Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011739.1 Kokia drynarioides strain JFW-HI SEQ_126733, 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: 477670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 61 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:650 original size:21 final size:21
Alignment explanation
Indices: 603--662 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
593 AATAGTATAG
* *
603 ACTTCTACCGATACAAGTGAT
1 ACTTCTATCGATACAAGTGAC
*
624 AGTTCTATCGATACAAGTGAC
1 ACTTCTATCGATACAAGTGAC
* *
645 ACTTCTATTGAAACAAGT
1 ACTTCTATCGATACAAGT
663 CTTACTTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (21 bp):
ACTTCTATCGATACAAGTGAC
Found at i:743 original size:21 final size:21
Alignment explanation
Indices: 719--770 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
709 CCTACAACTT
**
719 CTACCGATTCAAGTATTCAAA
1 CTACCGACACAAGTATTCAAA
740 CTACCGACACAAGTATTCAAA
1 CTACCGACACAAGTATTCAAA
761 CTACCGACAC
1 CTACCGACAC
771 TTCTAAACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.31, G:0.10, T:0.21
Consensus pattern (21 bp):
CTACCGACACAAGTATTCAAA
Found at i:7307 original size:31 final size:31
Alignment explanation
Indices: 7267--7325 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
7257 CTTAACAACT
*
7267 TAGTGACTTAAATAAAAACTTTTGAATAGTC
1 TAGTAACTTAAATAAAAACTTTTGAATAGTC
*
7298 TAGTAACTTAAATGAAAACTTTTGAATA
1 TAGTAACTTAAATAAAAACTTTTGAATA
7326 TTTTAGTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (31 bp):
TAGTAACTTAAATAAAAACTTTTGAATAGTC
Found at i:10357 original size:25 final size:25
Alignment explanation
Indices: 10329--10379 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
10319 TTGGGCTTCT
10329 TGGAAACATCTTCTTTTGGTCTCAA
1 TGGAAACATCTTCTTTTGGTCTCAA
10354 TGGAAACATCTTCTTTTGGTCTCAA
1 TGGAAACATCTTCTTTTGGTCTCAA
10379 T
1 T
10380 TTAGACTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.41
Consensus pattern (25 bp):
TGGAAACATCTTCTTTTGGTCTCAA
Found at i:14992 original size:21 final size:22
Alignment explanation
Indices: 14946--15004 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 22
14936 AATAGTGCAG
*
14946 ACTTCTACCGATACAAGTGACT
1 ACTTCTACCGATACAAATGACT
* *
14968 -CTTCTACCGAAACAAAT-ATT
1 ACTTCTACCGATACAAATGACT
*
14988 ACTTCTACTGATACAAA
1 ACTTCTACCGATACAAA
15005 AAACTCTAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.29
Consensus pattern (22 bp):
ACTTCTACCGATACAAATGACT
Found at i:15915 original size:104 final size:104
Alignment explanation
Indices: 15730--15958 Score: 289
Period size: 104 Copynumber: 2.2 Consensus size: 104
15720 ATTCATTTCC
* * ** * ** *
15730 TTTA-ATACTCACGATGAAACATAGCCATTGGACCTCTTTTTCCTTAAAGGAATCATACACTCAC
1 TTTATATACTCACAATGACACATAGCCATCAGACCTCATAATCCGTAAAGGAATCATACACTCAC
* ** *
15794 GATGACACATAGCCATCGAACTTTGTAACCCGTAAAGGA
66 GATGACACATAGCCATCGAACCTCATAACCCATAAAGGA
* * *
15833 TTTATATACTCACAATGACACATAGCCATCAGACCTCATAATCCGTAAAGGATTTATATACTCAC
1 TTTATATACTCACAATGACACATAGCCATCAGACCTCATAATCCGTAAAGGAATCATACACTCAC
* * *
15898 GATGACACATAGTCATCGGACCTCATAATCCATAAAGGA
66 GATGACACATAGCCATCGAACCTCATAACCCATAAAGGA
15937 TTTATATACTCACAATGACACA
1 TTTATATACTCACAATGACACA
15959 GAGTCATCGG
Statistics
Matches: 107, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
103 4 0.04
104 103 0.96
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (104 bp):
TTTATATACTCACAATGACACATAGCCATCAGACCTCATAATCCGTAAAGGAATCATACACTCAC
GATGACACATAGCCATCGAACCTCATAACCCATAAAGGA
Found at i:15968 original size:52 final size:52
Alignment explanation
Indices: 15730--15970 Score: 259
Period size: 52 Copynumber: 4.7 Consensus size: 52
15720 ATTCATTTCC
* * * * * ** *
15730 TTTA-ATACTCACGATGAAACATAGCCATTGGACCTCTTTTTCCTTAAAGGA
1 TTTATATACTCACAATGACACATAGTCATCGGACCTCATAATCCATAAAGGA
* * * * * * * ** * *
15781 ATCATACACTCACGATGACACATAGCCATCGAACTTTGTAACCCGTAAAGGA
1 TTTATATACTCACAATGACACATAGTCATCGGACCTCATAATCCATAAAGGA
* * *
15833 TTTATATACTCACAATGACACATAGCCATCAGACCTCATAATCCGTAAAGGA
1 TTTATATACTCACAATGACACATAGTCATCGGACCTCATAATCCATAAAGGA
*
15885 TTTATATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGA
1 TTTATATACTCACAATGACACATAGTCATCGGACCTCATAATCCATAAAGGA
*
15937 TTTATATACTCACAATGACACAGAGTCATCGGAC
1 TTTATATACTCACAATGACACATAGTCATCGGAC
15971 ATTTTTCATT
Statistics
Matches: 160, Mismatches: 29, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
51 2 0.01
52 158 0.99
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (52 bp):
TTTATATACTCACAATGACACATAGTCATCGGACCTCATAATCCATAAAGGA
Found at i:22132 original size:23 final size:21
Alignment explanation
Indices: 22098--22143 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
22088 ATAGCAAACA
22098 TTTTCTTCTTCTTTTCTTTTCTC
1 TTTTCTTCTTC-TTTCTTTT-TC
*
22121 TTTTCTTTTTCTTTCTTTTTC
1 TTTTCTTCTTCTTTCTTTTTC
22142 TT
1 TT
22144 ATTTTCCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 8 0.36
23 10 0.45
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTCTTCTTCTTTCTTTTTC
Found at i:22135 original size:10 final size:11
Alignment explanation
Indices: 22098--22143 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
22088 ATAGCAAACA
*
22098 TTTTCTTCTTC
1 TTTTCTTTTTC
22109 TTTTCTTTTCTC
1 TTTTCTTTT-TC
22121 TTTTCTTTTTC
1 TTTTCTTTTTC
22132 -TTTCTTTTTC
1 TTTTCTTTTTC
22142 TT
1 TT
22144 ATTTTCCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 10 0.31
11 11 0.34
12 11 0.34
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:33407 original size:21 final size:21
Alignment explanation
Indices: 33359--33411 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
33349 AATAGTGCAG
*
33359 ACTTCTACCGATACAAGTGGT
1 ACTTCTACCGATACAAGTGCT
**
33380 AGGTCTACCGATACAAGTGACT
1 ACTTCTACCGATACAAGTG-CT
33402 -CTTCTACCGA
1 ACTTCTACCGA
33412 AACAGATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGCT
Found at i:34345 original size:50 final size:52
Alignment explanation
Indices: 34164--34387 Score: 305
Period size: 52 Copynumber: 4.4 Consensus size: 52
34154 ATTCATTTCC
* ** *
34164 TTTA-ATACTCACGATGACACATAGTCATCGGAA-CTCTTGTTCCTTAAAGGA
1 TTTATATACTCACGATGACACATAGTCATC-GAACCTCATAATCCGTAAAGGA
* * * * *
34215 ATCAT-CACTCACGATGACACATAGTCATCGGACCTCGTAATCCGTAAAGGA
1 TTTATATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGA
*
34266 TTTATATACTCACGATGACACATAATCATCGAACCTCATAATCCGTAAAGGA
1 TTTATATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGA
*
34318 -TT-TATACTCACGATTACACATAGTCATCGAACCTCATAATCCGTAAAGGA
1 TTTATATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGA
34368 TTTATATACTCACGATGACA
1 TTTATATACTCACGATGACA
34388 GAGTCATCGG
Statistics
Matches: 151, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
50 48 0.32
51 46 0.30
52 57 0.38
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.28
Consensus pattern (52 bp):
TTTATATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGA
Found at i:34358 original size:102 final size:103
Alignment explanation
Indices: 34164--34387 Score: 328
Period size: 102 Copynumber: 2.2 Consensus size: 103
34154 ATTCATTTCC
* * ** *
34164 TTTA-ATACTCACGATGACACATAGTCATCGGAACTCTTGTTCCTTAAAGGAATCATCACTCACG
1 TTTATATACTCACGATGACACATAATCATCGGAACTCATAATCCGTAAAGGAATCATCACTCACG
* *
34228 ATGACACATAGTCATCGGACCTCGTAATCCGTAAAGGA
66 ATGACACATAGTCATCGAACCTCATAATCCGTAAAGGA
* *
34266 TTTATATACTCACGATGACACATAATCATC-GAACCTCATAATCCGTAAAGGATTTAT-ACTCAC
1 TTTATATACTCACGATGACACATAATCATCGGAA-CTCATAATCCGTAAAGGAATCATCACTCAC
*
34329 GATTACACATAGTCATCGAACCTCATAATCCGTAAAGGA
65 GATGACACATAGTCATCGAACCTCATAATCCGTAAAGGA
34368 TTTATATACTCACGATGACA
1 TTTATATACTCACGATGACA
34388 GAGTCATCGG
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
102 69 0.63
103 41 0.37
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.28
Consensus pattern (103 bp):
TTTATATACTCACGATGACACATAATCATCGGAACTCATAATCCGTAAAGGAATCATCACTCACG
ATGACACATAGTCATCGAACCTCATAATCCGTAAAGGA
Found at i:34393 original size:50 final size:51
Alignment explanation
Indices: 34164--34401 Score: 272
Period size: 50 Copynumber: 4.7 Consensus size: 51
34154 ATTCATTTCC
* ** *
34164 TTTA-ATACTCACGATGACACATAGTCATCGGAA-CTCTTGTTCCTTAAAGGA
1 TTTATATACTCACGATGA-ACATAGTCATC-GAACCTCATAATCCGTAAAGGA
* * * * *
34215 ATCAT-CACTCACGATGACACATAGTCATCGGACCTCGTAATCCGTAAAGGA
1 TTTATATACTCACGATGA-ACATAGTCATCGAACCTCATAATCCGTAAAGGA
*
34266 TTTATATACTCACGATGACACATAATCATCGAACCTCATAATCCGTAAAGGA
1 TTTATATACTCACGATGA-ACATAGTCATCGAACCTCATAATCCGTAAAGGA
*
34318 -TT-TATACTCACGATTACACATAGTCATCGAACCTCATAATCCGTAAAGGA
1 TTTATATACTCACGATGA-ACATAGTCATCGAACCTCATAATCCGTAAAGGA
* *
34368 TTTATATACTCACGATG-ACAGAGTCATCGGACCT
1 TTTATATACTCACGATGAACATAGTCATCGAACCT
34402 TTTTCATTTA
Statistics
Matches: 163, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
50 63 0.39
51 46 0.28
52 54 0.33
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (51 bp):
TTTATATACTCACGATGAACATAGTCATCGAACCTCATAATCCGTAAAGGA
Found at i:47626 original size:15 final size:15
Alignment explanation
Indices: 47608--47644 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
47598 ATGTTATTCT
47608 ACAAATCAATAGCTA
1 ACAAATCAATAGCTA
47623 ACAAATCAATAGCTA
1 ACAAATCAATAGCTA
*
47638 TCAAATC
1 ACAAATC
47645 CATCATAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.51, C:0.22, G:0.05, T:0.22
Consensus pattern (15 bp):
ACAAATCAATAGCTA
Found at i:50229 original size:31 final size:31
