTTCCTT
Found at i:177654 original size:3 final size:3
Alignment explanation
Indices: 177648--177692 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
177638 TATCTTCTTA
*
177648 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT TAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
177693 TTCAGAACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:177817 original size:14 final size:13
Alignment explanation
Indices: 177775--177820 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
177765 TTAATTATTA
177775 ATAAAAAT-G-AT
1 ATAAAAATCGTAT
*
177786 AAAAAAATCGTAT
1 ATAAAAATCGTAT
*
177799 ATAAAATTCGTAT
1 ATAAAAATCGTAT
177812 ATTAAAAAT
1 A-TAAAAAT
177821 AATTTTTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
11 7 0.25
12 1 0.04
13 14 0.50
14 6 0.21
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (13 bp):
ATAAAAATCGTAT
Found at i:202749 original size:15 final size:16
Alignment explanation
Indices: 202724--202755 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
202714 GCGTGTTTAA
202724 TTTTTATTTTTTATTT
1 TTTTTATTTTTTATTT
202740 TTTTTA-TTTTTATTT
1 TTTTTATTTTTTATTT
202755 T
1 T
202756 ATAGAAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTATTTTTTATTT
Found at i:205628 original size:17 final size:17
Alignment explanation
Indices: 205584--205638 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
205574 TCTCCATCAC
205584 AAAAAA-TGTT-GAAAA
1 AAAAAACTGTTCGAAAA
* *
205599 AAAATAGCAGTTCGAAAA
1 AAAA-AACTGTTCGAAAA
205617 AAAAAACTGTTCGAAAGA
1 AAAAAACTGTTCGAAA-A
205635 AAAA
1 AAAA
205639 GAAAAAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 4 0.12
16 1 0.03
17 13 0.41
18 14 0.44
ACGTcount: A:0.62, C:0.07, G:0.15, T:0.16
Consensus pattern (17 bp):
AAAAAACTGTTCGAAAA
Found at i:212876 original size:17 final size:18
Alignment explanation
Indices: 212854--212898 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 18
212844 AACTTTGTCA
212854 TCATTTTTTTTCA-TTTT
1 TCATTTTTTTTCATTTTT
212871 TCA-TTTTTTTCATTTTT
1 TCATTTTTTTTCATTTTT
212888 TCATTTTTTTT
1 TCATTTTTTTT
212899 ATAGAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.35
17 10 0.38
18 7 0.27
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (18 bp):
TCATTTTTTTTCATTTTT
Found at i:212878 original size:8 final size:8
Alignment explanation
Indices: 212859--212896 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
212849 TGTCATCATT
212859 TTTTTTCA
1 TTTTTTCA
212867 -TTTTTCA
1 TTTTTTCA
212874 TTTTTTTCA
1 -TTTTTTCA
212883 TTTTTTCA
1 TTTTTTCA
212891 TTTTTT
1 TTTTTT
212897 TTATAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.25
8 14 0.50
9 7 0.25
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCA
Found at i:212879 original size:9 final size:9
Alignment explanation
Indices: 212858--212897 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
212848 TTGTCATCAT
212858 TTTTTTTCA
1 TTTTTTTCA
212867 --TTTTTCA
1 TTTTTTTCA
212874 TTTTTTTCA
1 TTTTTTTCA
212883 -TTTTTTCA
1 TTTTTTTCA
212891 TTTTTTT
1 TTTTTTT
212898 TATAGAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 7 0.25
8 8 0.29
9 13 0.46
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:222672 original size:16 final size:16
Alignment explanation
Indices: 222651--222684 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
222641 GTGTACATGG
222651 TGCAGCCACCAGGGTT
1 TGCAGCCACCAGGGTT
222667 TGCAGCCACCAGGGTT
1 TGCAGCCACCAGGGTT
222683 TG
1 TG
222685 AACAAGTGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.29, G:0.32, T:0.21
Consensus pattern (16 bp):
TGCAGCCACCAGGGTT
Found at i:224396 original size:16 final size:16
Alignment explanation
