Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006568.1 Hibiscus syriacus cultivar Beakdansim tig00016070_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: 144477
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:3129 original size:36 final size:37
Alignment explanation
Indices: 3044--3129 Score: 88
Period size: 36 Copynumber: 2.4 Consensus size: 37
3034 TATTTTACCT
* * *
3044 TAAAATATGCATATGTTTTCTAAATATGATATTAAATA
1 TAAAATAT-AATATGTATTCTAAATATGATATAAAATA
* *
3082 TAGAACA-AATATGTATTCTAAATAT-A-ATGAAAATA
1 TAAAATATAATATGTATTCTAAATATGATAT-AAAATA
3117 TAAAATATAATAT
1 TAAAATATAATAT
3130 TATACCATGG
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
34 2 0.05
35 11 0.28
36 21 0.54
38 5 0.13
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (37 bp):
TAAAATATAATATGTATTCTAAATATGATATAAAATA
Found at i:3189 original size:17 final size:16
Alignment explanation
Indices: 3161--3196 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
3151 TCTTATGTAT
*
3161 ATAATAAAGTAATATA
1 ATAATAAAGTAAAATA
3177 ATAATATAAGTAAAATA
1 ATAATA-AAGTAAAATA
3194 ATA
1 ATA
3197 CCTAAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
ATAATAAAGTAAAATA
Found at i:4508 original size:14 final size:15
Alignment explanation
Indices: 4470--4514 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
4460 ATCTAGGTTG
*
4470 GGTTTTGGGTTTTTGA
1 GGTTTTGGG-TTATGA
4486 GGTTTTGGGTTATGA
1 GGTTTTGGGTTATGA
4501 GG-TTTGGGTTATGA
1 GGTTTTGGGTTATGA
4515 AAAATGGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 12 0.43
15 7 0.25
16 9 0.32
ACGTcount: A:0.11, C:0.00, G:0.40, T:0.49
Consensus pattern (15 bp):
GGTTTTGGGTTATGA
Found at i:6887 original size:34 final size:34
Alignment explanation
Indices: 6848--6917 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
6838 TATTATATTA
6848 TGCAAGGGGATTATGAGTCATGGATATTTGATTT
1 TGCAAGGGGATTATGAGTCATGGATATTTGATTT
6882 TGCAAGGGGATTATGAGTCATGGATATTTGATTT
1 TGCAAGGGGATTATGAGTCATGGATATTTGATTT
6916 TG
1 TG
6918 ATTTCAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.26, C:0.06, G:0.30, T:0.39
Consensus pattern (34 bp):
TGCAAGGGGATTATGAGTCATGGATATTTGATTT
Found at i:7950 original size:2 final size:2
Alignment explanation
Indices: 7943--7975 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7933 GGTTATTAGA
7943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7976 AATAAATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9151 original size:19 final size:19
Alignment explanation
Indices: 9127--9205 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 19
9117 AAGTCAACCC
9127 GACCTGACCCATTGACTTT
1 GACCTGACCCATTGACTTT
*
9146 GACCTGACCCGTTGACTTT
1 GACCTGACCCATTGACTTT
* * * *
9165 AACCCGACCCGTTGGCTTT
1 GACCTGACCCATTGACTTT
* *
9184 GACAC-AACCCATTAACTTT
1 GAC-CTGACCCATTGACTTT
9203 GAC
1 GAC
9206 TCGAGTTGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
19 49 0.98
20 1 0.02
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.28
Consensus pattern (19 bp):
GACCTGACCCATTGACTTT
Found at i:13387 original size:19 final size:19
Alignment explanation
Indices: 13365--13425 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
13355 CGAGTCAACC
13365 GACCTGACCCATTGACTTT
1 GACCTGACCCATTGACTTT
* *
13384 GACCTAACCCTTTGACTTT
1 GACCTGACCCATTGACTTT
* *
13403 GA-ATCGACCTATTGACTTT
1 GACCT-GACCCATTGACTTT
13422 GACC
1 GACC
13426 AGAGTTGATC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
18 1 0.03
19 32 0.97
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.33
Consensus pattern (19 bp):
GACCTGACCCATTGACTTT
Found at i:13451 original size:13 final size:13
Alignment explanation
Indices: 13430--13459 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
13420 TTGACCAGAG
*
13430 TTGATCGTTGACT
1 TTGACCGTTGACT
13443 TTGACCGTTGACT
1 TTGACCGTTGACT
13456 TTGA
1 TTGA
13460 ACCAAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (13 bp):