Alignment explanation
Indices: 50194--50253 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
50184 ACTTAATGAG
* *
50194 TAAACATTTATTAAAACGACGTAGTTTTGGA
1 TAAACATTTATCAAAACGACATAGTTTTGGA
*
50225 TAAACATTTATCAAAATGACATAGTTTTG
1 TAAACATTTATCAAAACGACATAGTTTTG
50254 CTTTTTCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (31 bp):
TAAACATTTATCAAAACGACATAGTTTTGGA
Found at i:68953 original size:23 final size:23
Alignment explanation
Indices: 68927--68981 Score: 83
Period size: 25 Copynumber: 2.3 Consensus size: 23
68917 TGTTGGTTTT
68927 ATTTTATATATATATACATCTTG
1 ATTTTATATATATATACATCTTG
*
68950 ATTTTGTATATATATATATATCTTG
1 A-TTT-TATATATATATACATCTTG
68975 ATTTTAT
1 ATTTTAT
68982 TTTAGTTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 4 0.14
24 6 0.21
25 19 0.66
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (23 bp):
ATTTTATATATATATACATCTTG
Found at i:68965 original size:25 final size:25
Alignment explanation
Indices: 68931--68979 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
68921 GGTTTTATTT
68931 TATATATATATACATCTTGATTTTG
1 TATATATATATACATCTTGATTTTG
*
68956 TATATATATATATATCTTGATTTT
1 TATATATATATACATCTTGATTTT
68980 ATTTTAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (25 bp):
TATATATATATACATCTTGATTTTG
Found at i:70047 original size:29 final size:28
Alignment explanation
Indices: 69882--70338 Score: 212
Period size: 29 Copynumber: 15.7 Consensus size: 28
69872 CCCCTAAACT
* * * *
69882 TTCCAAAAATTACATTTTGATCCTCAAAC
1 TTCCAAAAATTCCATTTTTA-CCCCGAAC
* * *
69911 TTTCCAAAAATTACA-TTTAACCCCTAAAC
1 -TTCCAAAAATTCCATTTTTACCCC-GAAC
* ** **
69940 TTTCCAAAAATTACATTTCAACCCTTAAAC
1 -TTCCAAAAATTCCATTTTTACCC-CGAAC
* * * *
69970 TTTCAAAAAATCACATTTTAACCCCAAAC
1 TTCCAAAAATTC-CATTTTTACCCCGAAC
69999 TTTCCAAAAATT--ATTATTTTACCCCGAAC
1 -TTCCAAAAATTCCA-T-TTTTACCCCGAAC
* *
70028 TTCCAAAAATTCCATTTTTTATCTCGAAC
1 TTCCAAAAATTCCA-TTTTTACCCCGAAC
* *
70057 TTTCTCAAAATTTCCA-TTTTACCTCGAAAC
1 -TTC-CAAAAATTCCATTTTTACCCCG-AAC
* *** **
70087 TTCTAAAAATTCCATTTTTGACCTTTATTT
1 TTCCAAAAATTCCATTTTT-ACCCCGA-AC
*
70117 TTCCAAAAACTACCA-TTTTACCCCCGAAC
1 TTCCAAAAA-TTCCATTTTTA-CCCCGAAC
* * *
70146 TTCCAAAAATTCCATTTTTGATCTCAAAC
1 TTCCAAAAATTCCATTTTT-ACCCCGAAC
* * *
70175 TTTCTAAAAATTACCA--TTTCCCCCTAGAC
1 -TTCCAAAAATT-CCATTTTTACCCCGA-AC
**
70204 TTCCAAAAATTCCATTTTTACCCCGATTT
1 TTCCAAAAATTCCATTTTTACCCCGA-AC
** *
70233 TTCC-AAAATTACCATTTTGCCCCCGAGC
1 TTCCAAAAATT-CCATTTTTACCCCGAAC
* * *
70261 TTCTAAAAATTCTATTTTTAACCTCGAAC
1 TTCCAAAAATTCCATTTTT-ACCCCGAAC
* *
70290 TTCCCGAAAGTTACCA-TTTTACCCTCGAAC
1 TT-CCAAAAATT-CCATTTTTACCC-CGAAC
*
70320 TTCCAAAGATTCCATTTTT
1 TTCCAAAAATTCCATTTTT
70339 TACATCGAAG
Statistics
Matches: 333, Mismatches: 63, Indels: 63
0.73 0.14 0.14
Matches are distributed among these distances:
27 4 0.01
28 59 0.18
29 151 0.45
30 100 0.30
31 19 0.06
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (28 bp):
TTCCAAAAATTCCATTTTTACCCCGAAC
Found at i:70048 original size:59 final size:58
Alignment explanation
Indices: 69871--70338 Score: 360
Period size: 59 Copynumber: 8.0 Consensus size: 58
69861 TCATATTTCG
* * *
69871 ACCCCTAAACTTTCCAAAAATTA-CATTTTGATCCTCAAACTTTCCAAAAATTACA--TTTA
1 ACCCC-AAACTTTCCAAAAATTACCATTTT-A-CCCCGAAC-TTCCAAAAATTCCATTTTTA
* ** * *
69930 ACCCCTAAACTTTCCAAAAATTA-CATTTCAACCCTTAAACTTTCAAAAAATCACA-TTTTA
1 ACCCC-AAACTTTCCAAAAATTACCATTT-TACCC-CGAACTTCCAAAAATTC-CATTTTTA
** *
69990 ACCCCAAACTTTCCAAAAATTATTATTTTACCCCGAACTTCCAAAAATTCCATTTTTT
1 ACCCCAAACTTTCCAAAAATTACCATTTTACCCCGAACTTCCAAAAATTCCATTTTTA
* * * * * * *
70048 ATCTCGAACTTTCTC-AAAATTTCCATTTTACCTCGAAACTTCTAAAAATTCCATTTTTG
1 ACCCCAAACTTTC-CAAAAATTACCATTTTACCCCG-AACTTCCAAAAATTCCATTTTTA
*** ** * *
70107 ACCTTTATTTTTCCAAAAACTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTG
1 ACCCCAAACTTTCCAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATTCCATTTTTA
* * * * *
70166 ATCTCAAACTTTCTAAAAATTACCA-TTTCCCCCTAGACTTCCAAAAATTCCATTTTT-
1 ACCCCAAACTTTCCAAAAATTACCATTTTACCCCGA-ACTTCCAAAAATTCCATTTTTA
* ** * * * *
70223 ACCCCGATTTTTCC-AAAATTACCATTTTGCCCCCGAGCTTCTAAAAATTCTATTTTTA
1 ACCCCAAACTTTCCAAAAATTACCATTTT-ACCCCGAACTTCCAAAAATTCCATTTTTA
* * * * * *
70281 ACCTCGAACTTCCCGAAAGTTACCATTTTACCCTCGAACTTCCAAAGATTCCATTTTT
1 ACCCCAAACTTTCCAAAAATTACCATTTTACCC-CGAACTTCCAAAAATTCCATTTTT
70339 TACATCGAAG
Statistics
Matches: 333, Mismatches: 60, Indels: 32
0.78 0.14 0.08
Matches are distributed among these distances:
56 10 0.03
57 36 0.11
58 98 0.29
59 172 0.52
60 17 0.05
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (58 bp):
ACCCCAAACTTTCCAAAAATTACCATTTTACCCCGAACTTCCAAAAATTCCATTTTTA
Found at i:71996 original size:16 final size:17
Alignment explanation
Indices: 71961--72002 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
71951 AAATTAAGGG
*
71961 TTATTTTTTAATTTAAT
1 TTATTATTTAATTTAAT
*
71978 TTATTATTT-ATTTATT
1 TTATTATTTAATTTAAT
71994 TTATTATTT
1 TTATTATTT
72003 TTCACAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATTATTTAATTTAAT
Found at i:78675 original size:18 final size:18
Alignment explanation
Indices: 78652--78691 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
78642 ACCGCCTCTG
78652 CCAAAGCTACCATTGTTA
1 CCAAAGCTACCATTGTTA
78670 CCAAAGCTACCATTGTTA
1 CCAAAGCTACCATTGTTA
78688 CCAA
1 CCAA
78692 GGTATGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.30, G:0.10, T:0.25
Consensus pattern (18 bp):
CCAAAGCTACCATTGTTA
Found at i:88023 original size:6 final size:6
Alignment explanation
Indices: 88012--88050 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
88002 TGATCAAAAT
* * *
88012 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
88051 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:99801 original size:10 final size:10
Alignment explanation
Indices: 99782--99849 Score: 58
Period size: 9 Copynumber: 7.2 Consensus size: 10
99772 TTATATTGTT
99782 AAAAAA-TAA
1 AAAAAATTAA
99791 AAAAAATT-A
1 AAAAAATTAA
99800 AAAAAATCTAA
1 AAAAAAT-TAA
* *
99811 AGAATA-TAA
1 AAAAAATTAA
99820 AAAAAATT--
1 AAAAAATTAA
99828 -AAAAATTAA
1 AAAAAATTAA
99837 AAAAAATTTAA
1 AAAAAA-TTAA
99848 AA
1 AA
99850 TAATAAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
7 7 0.15
9 21 0.45
10 8 0.17
11 11 0.23
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:99805 original size:18 final size:18
Alignment explanation
Indices: 99782--99856 Score: 71
Period size: 19 Copynumber: 4.1 Consensus size: 18
99772 TTATATTGTT
* *
99782 AAAAAATAAAAAAAATTA
1 AAAAAATTAAAAAAATAA
*
99800 AAAAAATCTAAAGAATATAA
1 AAAAAAT-TAAA-AAAATAA
*
99820 AAAAAATT-AAAAATTAA
1 AAAAAATTAAAAAAATAA
*
99837 AAAAAATTTAAAATAATAA
1 AAAAAA-TTAAAAAAATAA
99856 A
1 A
99857 TTTGAGATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
17 11 0.24
18 11 0.24
19 12 0.26
20 12 0.26
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (18 bp):
AAAAAATTAAAAAAATAA
Found at i:99820 original size:19 final size:16
Alignment explanation
Indices: 99792--99841 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 16
99782 AAAAAATAAA
99792 AAAAATTAAAAAAATCT
1 AAAAATTAAAAAAAT-T
99809 AAAGAATATAAAAAAAATT
1 AAA-AAT-T-AAAAAAATT
99828 AAAAATTAAAAAAA
1 AAAAATTAAAAAAA
99842 ATTTAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 7 0.23
17 4 0.13
18 6 0.20
19 5 0.17
20 8 0.27
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (16 bp):
AAAAATTAAAAAAATT
Found at i:99849 original size:9 final size:9
Alignment explanation
Indices: 99782--99841 Score: 61
Period size: 9 Copynumber: 6.7 Consensus size: 9
99772 TTATATTGTT
*
99782 AAAAAATAA
1 AAAAAATTA
99791 AAAAAATTA
1 AAAAAATTA
99800 AAAAAATCTA
1 AAAAAAT-TA
* *
99810 AAGAATATAA
1 AA-AAAATTA
99820 AAAAAATT-
1 AAAAAATTA
99828 -AAAAATTA
1 AAAAAATTA
99836 AAAAAA
1 AAAAAA
99842 ATTTAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
7 7 0.17
9 24 0.57
10 7 0.17
11 4 0.10
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (9 bp):
AAAAAATTA
Found at i:101197 original size:35 final size:35
Alignment explanation
Indices: 101144--101236 Score: 134
Period size: 35 Copynumber: 2.7 Consensus size: 35
101134 TATTCGTTTA
*
101144 CTCCCTGTTGACCCAAAGGTCATTATGCTCACTTT
1 CTCCTTGTTGACCCAAAGGTCATTATGCTCACTTT
* * *
101179 CTCCTTGTTGACCTAAAGGTCATTCTGCTCATTTT
1 CTCCTTGTTGACCCAAAGGTCATTATGCTCACTTT
101214 CT-CTCTGTTGACCCAAAGGTCAT
1 CTCCT-TGTTGACCCAAAGGTCAT
101237 GCTTGTTACC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
34 2 0.04
35 50 0.96
ACGTcount: A:0.19, C:0.29, G:0.15, T:0.37
Consensus pattern (35 bp):
CTCCTTGTTGACCCAAAGGTCATTATGCTCACTTT
Found at i:106335 original size:40 final size:40
Alignment explanation
Indices: 106281--106412 Score: 210
Period size: 40 Copynumber: 3.3 Consensus size: 40
106271 TTCCTTTAAC
* * *
106281 CATATTCTTATTCTCATCTCAAGACATGAGTCTTCCTTAT
1 CATAATCTCATTCTCATCTCAAGATATGAGTCTTCCTTAT
*
106321 CATAAACTCATTCTCATCTCAAGATATGAGTCTTCCTTAT
1 CATAATCTCATTCTCATCTCAAGATATGAGTCTTCCTTAT
*
106361 CATAATCTCATTCTCATCTCGAGATATGAGTCTTCCTTATT
1 CATAATCTCATTCTCATCTCAAGATATGAGTCTTCCTTA-T
106402 CATAATCTCAT
1 CATAATCTCAT
106413 GCCCATTTTT
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 73 0.86
41 12 0.14
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (40 bp):
CATAATCTCATTCTCATCTCAAGATATGAGTCTTCCTTAT
Found at i:113407 original size:40 final size:40
Alignment explanation
Indices: 113362--113492 Score: 192