Indices: 224375--224407 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
224365 ATAGATTCAG
224375 GAGCAATATCTGATGA
1 GAGCAATATCTGATGA
224391 GAGCAATATCTGATGA
1 GAGCAATATCTGATGA
224407 G
1 G
224408 TTTTAAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.24
Consensus pattern (16 bp):
GAGCAATATCTGATGA
Found at i:224612 original size:3 final size:3
Alignment explanation
Indices: 224606--224630 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
224596 CCAAATGATG
224606 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
224631 GCAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:225060 original size:47 final size:48
Alignment explanation
Indices: 224977--225073 Score: 133
Period size: 47 Copynumber: 2.0 Consensus size: 48
224967 ATCATAACTT
* * *
224977 AAAAATTAATAAAATATTGTATTCAGCTTGTTCACTTGAAGTCAAGATTA
1 AAAAATAAATAAAATA-T-TATTCAACTTGTTCACTTAAAGTCAAGATTA
*
225027 AAAAATAAATAAAATA-TATTCAATTTGTTCACTTAAAGTCAAGATTA
1 AAAAATAAATAAAATATTATTCAACTTGTTCACTTAAAGTCAAGATTA
225074 TATTAGTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
47 28 0.65
50 15 0.35
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.35
Consensus pattern (48 bp):
AAAAATAAATAAAATATTATTCAACTTGTTCACTTAAAGTCAAGATTA
Found at i:225585 original size:112 final size:112
Alignment explanation
Indices: 225378--225592 Score: 326
Period size: 112 Copynumber: 1.9 Consensus size: 112
225368 AAATAAGTAC
* *
225378 TTAAAGAATGTCTCGAAAAACGATTTTGTGCTAAAATAATTTTTCGTTAAAAATAAATGTTTAAA
1 TTAAAGAATGTCTCGAAAAACGATTTTATGCTAAAATAATTTTTCGTTAAAAATAAATGTCTAAA
* *
225443 GTTTTCTTCATTACAGTTTTACATTGCCACCGTTAAAAATTATTGTT
66 GTTTTCTTCATTACAATTTTACATTGCCACCATTAAAAATTATTGTT
* *
225490 TTAAAGAATGTCTCGAAAAACG-TTTTAATGTTAAAATAATTTTTCGTTAAAAATAAGTGTCTAA
1 TTAAAGAATGTCTCGAAAAACGATTTT-ATGCTAAAATAATTTTTCGTTAAAAATAAATGTCTAA
* *
225554 AGTTTTCTTCATTATAATTTTAC-GTGTCCACCATTAAAA
65 AGTTTTCTTCATTACAATTTTACATTG-CCACCATTAAAA
225593 CTTACCGTTA
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
111 6 0.06
112 87 0.94
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (112 bp):
TTAAAGAATGTCTCGAAAAACGATTTTATGCTAAAATAATTTTTCGTTAAAAATAAATGTCTAAA
GTTTTCTTCATTACAATTTTACATTGCCACCATTAAAAATTATTGTT
Found at i:233831 original size:64 final size:64
Alignment explanation
Indices: 233746--233964 Score: 224
Period size: 64 Copynumber: 3.4 Consensus size: 64
233736 GAATGTACAC
** * * * *
233746 CGATGCATTGGTAGTGCATCGATGCA-CTCTTTTATAATAAAGACATCTAATGCAATTCGTGCAT
1 CGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAA-ACATCGAATGCAATTCGTGCAT
* * * *
233810 CGATGCATAAGTAGTGTATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATTGGTGCAT
1 CGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCGTGCAT
* * ** * * * * ** *
233874 CGATGCATAAGGAGTGCATCGATGCATCTCAGCAATAATACAACATCAAATACATTTTATGCAC
1 CGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCGTGCAT
*
233938 CGATGCATCAGTAGTGCATCGATGCAT
1 CGATGCATAAGTAGTGCATCGATGCAT
233965 ACCTTCATTA
Statistics
Matches: 128, Mismatches: 26, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
64 118 0.92
65 10 0.08
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (64 bp):
CGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCGTGCAT
Found at i:234659 original size:31 final size:31
Alignment explanation
Indices: 234621--234776 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
234611 AGGGTCGAGG
*
234621 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
234652 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
234683 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
234714 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
234745 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
234776 G
1 G
234777 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:237885 original size:64 final size:64
Alignment explanation
Indices: 237811--237971 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 64
237801 TTGTTTGAAT
** * *
237811 GTGCACCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGA-AACATCGAATGCAATTG
1 GTGCACCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAAT-ACAACATCGAATACAATTG
* * * * *
237875 GTGCATCGATGCATAAGGAGTGCATCGATGCATCGCAGCAATAATACAACATCGAATACATTTT
1 GTGCACCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATACAACATCGAATACAATTG
* *
237939 ATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 GTGCACCGATGCATAAGTAGTGCATCGATGCAT
237972 ACCTTCATTA
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
63 1 0.01
64 82 0.99
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (64 bp):
GTGCACCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATACAACATCGAATACAATTG
Found at i:238666 original size:31 final size:31
Alignment explanation
Indices: 238628--238721 Score: 154
Period size: 31 Copynumber: 3.0 Consensus size: 31
238618 AGGGTCGAGG
238628 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
238659 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
238690 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
238721 G
1 G
238722 GTCCTTCGGG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 59 0.98
32 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:239570 original size:10 final size:11
Alignment explanation
Indices: 239555--239584 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
239545 AAATAACCTC
239555 AAAAATGAG-A
1 AAAAATGAGAA
239565 AAAAATGAGAA
1 AAAAATGAGAA
239576 AAAAATGAG
1 AAAAATGAG
239585 TTAGTACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (11 bp):
AAAAATGAGAA
Found at i:241448 original size:2 final size:2
Alignment explanation
Indices: 241441--241521 Score: 50
Period size: 2 Copynumber: 43.0 Consensus size: 2
241431 ACTAAATGTA
* * *
241441 AT AT AT AT AT AT A- AT AC A- AT AT AT GT ACT AT GAT AT -T AG A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT -AT AT AT AT AT
* *
241481 AT AT AA AT AT AT AT AT AT A- AT AT -T AT A- AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
241520 AT
1 AT
241522 GACAAATTGT
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
1 7 0.11
2 51 0.82
3 4 0.06
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (2 bp):
AT
Found at i:241483 original size:27 final size:27
Alignment explanation
Indices: 241458--241521 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
241448 TATATAATAC
* *
241458 AATATATGTACTATGATATTAGAATATA
1 AATATATATA-TATAATATTAGAATATA
*
241486 AATATATATATATAATATTATAATATA
1 AATATATATATATAATATTAGAATATA
* *
241513 TATAAATAT
1 AATATATAT
241522 GACAAATTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
27 22 0.71
28 9 0.29
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (27 bp):
AATATATATATATAATATTAGAATATA
Found at i:242307 original size:9 final size:9
Alignment explanation
Indices: 242285--242344 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
242275 CCGATTTTCA
242285 ACCGGTTCTG
1 ACCGGTT-TG
242295 ACCGGTTTG
1 ACCGGTTTG
242304 ACCGGTTTCG
1 ACCGGTTT-G
**
242314 ACCGGTCCG
1 ACCGGTTTG
242323 AACCGGTTTG
1 -ACCGGTTTG
*
242333 ACCGGTCTG
1 ACCGGTTTG
242342 ACC
1 ACC
242345 CGACCCGACC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
9 22 0.51
10 21 0.49
ACGTcount: A:0.13, C:0.32, G:0.30, T:0.25
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:242309 original size:19 final size:18
Alignment explanation