Period size: 40 Copynumber: 3.2 Consensus size: 40
113352 AACCATATTG
*
113362 TCATTCTCATCTCAAGACATGAGTCTTCCTTATCATAATC
1 TCATTCTCATCTCAAGATATGAGTCTTCCTTATCATAATC
*
113402 TCATTCTTATCT-AGAGATATGAGTCTTCCTTATCATAATC
1 TCATTCTCATCTCA-AGATATGAGTCTTCCTTATCATAATC
* *
113442 TCATTCTCATCTCGAGATATGAGTCTTACTTATTCATAATC
1 TCATTCTCATCTCAAGATATGAGTCTTCCTTA-TCATAATC
*
113483 TCATGCTCAT
1 TCATTCTCAT
113493 TTTCGAGTCA
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
39 1 0.01
40 64 0.78
41 17 0.21
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.40
Consensus pattern (40 bp):
TCATTCTCATCTCAAGATATGAGTCTTCCTTATCATAATC
Found at i:116977 original size:25 final size:25
Alignment explanation
Indices: 116949--117029 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
116939 AGCCCATCAA
116949 AATATCGCTCTTATGAGCCAGACAG
1 AATATCGCTCTTATGAGCCAGACAG
* * *
116974 AATACCGCTCTTACGAGCCAGATAG
1 AATATCGCTCTTATGAGCCAGACAG
*
116999 AATATTGCTCTT-TCGAGCCAGAATCAG
1 AATATCGCTCTTAT-GAGCCAG-A-CAG
117026 AATA
1 AATA
117030 ATGCTTCTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
25 39 0.85
26 1 0.02
27 6 0.13
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (25 bp):
AATATCGCTCTTATGAGCCAGACAG
Found at i:117003 original size:50 final size:53
Alignment explanation
Indices: 116931--117047 Score: 129
Period size: 50 Copynumber: 2.3 Consensus size: 53
116921 CAGAATATTA
* *
116931 CTCTTACGAGCC-CATCAAAATATCGCTCTTAT-GAGCCAG-A-CAGAATACCG
1 CTCTTACGAGCCAGATCAAAATATCGCTCTT-TCGAGCCAGAATCAGAATAACG
* * *
116981 CTCTTACGAGCCAGAT-AGAATATTGCTCTTTCGAGCCAGAATCAGAATAATG
1 CTCTTACGAGCCAGATCAAAATATCGCTCTTTCGAGCCAGAATCAGAATAACG
117033 CTTCTT-CGAGCCAGA
1 C-TCTTACGAGCCAGA
117048 ATCAGATTAC
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
49 1 0.02
50 31 0.54
51 3 0.05
52 18 0.32
53 4 0.07
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (53 bp):
CTCTTACGAGCCAGATCAAAATATCGCTCTTTCGAGCCAGAATCAGAATAACG
Found at i:117040 original size:27 final size:26
Alignment explanation
Indices: 116963--117053 Score: 100
Period size: 25 Copynumber: 3.5 Consensus size: 26
116953 TCGCTCTTAT
**
116963 GAGCCAG-A-CAGAATACCGCTCTTAC
1 GAGCCAGAATCAGAATAATGCTCTT-C
*
116988 GAGCCAG-AT-AGAATATTGCTCTTTC
1 GAGCCAGAATCAGAATAATGCTC-TTC
117013 GAGCCAGAATCAGAATAATGCTTCTTC
1 GAGCCAGAATCAGAATAATGC-TCTTC
117040 GAGCCAGAATCAGA
1 GAGCCAGAATCAGA
117054 TTACTCCTCA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
25 26 0.45
26 4 0.07
27 26 0.45
28 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (26 bp):
GAGCCAGAATCAGAATAATGCTCTTC
Found at i:122029 original size:25 final size:25
Alignment explanation
Indices: 121980--122099 Score: 96
Period size: 25 Copynumber: 4.7 Consensus size: 25
121970 ACAGAGTTTA
* * * *
121980 GCTCTTACGAGCCCAGACAAAATATT
1 GCTCTTACAAG-CCAGATAGAATATC
*
122006 GCTCTTACAAGCCAGATAGGATATC
1 GCTCTTACAAGCCAGATAGAATATC
* *
122031 ACTCTTACAAGCCAGACAGAATATC
1 GCTCTTACAAGCCAGATAGAATATC
* * * * *
122056 GCTCTTTCGAGCCAAAATCAGAATGTT
1 GCTCTTACAAGCC-AGAT-AGAATATC
*
122083 GCTCTTTCAAGCCAGAT
1 GCTCTTACAAGCCAGAT
122100 CAGATTACTC
Statistics
Matches: 75, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
25 42 0.56
26 15 0.20
27 18 0.24
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.25
Consensus pattern (25 bp):
GCTCTTACAAGCCAGATAGAATATC
Found at i:122287 original size:18 final size:18
Alignment explanation
Indices: 122260--122294 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
122250 ATTTTCCCTT
122260 ATTCTCGATCTACTACAC
1 ATTCTCGATCTACTACAC
* *
122278 ATTCTTGATCTATTACA
1 ATTCTCGATCTACTACA
122295 ATAATTCAAT
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:0.29, C:0.26, G:0.06, T:0.40
Consensus pattern (18 bp):
ATTCTCGATCTACTACAC
Found at i:123726 original size:14 final size:15
Alignment explanation
Indices: 123707--123740 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
123697 ACTAACTTTT
*
123707 AATTCACTAATT-AA
1 AATTCACCAATTCAA
123721 AATTCACCAATTCAA
1 AATTCACCAATTCAA
123736 AATTC
1 AATTC
123741 TATATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (15 bp):
AATTCACCAATTCAA
Found at i:125414 original size:13 final size:13
Alignment explanation
Indices: 125396--125420 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
125386 TTTCTCTTTC
125396 TTTTTCTTTTTAT
1 TTTTTCTTTTTAT
125409 TTTTTCTTTTTA
1 TTTTTCTTTTTA
125421 CAATACTTCT
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:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTCTTTTTAT
Found at i:127349 original size:60 final size:62
Alignment explanation
Indices: 127285--127423 Score: 153
Period size: 59 Copynumber: 2.3 Consensus size: 62
127275 TAGTGAGAAA
** * **
127285 TTTCAAAAATTTGAAGGGTTTAATTAAAATTTTCTAAAAATT-TCAAGAAAT-AAT-AAAAAT
1 TTTCAAAAATTTGAAGGGGCTAATTAAAACTTTAGAAAAATTCT-AAGAAATAAATAAAAAAT
*
127345 TTTCAAAAATTT--AGTGGGCTAATTAAAACTTTAGAAAAATTCTAATAAATAAATAAAAAAT
1 TTTCAAAAATTTGAAG-GGGCTAATTAAAACTTTAGAAAAATTCTAAGAAATAAATAAAAAAT
*
127406 TTTCAAAATTTTAGAAGG
1 TTTCAAAAATTT-GAAGG
127424 ACCAAGGCCA
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
58 2 0.03
59 27 0.42
60 16 0.25
61 17 0.26
63 1 0.02
64 2 0.03
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (62 bp):
TTTCAAAAATTTGAAGGGGCTAATTAAAACTTTAGAAAAATTCTAAGAAATAAATAAAAAAT
Found at i:127370 original size:59 final size:61
Alignment explanation
Indices: 127305--127419 Score: 155
Period size: 59 Copynumber: 1.9 Consensus size: 61
127295 TTGAAGGGTT
* **
127305 TAATTAAAATTTTCTAAAAATT-TCAAGAAAT-AAT-AAAAATTTTCAAAAATTTAGTGGGC
1 TAATTAAAACTTTAGAAAAATTCT-AAGAAATAAATAAAAAATTTTCAAAAATTTAGTGGGC
* *
127364 TAATTAAAACTTTAGAAAAATTCTAATAAATAAATAAAAAATTTTCAAAATTTTAG
1 TAATTAAAACTTTAGAAAAATTCTAAGAAATAAATAAAAAATTTTCAAAAATTTAG
127420 AAGGACCAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 25 0.52
60 4 0.08
61 19 0.40
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (61 bp):
TAATTAAAACTTTAGAAAAATTCTAAGAAATAAATAAAAAATTTTCAAAAATTTAGTGGGC
Found at i:129067 original size:29 final size:29
Alignment explanation
Indices: 129025--129082 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
129015 ATCAACATGC
*
129025 GATAACATAACACA-AATTAAAATCACACA
1 GATAACACAACACAGAA-TAAAATCACACA
*
129054 GATAACACAACACAGAATAATATCACACA
1 GATAACACAACACAGAATAAAATCACACA
129083 AGGTGTGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.57, C:0.22, G:0.05, T:0.16
Consensus pattern (29 bp):
GATAACACAACACAGAATAAAATCACACA
Found at i:129626 original size:20 final size:19
Alignment explanation
Indices: 129585--129626 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
129575 TCAAGTTCGG
*
129585 GTTAACGGGTCAGGTTTGA
1 GTTAACGGGTCAGGTATGA
*
129604 GTTAATGGGTCAGGTCATGA
1 GTTAACGGGTCAGGT-ATGA
129624 GTT
1 GTT
129627 CACAAGTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.21, C:0.10, G:0.36, T:0.33
Consensus pattern (19 bp):
GTTAACGGGTCAGGTATGA
Found at i:135896 original size:29 final size:29
Alignment explanation
Indices: 135843--135900 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
135833 ATCAACATAC
*
135843 GATAACACAACATAGATTAAAATCACACA
1 GATAACACAACACAGATTAAAATCACACA
*
135872 GATAACACAACACAGGA-TAATATCACACA
1 GATAACACAACACA-GATTAAAATCACACA
135901 AGGTGTGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.53, C:0.22, G:0.09, T:0.16
Consensus pattern (29 bp):
GATAACACAACACAGATTAAAATCACACA
Found at i:136368 original size:11 final size:11
Alignment explanation
Indices: 136354--136378 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
136344 TGTTTTAAAA
136354 AGTCAATAGTC
1 AGTCAATAGTC
136365 AGTCAATAGTC
1 AGTCAATAGTC
136376 AGT
1 AGT
136379 AGTCAACATT
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:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (11 bp):
AGTCAATAGTC
Found at i:136397 original size:20 final size:22
Alignment explanation
Indices: 136367--136411 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
136357 CAATAGTCAG
* *
136367 TCAATAGTCAGTAGTCAAC-AT
1 TCAATAGTCAGCAATCAACAAT
136388 TCAA-AGTCAGCAATCAACAAT
1 TCAATAGTCAGCAATCAACAAT
136409 TCA
1 TCA
136412 GGTTCGGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.24
Consensus pattern (22 bp):
TCAATAGTCAGCAATCAACAAT
Found at i:142785 original size:3 final size:3
Alignment explanation
Indices: 142777--142829 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
142767 GTGCAACGTA
* *
142777 TTC TTC TTC TTCC TTC -TC TTC TTT TTC TTC TCC TT- TTC -TC TTC
1 TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
142820 -TC TTC TTC TT
1 TTC TTC TTC TT
142830 TTGCTTCAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
2 8 0.20
3 30 0.73
4 3 0.07
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:142804 original size:24 final size:21
Alignment explanation
Indices: 142778--142829 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
142768 TGCAACGTAT
*
142778 TCTTCTTCTTC-CTTCTCTTC
1 TCTTCTTCTTCTTTTCTCTTC
* *
142798 TTTTTCTTCTCCTTTTCTCTTC
1 -TCTTCTTCTTCTTTTCTCTTC
142820 TCTTCTTCTT
1 TCTTCTTCTT
142830 TTGCTTCAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (21 bp):
TCTTCTTCTTCTTTTCTCTTC
Found at i:150224 original size:18 final size:17
Alignment explanation
Indices: 150201--150234 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
150191 TTTAAAAGAA
150201 AATCAACAAAAGATTAGT
1 AATCAACAAAAG-TTAGT
*
150219 AATCAATAAAAGTTAG
1 AATCAACAAAAGTTAG
150235 AAAAAGAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.24
Consensus pattern (17 bp):
AATCAACAAAAGTTAGT
Found at i:153445 original size:2 final size:2
Alignment explanation
Indices: 153438--153462 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
153428 TTTATGTGAT
153438 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 T
153463 TTCTAAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:154226 original size:20 final size:21
Alignment explanation
Indices: 154187--154239 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
154177 TTTTCCAAAC
*
154187 AGTATCGATACCCTTTTTAAA
1 AGTATCGATACCCTTCTTAAA
*
154208 AGTATTGATA-CCTTCTTAAA
1 AGTATCGATACCCTTCTTAAA
* *
154228 AATATCAATACC
1 AGTATCGATACC
154240 AACATAGCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.36
Consensus pattern (21 bp):
AGTATCGATACCCTTCTTAAA
Found at i:155157 original size:31 final size:27
Alignment explanation
Indices: 155103--155158 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 27
155093 GAGTCTTATG
*
155103 TTATTATATAATATATTTGCATGGGCT
1 TTATTATATAATATATTTACATGGGCT
155130 TTATTATATAAAGTATATATATACATGGG
1 TTATTATAT-AA-TATAT-T-TACATGGG
155159 TTATGGTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 9 0.38
28 2 0.08
29 5 0.21
30 1 0.04
31 7 0.29
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (27 bp):
TTATTATATAATATATTTACATGGGCT
Found at i:155175 original size:2 final size:2
Alignment explanation
Indices: 155168--155194 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
155158 GTTATGGTGT
155168 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
155195 TTATGGGATG
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:165809 original size:18 final size:18
Alignment explanation
Indices: 165752--165811 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
165742 CATTCGAGCT
*
165752 TGTGGTTGCATCTGG-CTA
1 TGTGATTGCATCTGGTC-A
* * * **
165770 TATGAATGCATCTGATTT
1 TGTGATTGCATCTGGTCA
165788 TGTGATTGCATCTGGTCA
1 TGTGATTGCATCTGGTCA
165806 TGTGAT
1 TGTGAT
165812 CACATATTAT
Statistics
Matches: 30, Mismatches: 11, Indels: 2
0.70 0.26 0.05
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.18, C:0.13, G:0.27, T:0.42
Consensus pattern (18 bp):
TGTGATTGCATCTGGTCA
Found at i:167384 original size:24 final size:24
Alignment explanation
Indices: 167336--167382 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
167326 AAGAGTTAAT
167336 TTGTTAATGCAAATATAAAATAAA
1 TTGTTAATGCAAATATAAAATAAA
*
167360 TTGTTAGA-GCAAAT-TAAGATAAA
1 TTGTTA-ATGCAAATATAAAATAAA
167383 ATGAATAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.32
Consensus pattern (24 bp):
TTGTTAATGCAAATATAAAATAAA
Found at i:175703 original size:17 final size:17
Alignment explanation
Indices: 175666--175710 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
175656 TGACAAATAG
*
175666 AAATGCAATGATAACGC
1 AAATGCAATGATAACGA
**
175683 AAATGCAATGATAATTA
1 AAATGCAATGATAACGA
*
175700 AAATGTAATGA
1 AAATGCAATGA
175711 CAATGGGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.24
Consensus pattern (17 bp):
AAATGCAATGATAACGA
Found at i:179150 original size:12 final size:12
Alignment explanation
Indices: 179133--179162 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
179123 GACTCTTCGT
*
179133 AGAATTATTATA
1 AGAATTATCATA
179145 AGAATTATCATA
1 AGAATTATCATA
179157 AGAATT
1 AGAATT
179163 TCCACGGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.37
Consensus pattern (12 bp):
AGAATTATCATA
Found at i:182555 original size:23 final size:23
Alignment explanation
Indices: 182529--182581 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
182519 ACGACAGTAC
182529 AATAAAAGTGTCTTTTAAATCCA
1 AATAAAAGTGTCTTTTAAATCCA
182552 AATAAAAGTGTCTTTTAAATCCA
1 AATAAAAGTGTCTTTTAAATCCA
182575 AATAAAA
1 AATAAAA
182582 ACCAGTTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (23 bp):
AATAAAAGTGTCTTTTAAATCCA
Found at i:189835 original size:18 final size:19
Alignment explanation
Indices: 189802--189840 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
189792 TGCTCATCCA
*
189802 TCTTTCCCCCTCTTCATTG
1 TCTTTCCCCCTCTTCAATG
*
189821 TCTTT-CCCTTCTTCAATG
1 TCTTTCCCCCTCTTCAATG
189839 TC
1 TC
189841 CTCCTCATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.08, C:0.38, G:0.05, T:0.49
Consensus pattern (19 bp):
TCTTTCCCCCTCTTCAATG
Found at i:193402 original size:11 final size:10
Alignment explanation
Indices: 193381--193423 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
193371 GAAATTAAAC
193381 AAATAAATAA
1 AAATAAATAA
193391 AAATATAATAA
1 AAATA-AATAA
193402 AAATAAATAA
1 AAATAAATAA
*
193412 ATA-AAATAA
1 AAATAAATAA
193421 AAA
1 AAA
193424 GAATCGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
9 8 0.27
10 12 0.40
11 10 0.33
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAATAAATAA
Found at i:193413 original size:19 final size:20
Alignment explanation
Indices: 193381--193423 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
193371 GAAATTAAAC
*
193381 AAATAAATAAAAATATAATAA
1 AAATAAAT-AAAATAAAATAA
193402 AAATAAAT-AAATAAAATAA
1 AAATAAATAAAATAAAATAA
193421 AAA
1 AAA
193424 GAATCGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.62
21 8 0.38
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (20 bp):
AAATAAATAAAATAAAATAA
Found at i:200226 original size:16 final size:16
Alignment explanation
Indices: 200205--200237 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
200195 TTCTAATTTA
200205 AAACATGGCTCCTCTT
1 AAACATGGCTCCTCTT
200221 AAACATGGCTCCTCTT
1 AAACATGGCTCCTCTT
200237 A
1 A
200238 TGCTTGGAGA
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:0.27, C:0.30, G:0.12, T:0.30
Consensus pattern (16 bp):
AAACATGGCTCCTCTT
Found at i:203944 original size:7 final size:7
Alignment explanation
Indices: 203932--203956 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
203922 TGAACTCAAG
203932 AAATTTA
1 AAATTTA
203939 AAATTTA
1 AAATTTA
203946 AAATTTA
1 AAATTTA
203953 AAAT
1 AAAT
203957 AATATCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:220764 original size:22 final size:21
Alignment explanation
Indices: 220716--220765 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
220706 GATGATGACA
*
220716 AAATAA-AAATATATAAATAC
1 AAATAATAAATAAATAAATAC
**
220736 ATTTAATAACATAAATAAATAC
1 AAATAATAA-ATAAATAAATAC
220758 AAATAATA
1 AAATAATA
220766 CTAGTAGTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 4 0.17
21 2 0.09
22 17 0.74
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATAATAAATAAATAAATAC
Found at i:224798 original size:20 final size:20
Alignment explanation
Indices: 224749--224802 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
224739 GAAATAGGCG
224749 ATTTATTTTATAATACAATT
1 ATTTATTTTATAATACAATT
* *
224769 ATTT-TTTTATATGTATAA-T
1 ATTTATTTTATA-ATACAATT
224788 ATTTATTTTATAATA
1 ATTTATTTTATAATA
224803 TTGATGATCC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
ATTTATTTTATAATACAATT
Found at i:224855 original size:32 final size:34
Alignment explanation
Indices: 224817--224885 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
224807 TGATCCTCTA
* * *
224817 ATTTTTATATGAAAA-AATAATGATATTTGAAAT
1 ATTTTAATATAAAAATAATAATGATATTTAAAAT
*
224850 ATTTTACATATAAAAATAATAATTATATTTAAAAT
1 ATTTTA-ATATAAAAATAATAATGATATTTAAAAT
224885 A
1 A
224886 ATTATTTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.17
34 8 0.27
35 17 0.57
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (34 bp):
ATTTTAATATAAAAATAATAATGATATTTAAAAT
Found at i:232620 original size:31 final size:30
Alignment explanation
Indices: 232531--232644 Score: 101
Period size: 31 Copynumber: 3.8 Consensus size: 30
232521 ATTTCTTAAC
* * *
232531 TAAACTTGATATATTTTTTTAATTTGATATT
1 TAAATTTGATAT-TTTTTCTAATTTGATACT
* *
232562 TAAATTT--T-TTTTATCCAATTT-AGTACT
1 TAAATTTGATATTTTTTCTAATTTGA-TACT
232589 TAAATTTGATACTTTTTTCTAATTTGATACT
1 TAAATTTGATA-TTTTTTCTAATTTGATACT
* *
232620 TGAATTTGATATATTTTTTTAATTT
1 TAAATTTGATAT-TTTTTCTAATTT
232645 TTTAAATATT
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
26 1 0.01
27 19 0.28
28 1 0.01
29 2 0.03
30 1 0.01
31 42 0.63
32 1 0.01
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (30 bp):
TAAATTTGATATTTTTTCTAATTTGATACT
Found at i:232838 original size:28 final size:28
Alignment explanation
Indices: 232783--232895 Score: 97
Period size: 28 Copynumber: 3.9 Consensus size: 28
232773 AGTATTTAAT
*
232783 AAATTTAGGTACCAAATT--GAATCTAAAA
1 AAATTTAGGTACCAAATTAAGAA--AAAAA
*
232811 AAATTTAGGTATCAAATTAAGAAAAAAA
1 AAATTTAGGTACCAAATTAAGAAAAAAA
* * * *
232839 TGTCAAATTCAAGTACCAAATTAGGTAAAAAA
1 ----AAATTTAGGTACCAAATTAAGAAAAAAA
232871 AAATTTAGGTACCAAATTAA-AAAAA
1 AAATTTAGGTACCAAATTAAGAAAAA
232896 TTTATCAAGT
Statistics
Matches: 68, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
27 4 0.06
28 38 0.56
30 3 0.04
32 23 0.34
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.26
Consensus pattern (28 bp):
AAATTTAGGTACCAAATTAAGAAAAAAA
Found at i:232876 original size:60 final size:59
Alignment explanation
Indices: 232807--232918 Score: 161
Period size: 59 Copynumber: 1.9 Consensus size: 59
232797 AATTGAATCT
* *
232807 AAAAAAATTTAGGTATCAAATTAAGAAAAAAATGTCAAATTCAAGTACCAAATTAGGTAA
1 AAAAAAATTTAGGTACCAAATTAA-AAAAAAATATCAAATTCAAGTACCAAATTAGGTAA