Indices: 242285--242344 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 18
242275 CCGATTTTCA
*
242285 ACCGGTTCTGACCGGTTTG
1 ACCGGTT-TGACCGGTCTG
*
242304 ACCGGTTTCGACCGGTCCG
1 ACCGGTTT-GACCGGTCTG
242323 AACCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTCTG
242342 ACC
1 ACC
242345 CGACCCGACC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.11
19 24 0.67
20 8 0.22
ACGTcount: A:0.13, C:0.32, G:0.30, T:0.25
Consensus pattern (18 bp):
ACCGGTTTGACCGGTCTG
Found at i:242317 original size:29 final size:29
Alignment explanation
Indices: 242280--242338 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
242270 TTCAACCGAT
*
242280 TTTCAACCGGTTCTG-ACCGGTTTGACCGG
1 TTTCAACCGG-TCCGAACCGGTTTGACCGG
*
242309 TTTCGACCGGTCCGAACCGGTTTGACCGG
1 TTTCAACCGGTCCGAACCGGTTTGACCGG
242338 T
1 T
242339 CTGACCCGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 3 0.11
29 24 0.89
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (29 bp):
TTTCAACCGGTCCGAACCGGTTTGACCGG
Found at i:242352 original size:29 final size:29
Alignment explanation
Indices: 242295--242352 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
242285 ACCGGTTCTG
* **
242295 ACCGGTTTGACCGGTTTCGACCGGTCCGA
1 ACCGGTTTGACCGGTCTCGACCGACCCGA
242324 ACCGGTTTGACCGGTCT-GACCCGACCCGA
1 ACCGGTTTGACCGGTCTCGA-CCGACCCGA
242353 CCGTTGACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.16, C:0.34, G:0.29, T:0.21
Consensus pattern (29 bp):
ACCGGTTTGACCGGTCTCGACCGACCCGA
Found at i:242367 original size:22 final size:22
Alignment explanation
Indices: 242341--242383 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
242331 TGACCGGTCT
242341 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
242363 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
242384 GTTGACCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:247042 original size:33 final size:32
Alignment explanation
Indices: 246991--247063 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 32
246981 AACCCGAACC
*
246991 CGACCCGACCCGAGTATCACACTTAAAATAACT
1 CGACCCGACCCGAATATCACACTTAAAA-AACT
*
247024 CGACCCGACTCGAATATCACACTTAAAAAACT
1 CGACCCGACCCGAATATCACACTTAAAAAACT
*
247056 TGACCCGA
1 CGACCCGA
247064 ACAAAATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
32 11 0.30
33 26 0.70
ACGTcount: A:0.37, C:0.33, G:0.12, T:0.18
Consensus pattern (32 bp):
CGACCCGACCCGAATATCACACTTAAAAAACT
Found at i:248483 original size:3 final size:3
Alignment explanation
Indices: 248475--248555 Score: 146
Period size: 3 Copynumber: 27.0 Consensus size: 3
248465 CATTGGCATA
248475 TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
248520 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
248556 ATCGGATATA
Statistics
Matches: 76, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.03
3 71 0.93
4 3 0.04
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:249289 original size:29 final size:29
Alignment explanation
Indices: 249244--249305 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
249234 TCCCCAAGCA
* * *
249244 TAGGTCGCCAAGTACTCCGGGCGACCTTG
1 TAGGTCGCCAAGCACTCCAGGCGACATTG
249273 TAGGTCGCCAAGCACTCCAGGCGACATTG
1 TAGGTCGCCAAGCACTCCAGGCGACATTG
249302 TAGG
1 TAGG
249306 ACACCATACA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.21, C:0.29, G:0.31, T:0.19
Consensus pattern (29 bp):
TAGGTCGCCAAGCACTCCAGGCGACATTG
Found at i:250313 original size:5 final size:5
Alignment explanation
Indices: 250303--250360 Score: 116
Period size: 5 Copynumber: 11.6 Consensus size: 5
250293 AAAGAAACAA
250303 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG
250353 GAAAG GAA
1 GAAAG GAA