** * *
232867 AAAAAAATTTAGGTACCAAATTAAAAAAATTTATCAAGTTCAAGTATCAAAT
1 AAAAAAATTTAGGTACCAAATTAAAAAAAAATATCAAATTCAAGTACCAAAT
232919 ATTATATTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 23 0.50
60 23 0.50
ACGTcount: A:0.54, C:0.09, G:0.10, T:0.27
Consensus pattern (59 bp):
AAAAAAATTTAGGTACCAAATTAAAAAAAAATATCAAATTCAAGTACCAAATTAGGTAA
Found at i:240916 original size:15 final size:16
Alignment explanation
Indices: 240898--240932 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
240888 CGGTTTGGAC
240898 TTGGTTCA-ATTGGGT
1 TTGGTTCACATTGGGT
*
240913 TTGGTTCACTTTGGGT
1 TTGGTTCACATTGGGT
240929 TTGG
1 TTGG
240933 GTTATTGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.09, C:0.09, G:0.34, T:0.49
Consensus pattern (16 bp):
TTGGTTCACATTGGGT
Found at i:247911 original size:17 final size:16
Alignment explanation
Indices: 247884--247915 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
247874 AACGGTCAAT
247884 GGTTTGACTTGGTTTG
1 GGTTTGACTTGGTTTG
247900 GGTTTGGACTTGGTTT
1 GGTTT-GACTTGGTTT
247916 AATGGGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.06, C:0.06, G:0.38, T:0.50
Consensus pattern (16 bp):
GGTTTGACTTGGTTTG
Found at i:263096 original size:28 final size:28
Alignment explanation
Indices: 263064--263121 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
263054 GTAATCATAG
* *
263064 AGGCGCCCTTGAGCAAAGATAGCCACAA
1 AGGCGCCCTTAAACAAAGATAGCCACAA
**
263092 AGGCGTTCTTAAACAAAGATAGCCACAA
1 AGGCGCCCTTAAACAAAGATAGCCACAA
263120 AG
1 AG
263122 ACGTTCCCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (28 bp):
AGGCGCCCTTAAACAAAGATAGCCACAA
Found at i:266455 original size:13 final size:13
Alignment explanation
Indices: 266437--266463 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
266427 TAACTATTTG
266437 TCAATAATGACAA
1 TCAATAATGACAA
266450 TCAATAATGACAA
1 TCAATAATGACAA
266463 T
1 T
266464 AAGTTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (13 bp):
TCAATAATGACAA
Found at i:276037 original size:23 final size:23
Alignment explanation
Indices: 275978--276044 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
275968 CAACAGGTCG
* *
275978 GGTCAAAGTCAATAGGACGGGTT
1 GGTCAAAGTCAATGGGTCGGGTT
*
276001 AGTCAAAGTCAATGGGTCGGGTT
1 GGTCAAAGTCAATGGGTCGGGTT
276024 GGTCAAAGTCAATGGGTCGGG
1 GGTCAAAGTCAATGGGTCGGG
276045 CTCGATTTGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.27, C:0.13, G:0.37, T:0.22
Consensus pattern (23 bp):
GGTCAAAGTCAATGGGTCGGGTT
Found at i:293331 original size:3 final size:3
Alignment explanation
Indices: 293318--293348 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
293308 TACAATCCAA
293318 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
293349 CAAAATCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:304238 original size:23 final size:24
Alignment explanation
Indices: 304215--304332 Score: 100
Period size: 25 Copynumber: 4.8 Consensus size: 24
304205 TTTAATCACA
304215 TTAGTCACATGAATATTTCAACAT
1 TTAGTCACATGAATATTTCAACAT
*
304239 TTA-TCACATCACATATTAATC-ACAT
1 TTAGTCACATGA-ATATT--TCAACAT
*
304264 TTAGTCACATGAATATTTCAAAAT
1 TTAGTCACATGAATATTTCAACAT
*
304288 TTA-TCACATCACATATTAATC-ACAT
1 TTAGTCACATGA-ATATT--TCAACAT
* * *
304313 TTAATCAAATTAATATTTCA
1 TTAGTCACATGAATATTTCA
304333 GCACAAATGA
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
23 18 0.23
24 19 0.25
25 23 0.30
26 17 0.22
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (24 bp):
TTAGTCACATGAATATTTCAACAT
Found at i:304251 original size:28 final size:28
Alignment explanation
Indices: 304219--304301 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 28
304209 ATCACATTAG
304219 TCACATGAATATTTCAACATTTATCACA
1 TCACATGAATATTTCAACATTTATCACA
* * *
304247 TCACAT-ATTA-ATC-ACA-TT-T-A-G
1 TCACATGAATATTTCAACATTTATCACA
*
304268 TCACATGAATATTTCAAAATTTATCACA
1 TCACATGAATATTTCAACATTTATCACA
304296 TCACAT
1 TCACAT
304302 ATTAATCACA
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
21 6 0.15
22 4 0.10
23 3 0.07
24 4 0.10
25 5 0.12
26 3 0.07
27 4 0.10
28 12 0.29
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.36
Consensus pattern (28 bp):
TCACATGAATATTTCAACATTTATCACA
Found at i:304274 original size:49 final size:49
Alignment explanation
Indices: 304199--304332 Score: 218
Period size: 49 Copynumber: 2.8 Consensus size: 49
304189 ATCATATATA
*
304199 ATCACAT-TTAATCACA-TTAGTCACATGAATATTTCAACATTTATCAC
1 ATCACATATTAATCACATTTAGTCACATGAATATTTCAAAATTTATCAC
304246 ATCACATATTAATCACATTTAGTCACATGAATATTTCAAAATTTATCAC
1 ATCACATATTAATCACATTTAGTCACATGAATATTTCAAAATTTATCAC
* * *
304295 ATCACATATTAATCACATTTAATCAAATTAATATTTCA
1 ATCACATATTAATCACATTTAGTCACATGAATATTTCA
304333 GCACAAATGA
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
47 7 0.09
48 9 0.11
49 65 0.80
ACGTcount: A:0.41, C:0.19, G:0.03, T:0.37
Consensus pattern (49 bp):
ATCACATATTAATCACATTTAGTCACATGAATATTTCAAAATTTATCAC
Found at i:304348 original size:23 final size:23
Alignment explanation
Indices: 304315--304447 Score: 158
Period size: 23 Copynumber: 5.8 Consensus size: 23
304305 AATCACATTT
* *
304315 AATCAAATTAATATTTCAGCACA
1 AATCACATTAATATTTAAGCACA
* **
304338 AATGACATTAATATTTAAAAACA
1 AATCACATTAATATTTAAGCACA
* *
304361 AATGACATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCACA
* * *
304384 AATCACATTAATTTTTAAGTATA
1 AATCACATTAATATTTAAGCACA
* *
304407 AATCATATTAACATTTAAGCACA
1 AATCACATTAATATTTAAGCACA
304430 AATCACATTAATATTTAA
1 AATCACATTAATATTTAA
304448 TTATCTTTTA
Statistics
Matches: 92, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 92 1.00
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.35
Consensus pattern (23 bp):
AATCACATTAATATTTAAGCACA
Found at i:304528 original size:10 final size:10
Alignment explanation
Indices: 304513--304575 Score: 65
Period size: 10 Copynumber: 6.3 Consensus size: 10
304503 TCATCACAAG
304513 TTTAATCACA
1 TTTAATCACA
304523 TTTAATCACA
1 TTTAATCACA
* *
304533 TATAACCACA
1 TTTAATCACA
* *
304543 TATAGTCAC-
1 TTTAATCACA
304552 TTATAATCACA
1 TT-TAATCACA
*
304563 TTTAATCATA
1 TTTAATCACA
304573 TTT
1 TTT
304576 TTATGATAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
9 1 0.02
10 41 0.93
11 2 0.05
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.40
Consensus pattern (10 bp):
TTTAATCACA
Found at i:305054 original size:36 final size:36
Alignment explanation
Indices: 305022--305210 Score: 247
Period size: 36 Copynumber: 5.2 Consensus size: 36
305012 CAATATAATC
*
305022 ACTGTCACATGACATGAA-AATCATACCCATATATTT
1 ACTGTCACATGACATGAATAA-CATACCCACATATTT
* * * *
305058 ATTGTCACATGGCATGAATAACACACCTACATATTT
1 ACTGTCACATGACATGAATAACATACCCACATATTT
*
305094 ACTATCACATGACATGAATAACATACCCACATATTT
1 ACTGTCACATGACATGAATAACATACCCACATATTT
* *
305130 ACTAT-ATCATGACATGAATAATATACCCACATATTT
1 ACTGTCA-CATGACATGAATAACATACCCACATATTT
* *
305166 ACTGTCACATGGCATGAATAACATACCCATATATTT
1 ACTGTCACATGACATGAATAACATACCCACATATTT
*
305202 ACTTTCACA
1 ACTGTCACA
305211 ACAGTCATCA
Statistics
Matches: 134, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
35 1 0.01
36 130 0.97
37 3 0.02
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.31
Consensus pattern (36 bp):
ACTGTCACATGACATGAATAACATACCCACATATTT
Found at i:307211 original size:36 final size:36
Alignment explanation
Indices: 307164--307252 Score: 160
Period size: 36 Copynumber: 2.5 Consensus size: 36
307154 CTTGGTCTTA
*
307164 ATGAAGAACAAACAATTCCTCCTGATGTTAGCATTG
1 ATGAAGAACAAACAATTCCTCCTAATGTTAGCATTG
*
307200 ATGAAGAACAAACAATTCCTCCTAATGTTGGCATTG
1 ATGAAGAACAAACAATTCCTCCTAATGTTAGCATTG
307236 ATGAAGAACAAACAATT
1 ATGAAGAACAAACAATT
307253 TCTTCTTTGG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (36 bp):
ATGAAGAACAAACAATTCCTCCTAATGTTAGCATTG
Found at i:307375 original size:55 final size:55
Alignment explanation
Indices: 307312--307424 Score: 217
Period size: 55 Copynumber: 2.1 Consensus size: 55
307302 AAACAAGGGA
*
307312 AATTTTAGTTGAAAAGGGGCCTATAAGAGAAATGAATCTTGATTTTCCTCTCGAT
1 AATTTTAGTTGAAAAAGGGCCTATAAGAGAAATGAATCTTGATTTTCCTCTCGAT
307367 AATTTTAGTTGAAAAAGGGCCTATAAGAGAAATGAATCTTGATTTTCCTCTCGAT
1 AATTTTAGTTGAAAAAGGGCCTATAAGAGAAATGAATCTTGATTTTCCTCTCGAT
307422 AAT
1 AAT
307425 AATAATATAC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (55 bp):
AATTTTAGTTGAAAAAGGGCCTATAAGAGAAATGAATCTTGATTTTCCTCTCGAT
Found at i:314768 original size:18 final size:18
Alignment explanation
Indices: 314745--314811 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
314735 CATCCTGATC
314745 AGATGCAGTCACATACTG
1 AGATGCAGTCACATACTG
* * *
314763 AGATGCAGTCATATAATC
1 AGATGCAGTCACATACTG
** *
314781 AGATGCAACCACATGCTTG
1 AGATGCAGTCACATAC-TG
314800 A-ATGCAGTCACA
1 AGATGCAGTCACA
314812 ACAGATTGTG
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
18 35 0.95
19 2 0.05
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (18 bp):
AGATGCAGTCACATACTG
Found at i:316879 original size:25 final size:26
Alignment explanation
Indices: 316851--316906 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 26
316841 CATTGCAATC
316851 TTTCTATTT-ACTT-TTTGTCTTTTA-T
1 TTTCTATTTAACTTGTTT-TC-TTTAGT
316876 TTTCT-TTTAACTTGTTTTCTTTAGT
1 TTTCTATTTAACTTGTTTTCTTTAGT
316901 TTTCTA
1 TTTCTA
316907 CAGGAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
24 7 0.26
25 17 0.63
26 3 0.11
ACGTcount: A:0.12, C:0.12, G:0.05, T:0.70