250361 GAAGGCATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 53 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:250407 original size:14 final size:14
Alignment explanation
Indices: 250388--250414 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
250378 GTAATTTATT
250388 ATTTTTTGTTGTTC
1 ATTTTTTGTTGTTC
250402 ATTTTTTGTTGTT
1 ATTTTTTGTTGTT
250415 GTGTATGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (14 bp):
ATTTTTTGTTGTTC
Found at i:250501 original size:17 final size:17
Alignment explanation
Indices: 250479--250517 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
250469 ATTTATTCCC
250479 GTTTAAAAAAATATT-GT
1 GTTTAAAAAAAT-TTAGT
*
250496 GTTTAAAAATATTTAGT
1 GTTTAAAAAAATTTAGT
250513 GTTTA
1 GTTTA
250518 TTTTATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (17 bp):
GTTTAAAAAAATTTAGT
Found at i:250535 original size:83 final size:83
Alignment explanation
Indices: 250436--250598 Score: 290
Period size: 83 Copynumber: 2.0 Consensus size: 83
250426 AATTAGTTAG
* *
250436 TTTATATTAGAGTATATAAAATTAATTTGATTAATTTATTCCCGTTTAAAAAAATATTGTGTTTA
1 TTTATATTAGAGTATATAAAATTAATTTGATTAATTTATTACAGTTTAAAAAAATATTGTGTTTA
250501 AAAATATTTAGTGTTTAT
66 AAAATATTTAGTGTTTAT
* *
250519 TTTATATTAGATTATATAAAATTAATTTGTTTAATTTATTACAGTTTAAAAAAATATTGTGTTTA
1 TTTATATTAGAGTATATAAAATTAATTTGATTAATTTATTACAGTTTAAAAAAATATTGTGTTTA
250584 AAAATATTTAGTGTT
66 AAAATATTTAGTGTT
250599 GTTTTAAAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.49
Consensus pattern (83 bp):
TTTATATTAGAGTATATAAAATTAATTTGATTAATTTATTACAGTTTAAAAAAATATTGTGTTTA
AAAATATTTAGTGTTTAT
Found at i:253674 original size:21 final size:21
Alignment explanation
Indices: 253644--253754 Score: 73
Period size: 21 Copynumber: 4.9 Consensus size: 21
253634 TGATTAGTAA
*
253644 TAATGAATTTATTATTAATATT
1 TAATG-ATTTATTAGTAATATT
*
253666 TAATGATTTAGTAGTAATGATTAGT
1 TAATGATTTATTAGTAAT-A-T--T
*
253691 AATAATGATATTATTATTAATATT
1 --TAATGAT-TTATTAGTAATATT
253715 TAATGATTTGA-TAGTAATGATT
1 TAATGATTT-ATTAGTAAT-ATT
* *
253737 TAAT-AATTATTACTAATA
1 TAATGATTTATTAGTAATA
253755 ATTATGGAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
20 2 0.03
21 28 0.39
22 21 0.29
23 1 0.01
24 1 0.01
25 1 0.01
26 1 0.01
27 8 0.11
28 9 0.12
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (21 bp):
TAATGATTTATTAGTAATATT
Found at i:253686 original size:49 final size:49
Alignment explanation
Indices: 253628--253743 Score: 186
Period size: 49 Copynumber: 2.4 Consensus size: 49
253618 TTGTCTGATT
253628 TAGTAATGATTAGTAATAATGA-ATTTATTATTAATATTTAATGATTT-A
1 TAGTAATGATTAGTAATAATGATA-TTATTATTAATATTTAATGATTTGA
253676 GTAGTAATGATTAGTAATAATGATATTATTATTAATATTTAATGATTTGA
1 -TAGTAATGATTAGTAATAATGATATTATTATTAATATTTAATGATTTGA
253726 TAGTAATGATT--TAATAAT
1 TAGTAATGATTAGTAATAAT
253744 TATTACTAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
47 7 0.11
49 56 0.86
50 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGATATTATTATTAATATTTAATGATTTGA
Found at i:253903 original size:59 final size:57
Alignment explanation
Indices: 253828--253954 Score: 159
Period size: 59 Copynumber: 2.2 Consensus size: 57
253818 TCGAATTTAT
*
253828 TAATGATTTTTAAATATTTAATGATTTAATACTAATGATT-TAGTAAT-TATTATTAA
1 TAATGATTTTTAAATATTTAATGATTTAATACTAATGATTATAGTAATAAATTA-TAA
* *
253884 TAATGATTTATTAATAATATTTAATTATTTGATACTAATGATTACTAGTAATGAAATTATAA
1 TAATGATTT-TT-A-AATATTTAATGATTTAATACTAATGATTA-TAGTAAT-AAATTATAA
253946 TAATGATTT
1 TAATGATTT
253955 GATACTAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
56 9 0.15
57 2 0.03
58 1 0.02
59 26 0.43
61 7 0.11
62 12 0.20
63 4 0.07
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (57 bp):
TAATGATTTTTAAATATTTAATGATTTAATACTAATGATTATAGTAATAAATTATAA