Consensus pattern (26 bp):
TTTCTATTTAACTTGTTTTCTTTAGT
Found at i:325829 original size:25 final size:25
Alignment explanation
Indices: 325792--325857 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
325782 ACTTTGTTTG
* *
325792 GGCTCATACGAGCTAACCTTATCTA
1 GGCTCATAAGAGCTAACCCTATCTA
* *
325817 GGCTCGTAAGAGCTAACCCTCTCTA
1 GGCTCATAAGAGCTAACCCTATCTA
*
325842 GGCTCATATGAGCTAA
1 GGCTCATAAGAGCTAA
325858 ATTTCTAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (25 bp):
GGCTCATAAGAGCTAACCCTATCTA
Found at i:332943 original size:13 final size:13
Alignment explanation
Indices: 332925--332960 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
332915 TTCTCATCAA
332925 CTTTTGTGAGCAG
1 CTTTTGTGAGCAG
*
332938 CTTTTGTAAGCAG
1 CTTTTGTGAGCAG
*
332951 CATTTGTGAG
1 CTTTTGTGAG
332961 TGGGTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.14, G:0.28, T:0.39
Consensus pattern (13 bp):
CTTTTGTGAGCAG
Found at i:333072 original size:82 final size:82
Alignment explanation
Indices: 332935--333117 Score: 294
Period size: 82 Copynumber: 2.2 Consensus size: 82
332925 CTTTTGTGAG
* *
332935 CAGCTTTTGTAAGCAGCATTTGTGAGTGGGTAATTTGGACCGTATCGATGGCTGAGTTTTTGCAT
1 CAGCTTGTGTGAGCAGCATTTGTGAGTGGGTAATTTGGACCGTATCGATGGCTGAGTTTTTGCAT
* *
333000 ATGTTGCAAATTCTCAT
66 ATGTTACAAATCCTCAT
*
333017 CAGCTTGTGTGAGCAGCATTTGTGAGTGGGTAATTTGGACCGTTTCGATGGCTGAGTTTTTGCAT
1 CAGCTTGTGTGAGCAGCATTTGTGAGTGGGTAATTTGGACCGTATCGATGGCTGAGTTTTTGCAT
**
333082 ATGTTACGGATCCTCAT
66 ATGTTACAAATCCTCAT
*
333099 CAACTTGTGTGAGCAGCAT
1 CAGCTTGTGTGAGCAGCAT
333118 CATATACTGG
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 93 1.00
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (82 bp):
CAGCTTGTGTGAGCAGCATTTGTGAGTGGGTAATTTGGACCGTATCGATGGCTGAGTTTTTGCAT
ATGTTACAAATCCTCAT
Found at i:333182 original size:25 final size:25
Alignment explanation
Indices: 333148--333257 Score: 121
Period size: 25 Copynumber: 4.4 Consensus size: 25
333138 TCCGGGCTTG
* * **
333148 TAAGAGCTAACCTTATTTTTGCTCA
1 TAAGAGCTAACCCTATCTGGGCTCA
*
333173 TAAGAACTAACCCTATCTGGGCTCA
1 TAAGAGCTAACCCTATCTGGGCTCA
* *
333198 TAAGAGCTAACCCTATCTAGGCTCG
1 TAAGAGCTAACCCTATCTGGGCTCA
* * *
333223 TATGAGCTAATCCTATCTGGGCTCG
1 TAAGAGCTAACCCTATCTGGGCTCA
*
333248 TATGAGCTAA
1 TAAGAGCTAA
333258 ATTTCTGAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 74 1.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (25 bp):
TAAGAGCTAACCCTATCTGGGCTCA
Found at i:335977 original size:26 final size:26
Alignment explanation
Indices: 335926--335998 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
335916 TAATTTAAAT
335926 TATTTGCATTAATTAAATTTTTTTGAA
1 TATTTGCATTAATT-AATTTTTTTGAA
*
335953 TATTTTCATTAATTAATTTTTTTGAA
1 TATTTGCATTAATTAATTTTTTTGAA
*
335979 TAATTGCATTAATTAATTTT
1 TATTTGCATTAATTAATTTT
335999 AGTTACTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
26 30 0.70
27 13 0.30
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (26 bp):
TATTTGCATTAATTAATTTTTTTGAA
Found at i:339735 original size:25 final size:25
Alignment explanation
Indices: 339706--339757 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
339696 ATACTAGTTA
339706 AACTCTACTTGGGCTCGTAAGAGCT
1 AACTCTACTTGGGCTCGTAAGAGCT
* *
339731 AACTCTATTTGGGCTCGTATGAGCT
1 AACTCTACTTGGGCTCGTAAGAGCT
339756 AA
1 AA
339758 ATTTCTGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (25 bp):
AACTCTACTTGGGCTCGTAAGAGCT
Found at i:341419 original size:20 final size:20
Alignment explanation
Indices: 341395--341443 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
341385 AATCCAAATA
341395 AAAAATCCAAAGTCCAAAACC
1 AAAAA-CCAAAGTCCAAAACC
* *
341416 AAAAACCAAATTCCAAAATC
1 AAAAACCAAAGTCCAAAACC
*
341436 AAATACCA
1 AAAAACCA
341444 CAGTAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.59, C:0.27, G:0.02, T:0.12
Consensus pattern (20 bp):
AAAAACCAAAGTCCAAAACC
Found at i:343110 original size:23 final size:23
Alignment explanation
Indices: 343084--343377 Score: 403
Period size: 23 Copynumber: 12.8 Consensus size: 23
343074 GCATTACATG
*
343084 TTAAAAGTTAATGTGATTTACGC
1 TTAAAAGTTAATGTGATTTATGC
* *
343107 TTAAAAGATAATGTGATTTACGC
1 TTAAAAGTTAATGTGATTTATGC
**
343130 TTAAAAGTTAATGTGATTTACAC
1 TTAAAAGTTAATGTGATTTATGC
343153 TTAAAAGTTAATGTGATTTATGC
1 TTAAAAGTTAATGTGATTTATGC
*
343176 TTAAAATTTAATGTGATTTATGC
1 TTAAAAGTTAATGTGATTTATGC
* *
343199 TTAAAAGTTAATGTGATTTTTGG
1 TTAAAAGTTAATGTGATTTATGC
343222 TTAAAAG-TATATGTGATTTATGC
1 TTAAAAGTTA-ATGTGATTTATGC
* *
343245 TTAAAATTTAATGTGATTTTTGC
1 TTAAAAGTTAATGTGATTTATGC
* *
343268 TTAAAAGTTAAAGTGGTTTATGC
1 TTAAAAGTTAATGTGATTTATGC
*
343291 TTAAAATTTAATGTGATTTATGC
1 TTAAAAGTTAATGTGATTTATGC
*
343314 TTAAATG-TATATGTGATTTATGC
1 TTAAAAGTTA-ATGTGATTTATGC
343337 TTAAAAGTTAATGTGATTTATGC
1 TTAAAAGTTAATGTGATTTATGC
* * *
343360 TCAAATGATAATGTGATT
1 TTAAAAGTTAATGTGATT
343378 AATGTGTAAA
Statistics
Matches: 241, Mismatches: 26, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
22 4 0.02
23 233 0.97
24 4 0.02
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.44
Consensus pattern (23 bp):
TTAAAAGTTAATGTGATTTATGC
Found at i:344511 original size:3 final size:3
Alignment explanation
Indices: 344503--344540 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
344493 TAGTGTGGGT
*
344503 TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
344541 GAATTTAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:350649 original size:43 final size:43
Alignment explanation
Indices: 350588--350772 Score: 201
Period size: 43 Copynumber: 4.3 Consensus size: 43
350578 TTATGAGGAA
* * *
350588 AAACGCCGCTATAGAACATGGTATTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTATTTAGCGGCACTTTCCCCAC
** * * *
350631 AAACGCCGCTGTAGAACATGGTCTTTAGCGACACATTCCCCAC
1 AAACGCCGCTAAAGAACATGGTATTTAGCGGCACTTTCCCCAC
* **
350674 AAATGGTGCTAAAGAACATGG-ACTTTAGCGGCACTTTCCCCAC
1 AAACGCCGCTAAAGAACATGGTA-TTTAGCGGCACTTTCCCCAC
* *** *
350717 AAACGCCGCTAAAGAACATGGTCTTTAGCGGTGTTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTATTTAGCGGCACTTTCCCCAC
*
350760 AAACGCCACTAAA
1 AAACGCCGCTAAA
350773 ATTAACAGAT
Statistics
Matches: 117, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
43 117 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTATTTAGCGGCACTTTCCCCAC
Found at i:350772 original size:86 final size:86
Alignment explanation
Indices: 350588--350746 Score: 230
Period size: 86 Copynumber: 1.8 Consensus size: 86
350578 TTATGAGGAA
* * * **
350588 AAACGCCGCTATAGAACATGGTATTTAGCGGCGCTTTTCCCACAAACGCCGCTGTAGAACATGGT
1 AAACGCCGCTAAAGAACATGGTATTTAGCGGCACTTTCCCCACAAACGCCGCTAAAGAACATGGT
350653 CTTTAGCGACACATTCCCCAC
66 CTTTAGCGACACATTCCCCAC
* **
350674 AAATGGTGCTAAAGAACATGG-ACTTTAGCGGCACTTTCCCCACAAACGCCGCTAAAGAACATGG
1 AAACGCCGCTAAAGAACATGGTA-TTTAGCGGCACTTTCCCCACAAACGCCGCTAAAGAACATGG
350738 TCTTTAGCG
65 TCTTTAGCG
350747 GTGTTTTTCC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
85 1 0.02
86 63 0.98
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (86 bp):
AAACGCCGCTAAAGAACATGGTATTTAGCGGCACTTTCCCCACAAACGCCGCTAAAGAACATGGT
CTTTAGCGACACATTCCCCAC
Found at i:352604 original size:14 final size:14
Alignment explanation
Indices: 352561--352593 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
352551 AGTATTATAA
352561 ATTACATTAACTTT
1 ATTACATTAACTTT
352575 ATTACATTAACTTT
1 ATTACATTAACTTT
352589 ATTAC
1 ATTAC
352594 CTTACTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTACATTAACTTT
Found at i:357250 original size:20 final size:21
Alignment explanation
Indices: 357206--357256 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
357196 TATTTAATAT
*
357206 AATTAAATAATTTAATATTTTG
1 AATTAAAT-ATTTAATATTTAG
*
357228 AATTAAATATTT-CTATTTAG
1 AATTAAATATTTAATATTTAG
*
357248 AATTTAATA
1 AATTAAATA
357257 AATAACTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 14 0.54
21 4 0.15
22 8 0.31
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (21 bp):
AATTAAATATTTAATATTTAG
Found at i:358382 original size:14 final size:14
Alignment explanation
Indices: 358339--358371 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
358329 AGTATTATAA
358339 ATTACATTAACTTT
1 ATTACATTAACTTT
358353 ATTACATTAACTTT
1 ATTACATTAACTTT
358367 ATTAC
1 ATTAC
358372 CTTACTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTACATTAACTTT
Found at i:363028 original size:20 final size:21
Alignment explanation
Indices: 362984--363138 Score: 60
Period size: 22 Copynumber: 7.6 Consensus size: 21
362974 TATTTAATAT
*
362984 AATTAAATAATTTAATATTTTG
1 AATTAAAT-ATTTAATATTTAG
*
363006 AATTAAATATTT-CTATTTAG
1 AATTAAATATTTAATATTTAG
* ** *
363026 AATTTAATAAATAACTATTTAA
1 AATTAAATATTTAA-TATTTAG
*
363048 ATATTTAATTATTTTAATATTT-G
1 A-A-TTAAATA-TTTAATATTTAG
** * *
363071 --TTTTATTTTTAATAATT-G
1 AATTAAATATTTAATATTTAG
**
363089 AA-TATTTATTTAATA--T--
1 AATTAAATATTTAATATTTAG
*
363105 AATTAAATAATTTAATATTTTG
1 AATTAAAT-ATTTAATATTTAG
363127 AATTAAATATTT
1 AATTAAATATTT
363139 GAGTTTTGGG
Statistics
Matches: 98, Mismatches: 22, Indels: 27
0.67 0.15 0.18
Matches are distributed among these distances:
16 2 0.02
17 4 0.04
18 18 0.18
19 13 0.13
20 16 0.16
21 8 0.08
22 23 0.23
23 1 0.01
24 10 0.10
25 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (21 bp):
AATTAAATATTTAATATTTAG
Found at i:363068 original size:121 final size:122
Alignment explanation
Indices: 362920--363462 Score: 853
Period size: 122 Copynumber: 4.5 Consensus size: 122
362910 CTTTATTTAA
* *
362920 TAATTAAAT-ATGTAATTATTTTAATATTTGTTATGTTTTTAATAATTGAATATTTATTT-AATA
1 TAATTAAATAAT-TAATTATTTTAATATTTATTATATTTTTAATAATTGAATATTTATTTAAATA
* *
362983 TAATTAAATAATTTAATATTTTGAATTAAATATTTCTA-TTTAGAATTTAATAAATAAC
65 TAATTAAATAATTTAATATTTTGAATTAAATATTT-GAGTTTAGGATTTAATAAATAAC
* * * *
363041 TATTTAAATATTTAATTATTTTAATATTTGTTTTATTTTTAATAATTGAATATTTATTT-AATAT
1 TAATTAAATAATTAATTATTTTAATATTTATTATATTTTTAATAATTGAATATTTATTTAAATAT
* *
363105 AATTAAATAATTTAATATTTTGAATTAAATATTTGAGTTTTGGGTTTAATAAATAAC
66 AATTAAATAATTTAATATTTTGAATTAAATATTTGAGTTTAGGATTTAATAAATAAC
*
363162 TAATTAAATAATTAATTATTTTAATATTTATTCTATTTTTAATAATTGAATATTTATTTAAATAT
1 TAATTAAATAATTAATTATTTTAATATTTATTATATTTTTAATAATTGAATATTTATTTAAATAT
* * *
363227 AATTAAATAATTTAATATTTTGAATTAAATATTTGAGTTTTGGGTTTAATAAATAAG
66 AATTAAATAATTTAATATTTTGAATTAAATATTTGAGTTTAGGATTTAATAAATAAC
*
363284 TAATTAAATAATTAATTATTTTAATATTTATTATATTTTTAATAATTAAATATTTATTTAAATAT
1 TAATTAAATAATTAATTATTTTAATATTTATTATATTTTTAATAATTGAATATTTATTTAAATAT
*
363349 AATTAAATAATTTAATATTTTGAATTAAATATTTTGA-CTTAGGATTTAATAAATAAC
66 AATTAAATAATTTAATATTTTGAATTAAATA-TTTGAGTTTAGGATTTAATAAATAAC
* *
363406 TAATTAAATAATTAATTATTTTAATATTTATTCTATTTTTAATAATTAAATAATTTA
1 TAATTAAATAATTAATTATTTTAATATTTATTATATTTTTAATAATTGAAT-ATTTA
363463 ATATTTTGAA
Statistics
Matches: 397, Mismatches: 20, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
120 1 0.00
121 164 0.41
122 222 0.56
123 10 0.03
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (122 bp):
TAATTAAATAATTAATTATTTTAATATTTATTATATTTTTAATAATTGAATATTTATTTAAATAT
AATTAAATAATTTAATATTTTGAATTAAATATTTGAGTTTAGGATTTAATAAATAAC
Found at i:363246 original size:64 final size:64
Alignment explanation
Indices: 363162--363462 Score: 158
Period size: 58 Copynumber: 4.9 Consensus size: 64
363152 AATAAATAAC
*
363162 TAATTAAATAATTAATTATTTTAATATTTATTCTATTTTTAATAATTGAATATTTATTTAAATA
1 TAATTAAATAATTAATTATTTTAATATTTATTATATTTTTAATAATTGAATATTTATTTAAATA
** *** ** **
363226 TAATTAAATAATTTAA-TATTTTGAATTAAATATT-TGAGTTTTGGGT--TT-AATAAATAAGT-
1 TAATTAAATAA-TTAATTATTTT-AA-TATTTATTAT-A-TTTTTAATAATTGAATATTTATTTA
363285 AAT-
61 AATA
* * * *
363288 TAAATAATTAATT-ATT-TTAAT-A--TTTATTATATTTTTAATAATTAAATATTTATTTAAATA
1 TAATTAAATAATTAATTATT-TTAATATTTATTATATTTTTAATAATTGAATATTTATTTAAATA
* * * * ** *
363348 TAATTAAATAATTTAA-TATTTTGA-A-TTA-AATA-TTTT--GACTT-AGGATTTA-ATAAATA
1 TAATTAAATAA-TTAATTATTTTAATATTTATTATATTTTTAATAATTGAATATTTATTTAAAT-
363404 A
64 A
* *
363405 CTAATTAAATAATTAATTATTTTAATATTTATTCTATTTTTAATAATTAAATAATTTA
1 -TAATTAAATAATTAATTATTTTAATATTTATTATATTTTTAATAATTGAAT-ATTTA
363463 ATATTTTGAA
Statistics
Matches: 171, Mismatches: 37, Indels: 56
0.65 0.14 0.21
Matches are distributed among these distances:
55 5 0.03
56 10 0.06
57 14 0.08
58 28 0.16
59 5 0.03
60 19 0.11
61 13 0.08
62 20 0.12
63 3 0.02
64 27 0.16
65 10 0.06
66 12 0.07
67 5 0.03
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (64 bp):
TAATTAAATAATTAATTATTTTAATATTTATTATATTTTTAATAATTGAATATTTATTTAAATA
Found at i:363431 original size:16 final size:16
Alignment explanation
Indices: 363392--363465 Score: 58
Period size: 16 Copynumber: 4.5 Consensus size: 16
363382 TTGACTTAGG
* *
363392 ATTTAATAAATAACTA
1 ATTTAATAATTAATTA
*
363408 ATTAAATAATTAATTA
1 ATTTAATAATTAATTA
* * *
363424 TTTTAATATTTATTCTA
1 ATTTAATAATTAAT-TA
* *
363441 TTTTTAATAATTAAATA
1 -ATTTAATAATTAATTA
363458 ATTTAATA
1 ATTTAATA
363466 TTTTGAATTA
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
16 30 0.67
17 4 0.09
18 11 0.24
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTAATAATTAATTA
Found at i:363451 original size:100 final size:100
Alignment explanation
Indices: 363347--363534 Score: 333
Period size: 100 Copynumber: 1.9 Consensus size: 100
363337 TTATTTAAAT
363347 ATAATTAAATAATTTAATATTTTGAATTAAATATTTTGA-CTTAGGATTTAATAAATAACTAATT
1 ATAATTAAATAATTTAATATTTTGAATTAAATA-TTTGAGCTTAGGATTTAATAAATAACTAATT
363411 AAATAATTAATTATTTTAATATTTATTCTATTTTTA
65 AAATAATTAATTATTTTAATATTTATTCTATTTTTA
* * *
363447 ATAATTAAATAATTTAATATTTTGAATTATATATTTGAGTTTAGGGTTTAATAAATAACTAATTA
1 ATAATTAAATAATTTAATATTTTGAATTAAATATTTGAGCTTAGGATTTAATAAATAACTAATTA
363512 AATAATTAATTATTTTAATATTT
66 AATAATTAATTATTTTAATATTT
363535 CATAACCCTT
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
99 5 0.06
100 79 0.94
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (100 bp):
ATAATTAAATAATTTAATATTTTGAATTAAATATTTGAGCTTAGGATTTAATAAATAACTAATTA
AATAATTAATTATTTTAATATTTATTCTATTTTTA
Found at i:365083 original size:43 final size:42
Alignment explanation
Indices: 364987--365200 Score: 239
Period size: 43 Copynumber: 5.0 Consensus size: 42
364977 GCTACTATAG
* * * *
364987 AACATGGTCTTTAGCGGCGCTTTCTCATAAACACCGCTAAAG
1 AACATGGTCTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAA
365029 AACATGGTCTTTAGCGGCGCTTTCCTCACAAACGCCGCTAAAA
1 AACATGGTCTTTAGCGGCGCTTTCC-CACAAACGCCGCTAAAA
* * * * *
365072 AACATGATCTTTAACAGCGCTTCTGCCACAAACGCCGCTAAAG
1 AACATGGTCTTTAGCGGCGCTT-TCCCACAAACGCCGCTAAAA
* * *
365115 AACATGGTCTTTATCGACGCTTTTCCCACAAAAGCCGCTAAAA
1 AACATGGTCTTTAGCGGCGC-TTTCCCACAAACGCCGCTAAAA
* * * * *
365158 AACATGATCTGTAGTGACGCTTTTCCCACAAATGCCGCTAAAA
1 AACATGGTCTTTAGCGGCGC-TTTCCCACAAACGCCGCTAAAA
365201 TTAACTGATT
Statistics
Matches: 148, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
42 24 0.16
43 120 0.81
44 4 0.03
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (42 bp):
AACATGGTCTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAA
Found at i:365195 original size:129 final size:127
Alignment explanation
Indices: 364985--365216 Score: 299
Period size: 129 Copynumber: 1.8 Consensus size: 127
364975 ATGCTACTAT
* * * * * * *
364985 AGAACATGGTCTTTAGCGGCGCTTTCTCATAAACACCGCTAAAGAACATGGTCTTTAGCGGCGCT
1 AGAACATGGTCTTTAGCGACGCTTTCCCACAAACACCGCTAAAAAACATGATCTGTAGCGACGCT
365050 TTCCTCACAAACGCCGCTAAAA-AACATGATCTTTAACAGCGCTTCTGCCACAAACGCCGCTAA
66 TTCCTCACAAACGCCGCTAAAATAAC-TGAT-TTTAACAGCGCTTCTGCCACAAACGCCGCTAA
* *
365113 AGAACATGGTCTTTATCGACGCTTTTCCCACAAA-AGCCGCTAAAAAACATGATCTGTAGTGACG
1 AGAACATGGTCTTTAGCGACGC-TTTCCCACAAACA-CCGCTAAAAAACATGATCTGTAGCGACG
*
365177 CTTTTCC-CACAAATGCCGCTAAAATTAACTGATTTTAACA
64 C-TTTCCTCACAAACGCCGCTAAAA-TAACTGATTTTAACA
365217 CCTCATTTTA
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
128 21 0.24
129 56 0.63
130 9 0.10
131 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (127 bp):
AGAACATGGTCTTTAGCGACGCTTTCCCACAAACACCGCTAAAAAACATGATCTGTAGCGACGCT
TTCCTCACAAACGCCGCTAAAATAACTGATTTTAACAGCGCTTCTGCCACAAACGCCGCTAA
Found at i:367849 original size:26 final size:26
Alignment explanation
Indices: 367813--367865 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
367803 GAAGGCATTA
*
367813 TATCTTTTTACTACTTTATTAGGACC
1 TATCTTTTTACTACTCTATTAGGACC
*
367839 TATCTTTTTACTACTCTATTCGGACC
1 TATCTTTTTACTACTCTATTAGGACC
367865 T
1 T
367866 TGGGAAAGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.23, G:0.08, T:0.49
Consensus pattern (26 bp):
TATCTTTTTACTACTCTATTAGGACC
Found at i:371441 original size:16 final size:16
Alignment explanation
Indices: 371401--371469 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
371391 GGGTTTAAGG
* * *
371401 TTAAATAAATAACTAA
1 TTAAATAATTAATTAT
371417 TTAAATAATTAATTAT
1 TTAAATAATTAATTAT
*
371433 TTAAATAATTCGATTATT
1 TTAAATAATT-AATTA-T
*
371451 TTTAATAATTTAA-TAT
1 TTAAATAA-TTAATTAT
371467 TTA
1 TTA
371470 TTTAAATATA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
16 26 0.60
17 6 0.14
18 9 0.21
19 2 0.05
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (16 bp):
TTAAATAATTAATTAT
Found at i:371506 original size:108 final size:107
Alignment explanation
Indices: 371376--371605 Score: 329
Period size: 108 Copynumber: 2.1 Consensus size: 107
371366 GAGTTGTTTT
* * *
371376 AATAATTAAATAGTTGGGTTTAAGGTTAAATAAATAACTAATTAAATAATTAATTATTTAAAT-A
1 AATAATTAAATATTTGGATTTAAGGTTAAATAAATAACTAATAAAATAATTAATTATTTAAATGA
371440 ATTCGATTATTTTTAATAATTTAATA-TTTATTTAAATATAATTA
66 ATT---TTATTTTTAATAATTTAATATTTTATTTAAATATAATTA
** *
371484 AATAATTAAATATTTGGATTTAAGGTTTCATAAATAACTAATAAAATAATTAATTATTTAATTGA
1 AATAATTAAATATTTGGATTTAAGGTTAAATAAATAACTAATAAAATAATTAATTATTTAAATGA
* * *
371549 GTTTTGTTTTTAATAATTTAATATTTTTTTTAAATATAATTA
66 ATTTTATTTTTAATAATTTAATATTTTATTTAAATATAATTA
*
371591 AATAATTTAATATTT
1 AATAATTAAATATTT
371606 TGAATTAAAT
Statistics
Matches: 110, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
106 19 0.17
107 31 0.28
108 57 0.52
109 3 0.03
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (107 bp):
AATAATTAAATATTTGGATTTAAGGTTAAATAAATAACTAATAAAATAATTAATTATTTAAATGA
ATTTTATTTTTAATAATTTAATATTTTATTTAAATATAATTA
Found at i:372031 original size:82 final size:81
Alignment explanation
Indices: 371894--372059 Score: 287
Period size: 82 Copynumber: 2.0 Consensus size: 81
371884 GGATTGGGGC
*
371894 AATTTGTTTTATTATAAGGAACCACTTTCAAACAATCAAGAGAGAAGACAATTGCATAAAAAATG
1 AATTTGTTTTATTATAAGGAACCACTTTCAAACAATCAAGAGAGAAAACAATTGCATAAAAAA-G
*
371959 TTATCTGTATTCGAGTG
65 TTATCTGGATTCGAGTG
* *
371976 AATTTGTTTTATTCTAAGGAACTACTTTCAAACAATCAAGAGAGAAAACAATTGCATAAAAAAGT
1 AATTTGTTTTATTATAAGGAACCACTTTCAAACAATCAAGAGAGAAAACAATTGCATAAAAAAGT
372041 TATCTGGATTCGAGTG
66 TATCTGGATTCGAGTG
372057 AAT
1 AAT
372060 ATTGAATACG