Found at i:253910 original size:14 final size:14
Alignment explanation
Indices: 253846--253906 Score: 60
Period size: 14 Copynumber: 4.7 Consensus size: 14
253836 TTTAAATATT
* *
253846 TAATGATTTAATAC
1 TAATGATTTATTAA
*
253860 TAATGATTTAGTAA
1 TAATGATTTATTAA
253874 T--T-A-TTATTAA
1 TAATGATTTATTAA
253884 TAATGATTTATTAA
1 TAATGATTTATTAA
253898 TAAT-ATTTA
1 TAATGATTTA
253907 ATTATTTGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
10 7 0.17
11 1 0.03
12 2 0.05
13 6 0.15
14 24 0.60
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (14 bp):
TAATGATTTATTAA
Found at i:256268 original size:22 final size:23
Alignment explanation
Indices: 256240--256288 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
256230 ACAACTATTA
256240 AACTATTCTTTAATATAAC-TTT
1 AACTATTCTTTAATATAACTTTT
256262 AACTATTCTTTAATATAACTTTT
1 AACTATTCTTTAATATAACTTTT
256285 AACT
1 AACT
256289 GATAAACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (23 bp):
AACTATTCTTTAATATAACTTTT
Found at i:256337 original size:31 final size:31
Alignment explanation
Indices: 256262--256337 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 31
256252 ATATAACTTT
** * * *
256262 AACTATTCTTTAATATAACTTTTAACTGATA
1 AACTATTAATTAATATAACTTTAAACTAAAA
**
256293 AACTATTCTTTAATATAAC-TTAAACTAAAA
1 AACTATTAATTAATATAACTTTAAACTAAAA
256323 AACTAATTAATTAAT
1 AACT-ATTAATTAAT
256338 TTTTATATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 12 0.31
31 27 0.69
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (31 bp):
AACTATTAATTAATATAACTTTAAACTAAAA
Found at i:256532 original size:21 final size:21
Alignment explanation
Indices: 256506--256545 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
256496 TCTATATGAT
256506 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
256527 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
256546 ACTAATCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:256594 original size:18 final size:18
Alignment explanation
Indices: 256573--256625 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 18
256563 TTGTTTTACC
256573 CTAATTTATAATAATAAA
1 CTAATTTATAATAATAAA
*
256591 CTAATAATTTATAACAATAAA
1 C---TAATTTATAATAATAAA
256612 CTAATTTA-AATAAT
1 CTAATTTATAATAAT
256626 TATATAACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 5 0.17
18 8 0.27
21 17 0.57
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAATAATAAA
Found at i:256599 original size:21 final size:21
Alignment explanation
Indices: 256574--256616 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
256564 TGTTTTACCC
*
256574 TAATTTATAATAATAAACTAA
1 TAATTTATAACAATAAACTAA
256595 TAATTTATAACAATAAACTAA
1 TAATTTATAACAATAAACTAA
256616 T
1 T
256617 TTAAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATTTATAACAATAAACTAA
Found at i:256645 original size:35 final size:35
Alignment explanation
Indices: 256573--256676 Score: 93
Period size: 35 Copynumber: 2.9 Consensus size: 35
256563 TTGTTTTACC
*
256573 CTAATTTATAATAATAAACTAATAATTTATAAC-AATAAA
1 CTAATTTA-AATAAT-AA-TAA-AACTTA-AACTAATAAA
* *
256612 CTAATTTAAATAATTATATAACTTAAACTAATAAA
1 CTAATTTAAATAATAATAAAACTTAAACTAATAAA
* ** *
256647 CTATTTTTTATTATAATAAAACTTAAACTA
1 CTAATTTAAATAATAATAAAACTTAAACTA
256677 CTAATAAACT
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
34 3 0.05
35 35 0.64
36 2 0.04
37 1 0.02
38 6 0.11
39 8 0.15
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (35 bp):
CTAATTTAAATAATAATAAAACTTAAACTAATAAA
Found at i:256770 original size:27 final size:29
Alignment explanation
Indices: 256735--256799 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
256725 AAAATATAAC
*