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
81 20 0.25
82 60 0.75
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (81 bp):
AATTTGTTTTATTATAAGGAACCACTTTCAAACAATCAAGAGAGAAAACAATTGCATAAAAAAGT
TATCTGGATTCGAGTG
Found at i:374038 original size:23 final size:23
Alignment explanation
Indices: 374008--374063 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
373998 GGGGAGAAAC
374008 GGGATTTGAGAAAGGAGAAATTT
1 GGGATTTGAGAAAGGAGAAATTT
* ** **
374031 GGGATTTGGGGGATTAGAAATTT
1 GGGATTTGAGAAAGGAGAAATTT
374054 GGGATTTGAG
1 GGGATTTGAG
374064 GTTTTGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.39, T:0.30
Consensus pattern (23 bp):
GGGATTTGAGAAAGGAGAAATTT
Found at i:374115 original size:47 final size:47
Alignment explanation
Indices: 374057--374161 Score: 133
Period size: 47 Copynumber: 2.2 Consensus size: 47
374047 GAAATTTGGG
* *
374057 ATTTGAGGTTTTGAGA-GAGGATAAATGAAGAATT-AGAGATTAGAGAA
1 ATTTGAGGTTTTGAGACG-GGAGAAATGAAGAATTAAG-GATGAGAGAA
* *
374104 ATTTGAAGTTTTGAGACGGGAGAAATTAAGAATTAAGGATGAGAGAA
1 ATTTGAGGTTTTGAGACGGGAGAAATGAAGAATTAAGGATGAGAGAA
*
374151 AGTTGAGGTTT
1 ATTTGAGGTTT
374162 GGAAACAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
47 47 0.94
48 3 0.06
ACGTcount: A:0.40, C:0.01, G:0.30, T:0.29
Consensus pattern (47 bp):
ATTTGAGGTTTTGAGACGGGAGAAATGAAGAATTAAGGATGAGAGAA
Found at i:374394 original size:42 final size:41
Alignment explanation
Indices: 374285--374423 Score: 115
Period size: 41 Copynumber: 3.3 Consensus size: 41
374275 ATTGTTTAAC
* *
374285 TTTTAGC-AGCGTTTTTCTCATAAACGCCGTTAATGTTTTGGAT
1 TTTTAGCGA-CGTTTTTCTCATAAACGCCGCTAATG-CTT-GAT
* * *
374328 TTTTTGTCG-GGTTTTT-T-AGAAAACGCCGCTAATGCTCTGAT
1 TTTTAG-CGACGTTTTTCTCA-TAAACGCCGCTAATGCT-TGAT
* * * *
374369 TTTTAGCGATGTTTTTCTCATAAACGCTGCTAATGCTTTAC
1 TTTTAGCGACGTTTTTCTCATAAACGCCGCTAATGCTTGAT
374410 TTTTAGCGACGTTT
1 TTTTAGCGACGTTT
374424 AAGAGAAAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 16
0.73 0.11 0.15
Matches are distributed among these distances:
40 2 0.03
41 31 0.40
42 31 0.40
43 12 0.16
44 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.44
Consensus pattern (41 bp):
TTTTAGCGACGTTTTTCTCATAAACGCCGCTAATGCTTGAT
Found at i:376084 original size:41 final size:41
Alignment explanation
Indices: 376027--376128 Score: 150
Period size: 41 Copynumber: 2.5 Consensus size: 41
376017 TTAAGCACCG
* * *
376027 CTAATGCTCTGACCTTTAGCGGCGTTTATGTGGAAGCGCCA
1 CTAATGCTCTGACCTTTAGCGGCGTTAATGAGAAAGCGCCA
**
376068 CTAATGCTCTGACCTTTAGCGGCGTTAATGAGAAAGCGCTG
1 CTAATGCTCTGACCTTTAGCGGCGTTAATGAGAAAGCGCCA
*
376109 CTAATGCTCCGACCTTTAGC
1 CTAATGCTCTGACCTTTAGC
376129 AGCGCTTTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (41 bp):
CTAATGCTCTGACCTTTAGCGGCGTTAATGAGAAAGCGCCA
Found at i:377397 original size:39 final size:39
Alignment explanation
Indices: 377286--377509 Score: 268
Period size: 39 Copynumber: 5.7 Consensus size: 39
377276 CCTAATAAGA
* *** * **
377286 GGGCAGATTGAAGACCATCCAATCTTTTACCTTAATCAAA
1 GGGCAGATTGAAG-CAATCCAATCTTTTACCCCGACCATG
* *
377326 GGGCAGATTGAAGACCATCCAATCTTTTACCCCGGCCATG
1 GGGCAGATTGAAG-CAATCCAATCTTTTACCCCGACCATG
*
377366 GGGCAGATTGAAGCAATCTAATCTTTTACCCCGACCATG
1 GGGCAGATTGAAGCAATCCAATCTTTTACCCCGACCATG
* * * *
377405 GAGCAGATTGAAGTAATCTAGTCTTTTACCCCGACCATG
1 GGGCAGATTGAAGCAATCCAATCTTTTACCCCGACCATG
* *
377444 AGGCAGATTAAAGCAATCCAATCTTTTACCCCGACCATG
1 GGGCAGATTGAAGCAATCCAATCTTTTACCCCGACCATG
*
377483 GGGCAGATTGAAGACCATCCAATCTTT
1 GGGCAGATTGAAG-CAATCCAATCTTT
377510 ATCTCCCTGA
Statistics
Matches: 161, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
39 103 0.64
40 58 0.36
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (39 bp):
GGGCAGATTGAAGCAATCCAATCTTTTACCCCGACCATG
Found at i:378031 original size:63 final size:65
Alignment explanation
Indices: 377862--378043 Score: 205
Period size: 66 Copynumber: 2.8 Consensus size: 65
377852 CTAATTCCAT
* * * * *
377862 TTTTCTTATTA-TTATTTGTT-TAGTATGAATATAATAAACAAATATAAACTAATATTAATTTTG
1 TTTTATTATTATTTATTTATTATTGTATGAATATAATAAATAAATATAAAATAATATTAATTTTG
* *
377925 TTTTATTATTATTTATTTATTATTGTATCAATATAAATAAATAAATGTAAAATAATATTAATTTT
1 TTTTATTATTATTTATTTATTATTGTATGAATAT-AATAAATAAATATAAAATAATATTAATTTT
377990 G
65 G
* *
377991 TTTTGTTATTTATTT-TTTA-T-TT-TATGAATATAGATAAATAAATAAATAAATAA
1 TTTTATTA-TTATTTATTTATTATTGTATGAATATA-ATAAATAAATATA-AAATAA
378044 ACAAATAACC
Statistics
Matches: 102, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
62 1 0.01
63 29 0.28
64 16 0.16
65 11 0.11
66 39 0.38
67 6 0.06
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (65 bp):
TTTTATTATTATTTATTTATTATTGTATGAATATAATAAATAAATATAAAATAATATTAATTTTG
Found at i:379113 original size:30 final size:30
Alignment explanation
Indices: 379079--379230 Score: 166
Period size: 30 Copynumber: 5.1 Consensus size: 30
379069 AAAATTGTGT
*
379079 TTTGACCCCTTAACTTTCCAAAAATTCAAA
1 TTTGACCCCTAAACTTTCCAAAAATTCAAA
* * * *
379109 TTTGACACCC-GAACTTCCCAAAAATCCAAG
1 TTTGAC-CCCTAAACTTTCCAAAAATTCAAA
* * *
379139 TTTTA-CCCTCAAATTTTCCAAAAACTCAAA
1 TTTGACCCCT-AAACTTTCCAAAAATTCAAA
* *
379169 TTTGACCCCTGAACTTTCTAAAAATTCAAA
1 TTTGACCCCTAAACTTTCCAAAAATTCAAA
*
379199 TTTGA-CCCTAAATTTTCCAAAAATTCAAA
1 TTTGACCCCTAAACTTTCCAAAAATTCAAA
379228 TTT
1 TTT
379231 AACCTAGTTT
Statistics
Matches: 99, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
28 3 0.03
29 24 0.24
30 65 0.66
31 7 0.07
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.32
Consensus pattern (30 bp):
TTTGACCCCTAAACTTTCCAAAAATTCAAA
Found at i:379162 original size:60 final size:59
Alignment explanation
Indices: 379079--379230 Score: 198
Period size: 60 Copynumber: 2.5 Consensus size: 59
379069 AAAATTGTGT
* * *
379079 TTTGACCCCTTAACTTTCCAAAAATTCAAATTTGACACCC-GAACTTCCCAAAAATCCAAG
1 TTTGA-CCCTAAATTTTCCAAAAATTCAAATTTGAC-CCCTGAACTTCCCAAAAATCCAAA
* * * * *
379139 TTTTACCCTCAAATTTTCCAAAAACTCAAATTTGACCCCTGAACTTTCTAAAAATTCAAA
1 TTTGACCCT-AAATTTTCCAAAAATTCAAATTTGACCCCTGAACTTCCCAAAAATCCAAA
379199 TTTGACCCTAAATTTTCCAAAAATTCAAATTT
1 TTTGACCCTAAATTTTCCAAAAATTCAAATTT
379231 AACCTAGTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
59 29 0.36
60 51 0.64
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.32
Consensus pattern (59 bp):
TTTGACCCTAAATTTTCCAAAAATTCAAATTTGACCCCTGAACTTCCCAAAAATCCAAA
Found at i:382309 original size:21 final size:21
Alignment explanation
Indices: 382275--382320 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
382265 GGCTATAGCA
* * *
382275 GGCTTTGTGCCGGTGTATTTG
1 GGCTTCGTGCCGGTGAATTCG
*
382296 GGCTTCGTGTCGGTGAATTCG
1 GGCTTCGTGCCGGTGAATTCG
382317 GGCT
1 GGCT
382321 ATGTGCCTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.07, C:0.17, G:0.39, T:0.37
Consensus pattern (21 bp):
GGCTTCGTGCCGGTGAATTCG
Found at i:385860 original size:9 final size:9
Alignment explanation
Indices: 385846--385893 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
385836 AGGCAACCCA
385846 ATTTTATTT
1 ATTTTATTT
385855 ATTTTATTT
1 ATTTTATTT
385864 -TTTTATTT
1 ATTTTATTT
*
385872 ATATTATTT
1 ATTTTATTT
385881 -TTATT-TTT
1 ATT-TTATTT
385889 ATTTT
1 ATTTT
385894 CTTTCATGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
8 14 0.41
9 20 0.59
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
ATTTTATTT
Found at i:385869 original size:17 final size:17
Alignment explanation
Indices: 385847--385893 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
385837 GGCAACCCAA
385847 TTTTATTTATTTTATTT
1 TTTTATTTATTTTATTT
*
385864 TTTTATTTATATTATTT
1 TTTTATTTATTTTATTT
385881 TTATT-TTTATTTT
1 TT-TTATTTATTTT
385894 CTTTCATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 25 0.93
18 2 0.07
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTATTTATTTTATTT
Found at i:386760 original size:104 final size:104
Alignment explanation
Indices: 386652--386848 Score: 254
Period size: 104 Copynumber: 1.9 Consensus size: 104
386642 AGAAAATAAA
* *
386652 AAAATAACTTAGGAGTGTGTTGGGTTGAGT-ATCCAGGATG-GAGTGCTTGAGTTCTCATTCCAT
1 AAAATAAATTAGGAGTGTGTTGGGCTGAGTAAT-CAGGATGAG-GTGCTTGAGTTCTCATTCCAT
* *
386715 TTCACGTTAAAACGGTCAATACATTCTTAAGTAAAAAAATG
64 TTCACGTCAAAACGGCCAATACATTCTTAAGTAAAAAAATG
* * * *
386756 AAAATAAATTGGGAGTGTGTTGGGCTGAGTAATCGGGATGAGGTGCTTGGGTTGTCATTCCATTT
1 AAAATAAATTAGGAGTGTGTTGGGCTGAGTAATCAGGATGAGGTGCTTGAGTTCTCATTCCATTT
* * * *
386821 CGCGTCAATAGGGCCAATATATTCTTAA
66 CACGTCAAAACGGCCAATACATTCTTAA
386849 ACAAAAGAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
104 76 0.96
105 3 0.04
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.32
Consensus pattern (104 bp):
AAAATAAATTAGGAGTGTGTTGGGCTGAGTAATCAGGATGAGGTGCTTGAGTTCTCATTCCATTT
CACGTCAAAACGGCCAATACATTCTTAAGTAAAAAAATG
Found at i:389186 original size:40 final size:41
Alignment explanation
Indices: 389142--389242 Score: 107
Period size: 40 Copynumber: 2.5 Consensus size: 41
389132 TTTTTTTAAA
*
389142 ATATAATTTTTAATTTTTTTTATATTTTATAATA-ATATTT
1 ATATAATTTTTAATATTTTTTATATTTTATAATATATATTT
* * * * *
389182 ATAT-ATATTTAATAAGTTTTTATATTTTTTAATATTTTTTT
1 ATATAATTTTTAAT-ATTTTTTATATTTTATAATATATATTT
* *
389223 CTAAAATTTTTAATATTTTT
1 ATATAATTTTTAATATTTTT
389243 CTACCATAGT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
39 8 0.17
40 21 0.44
41 11 0.23
42 8 0.17
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (41 bp):
ATATAATTTTTAATATTTTTTATATTTTATAATATATATTT
Done.