256735 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
256762 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
256790 TTAATTATTT
1 TTAAATATTT
256800 TTTAATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:256911 original size:21 final size:20
Alignment explanation
Indices: 256863--256911 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
256853 ATATAACTTA
256863 AACTAAACTAACAATAATAT
1 AACTAAACTAACAATAATAT
256883 AACTTAAACTAACAAACTAAT-T
1 AAC-TAAACTAAC-AA-TAATAT
256905 AACTAAA
1 AACTAAA
256912 ATTTTGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 3 0.12
21 13 0.50
22 6 0.23
23 4 0.15
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.24
Consensus pattern (20 bp):
AACTAAACTAACAATAATAT
Found at i:256930 original size:39 final size:39
Alignment explanation
Indices: 256885--256969 Score: 161
Period size: 39 Copynumber: 2.2 Consensus size: 39
256875 AATAATATAA
256885 CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
*
256924 CTTAAACTAACTAACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
256963 CTTAAAC
1 CTTAAAC
256970 CATAAACTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.39
Consensus pattern (39 bp):
CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
Found at i:256993 original size:39 final size:37
Alignment explanation
Indices: 256896--256993 Score: 133
Period size: 39 Copynumber: 2.5 Consensus size: 37
256886 TTAAACTAAC
*
256896 AAACTAATTAACTAAAATTTTGTTTTACCTTAAACTA
1 AAACTAATTAACTAAAATTTTGTTTTACCTTAAACCA
256933 ACTAACTAATTAACTAAAATTTTGTTTTACCTTAAACCA
1 A--AACTAATTAACTAAAATTTTGTTTTACCTTAAACCA
**
256972 TAAACTAACAAACTAATAATTT
1 -AAACTAATTAACTAA-AATTT
256994 AAAATAATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
37 1 0.02
38 12 0.22
39 40 0.74
40 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (37 bp):
AAACTAATTAACTAAAATTTTGTTTTACCTTAAACCA
Found at i:257018 original size:9 final size:9
Alignment explanation
Indices: 256986--257023 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
256976 CTAACAAACT
256986 AATAATTTAA
1 AATAA-TTAA
256996 AATAA-TAA
1 AATAATTAA
*
257004 ACTAATTAA
1 AATAATTAA
257013 AATAATTAA
1 AATAATTAA
257022 AA
1 AA
257024 AACTTACCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 13 0.52
10 5 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:257433 original size:30 final size:28
Alignment explanation
Indices: 257398--257469 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 28
257388 GCCATGCACA
* *
257398 GCCATGCAGACACTCCAAGCTCGCCTGGAT
1 GCCATGC-GAC-CTCCAAGCTCACCCGGAT
257428 GCCATGGCGACCTCCAAGCTCACCCGGAT
1 GCCAT-GCGACCTCCAAGCTCACCCGGAT
*
257457 ACCATGGCGACCT
1 GCCAT-GCGACCT
257470 ACATGCACCC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 28 0.74
30 8 0.21
31 2 0.05
ACGTcount: A:0.22, C:0.39, G:0.24, T:0.15
Consensus pattern (28 bp):
GCCATGCGACCTCCAAGCTCACCCGGAT
Found at i:257444 original size:29 final size:29
Alignment explanation
Indices: 257410--257469 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
257400 CATGCAGACA
* * *
257410 CTCCAAGCTCGCCTGGATGCCATGGCGAC
1 CTCCAAGCTCACCCGGATACCATGGCGAC
257439 CTCCAAGCTCACCCGGATACCATGGCGAC
1 CTCCAAGCTCACCCGGATACCATGGCGAC
257468 CT
1 CT
257470 ACATGCACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.20, C:0.40, G:0.23, T:0.17
Consensus pattern (29 bp):
CTCCAAGCTCACCCGGATACCATGGCGAC
Found at i:257912 original size:75 final size:72
Alignment explanation
Indices: 257813--258014 Score: 226
Period size: 72 Copynumber: 2.8 Consensus size: 72
257803 CACCGGTTAC
* ** *
257813 ACTCCCTCCGGTTGTCAAGTCACCAATTATAGTTCCCCCGATGACTGTTCCTCCAGTAGTGAAGC
1 ACTCCCTCCGGTTGTAAAACCACCAATTACAGTTCCCCCGATGACTGTTCCTCCAGT--T-AAGC
* *
257878 CTCCAGTCGT
63 CACCAGTCGA
257888 ACTCCCTCCGGTTGTAAAACCACCAATTACAGTTCCCCC-AGTGACTGTTCCTCCAGTTAAGCCA
1 ACTCCCTCCGGTTGTAAAACCACCAATTACAGTTCCCCCGA-TGACTGTTCCTCCAGTTAAGCCA
*
257952 CCAGTTGA
65 CCAGTCGA
** * * * * * *
257960 ACTCCCTCCAATAGTAAAACCACCAGTCACGGTTCCTCCGGTGACTGTTCCTCCA
1 ACTCCCTCCGGTTGTAAAACCACCAATTACAGTTCCCCCGATGACTGTTCCTCCA
258015 AAGATTGTGC
Statistics
Matches: 110, Mismatches: 15, Indels: 7
0.83 0.11 0.05
Matches are distributed among these distances:
72 57 0.52
73 1 0.01
74 1 0.01
75 51 0.46
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (72 bp):
ACTCCCTCCGGTTGTAAAACCACCAATTACAGTTCCCCCGATGACTGTTCCTCCAGTTAAGCCAC
CAGTCGA
Found at i:258093 original size:60 final size:60
Alignment explanation
Indices: 258023--258178 Score: 258
Period size: 60 Copynumber: 2.6 Consensus size: 60
258013 CAAAGATTGT
*
258023 GCCATCAGTTAACCTGCCTCCGGTGACTGTTCCTCCAAAGATTGTGCCCCCAGTTGTGAA
1 GCCACCAGTTAACCTGCCTCCGGTGACTGTTCCTCCAAAGATTGTGCCCCCAGTTGTGAA
*
258083 GCCACCAGTTAACCTGCCTCCGGTGACTGTTCCTCCAAAGATTGTGCCTCCAGTTGTGAA
1 GCCACCAGTTAACCTGCCTCCGGTGACTGTTCCTCCAAAGATTGTGCCCCCAGTTGTGAA
* * * *
258143 GCCACCAATTAACCTCCCTCCTGTGACTGTCCCTCC
1 GCCACCAGTTAACCTGCCTCCGGTGACTGTTCCTCC
258179 GGTTGTAAAG
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 90 1.00
ACGTcount: A:0.19, C:0.35, G:0.19, T:0.26
Consensus pattern (60 bp):
GCCACCAGTTAACCTGCCTCCGGTGACTGTTCCTCCAAAGATTGTGCCCCCAGTTGTGAA
Found at i:258163 original size:45 final size:45
Alignment explanation
Indices: 258114--258209 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 45
258104 GGTGACTGTT
* * * *
258114 CCTCCAAAGATTGTGCCTCCAGTTGTGAAGCCACCAATTAACCTC
1 CCTCCAAAGACTGTCCCTCCAGTTGTAAAGCCACCAATCAACCTC
*** * *
258159 CCTCCTGTGACTGTCCCTCCGGTTGTAAAGCCACCGATCAACCTC
1 CCTCCAAAGACTGTCCCTCCAGTTGTAAAGCCACCAATCAACCTC
258204 CCTCCA
1 CCTCCA
258210 GTGACGGTGC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.22, C:0.39, G:0.16, T:0.24
Consensus pattern (45 bp):
CCTCCAAAGACTGTCCCTCCAGTTGTAAAGCCACCAATCAACCTC
Found at i:258214 original size:45 final size:45
Alignment explanation
Indices: 258129--258214 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
258119 AAAGATTGTG
* * *
258129 CCTCCAGTTGTGAAGCCACCAATTAACCTCCCTCCTGTGACTGTC
1 CCTCCAGTTGTAAAGCCACCAATCAACCTCCCTCCAGTGACTGTC
* *
258174 CCTCCGGTTGTAAAGCCACCGATCAACCTCCCTCCAGTGAC
1 CCTCCAGTTGTAAAGCCACCAATCAACCTCCCTCCAGTGAC
258215 GGTGCCACCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.21, C:0.40, G:0.16, T:0.23
Consensus pattern (45 bp):
CCTCCAGTTGTAAAGCCACCAATCAACCTCCCTCCAGTGACTGTC
Found at i:259306 original size:40 final size:38
Alignment explanation
Indices: 259254--259329 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 38
259244 ATTATAGAAG
* * *
259254 ATAATGATAATTAATCGATTATAAATTATAAAAGATAATA
1 ATAATAATAATTAATCAATCATAAATTA-AAAA-ATAATA
259294 ATAATAATAATTAATCAATCATAAATTAAAAAATAA
1 ATAATAATAATTAATCAATCATAAATTAAAAAATAA
259330 ACACATAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 4 0.12
39 4 0.12
40 25 0.76
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (38 bp):
ATAATAATAATTAATCAATCATAAATTAAAAAATAATA
Found at i:264017 original size:16 final size:15
Alignment explanation
Indices: 263987--264028 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
263977 TATGTATATA
263987 TTTCAAAAAATATGT
1 TTTCAAAAAATATGT
*
264002 TTTCAAAACTATATGT
1 TTTCAAAA-AATATGT
264018 TTTCCAAAAAA
1 TTT-CAAAAAA
264029 CCATTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 8 0.35
16 10 0.43
17 5 0.22
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (15 bp):
TTTCAAAAAATATGT
Done.