TTGACCGTTGACT
Found at i:17754 original size:19 final size:18
Alignment explanation
Indices: 17729--17801 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
17719 TCAACCCGAC
*
17729 CCATTGACTTTGACCCAA
1 CCATTGACTTTGACCAAA
*
17747 CTCGTTGACTTTGAACCAAA
1 C-CATTGACTTTG-ACCAAA
**
17767 CCATTGACTTTGACCTGA
1 CCATTGACTTTGACCAAA
*
17785 CCTATTGACTTTAACCA
1 CC-ATTGACTTTGACCA
17802 GAGTGTATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
18 7 0.16
19 32 0.71
20 6 0.13
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (18 bp):
CCATTGACTTTGACCAAA
Found at i:17793 original size:38 final size:37
Alignment explanation
Indices: 17729--17801 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 37
17719 TCAACCCGAC
*
17729 CCATTGACTTTGACCCAACTCGTTGACTTTGAACCAAA
1 CCATTGACTTTGACCCAACTCATTGACTTT-AACCAAA
**
17767 CCATTGACTTTGACCTGAC-CTATTGACTTTAACCA
1 CCATTGACTTTGACCCAACTC-ATTGACTTTAACCA
17802 GAGTGTATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 6 0.19
38 25 0.81
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (37 bp):
CCATTGACTTTGACCCAACTCATTGACTTTAACCAAA
Found at i:21181 original size:95 final size:96
Alignment explanation
Indices: 20996--21219 Score: 274
Period size: 95 Copynumber: 2.3 Consensus size: 96
20986 TACCGTTAAG
* * *
20996 GTAGTATCGATACCATTGTAAAGGTATCGATACCAAGCAAACATCGAATCTAATTTTGGTATCGA
1 GTAGTATCGATACCATGGTAAAGGTATCGATACCAAGCAAACATCGAACCTAATTTTGGAATCGA
* * *
21061 TACCGTACGGAGGTATCGGTGCCATAGTATA
66 TACCGGACGGAAGTATCGGTACCATAGTATA
* * *
21092 GTAGTATTGATACCATGGTAAGGGTATCGATACCAGGC-AACATCGAACCTAATTTTGGAATCGA
1 GTAGTATCGATACCATGGTAAAGGTATCGATACCAAGCAAACATCGAACCTAATTTTGGAATCGA
* *
21156 TACCCGGA-GGAAGTATTGGTACCATAGTATT
66 TA-CCGGACGGAAGTATCGGTACCATAGTATA
* * * *
21187 GAATTATCGGTACCATGGTAGTA-GTATCGATAC
1 GTAGTATCGATACCATGGTA-AAGGTATCGATAC
21220 TATTGATCTT
Statistics
Matches: 109, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
95 71 0.65
96 38 0.35
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (96 bp):
GTAGTATCGATACCATGGTAAAGGTATCGATACCAAGCAAACATCGAACCTAATTTTGGAATCGA
TACCGGACGGAAGTATCGGTACCATAGTATA
Found at i:21737 original size:34 final size:34
Alignment explanation
Indices: 21678--21742 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
21668 TCATAGCTAA
*
21678 AATGCACATGGATGCTTTATCGGCATAAAAGAAT
1 AATGCACATGGATGCATTATCGGCATAAAAGAAT
* * * *
21712 AATGCATATGGGTGCATTATTGGCATGAAAG
1 AATGCACATGGATGCATTATCGGCATAAAAG
21743 GATGGCCTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (34 bp):
AATGCACATGGATGCATTATCGGCATAAAAGAAT
Found at i:21760 original size:79 final size:79
Alignment explanation
Indices: 21623--21787 Score: 267
Period size: 79 Copynumber: 2.1 Consensus size: 79
21613 AAATGAATGA
* *
21623 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTAAAATGCACATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGGCATACCTAAAATGCACATG
*
21688 GATGCTTTATCGGC
66 GATGCATTATCGGC
* * *
21702 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGGCCTACCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGGCATACCTAAAATGCACATG
*
21767 GGTGCATTATCGGC
66 GATGCATTATCGGC
21781 ATAAAAG
1 ATAAAAG
21788 TATACCACAT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.27
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGGCATACCTAAAATGCACATG
GATGCATTATCGGC
Found at i:49042 original size:17 final size:17
Alignment explanation
Indices: 49020--49054 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
49010 CTGCACAAAT
49020 GTTTAGAATTTTGTGAG
1 GTTTAGAATTTTGTGAG
49037 GTTTAGAATTTTGTGAG
1 GTTTAGAATTTTGTGAG
49054 G
1 G
49055 AGGTCTGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (17 bp):
GTTTAGAATTTTGTGAG
Found at i:51637 original size:14 final size:14
Alignment explanation
Indices: 51602--51637 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
51592 ATATAATGAT
*
51602 TAATTTAAGTACAA
1 TAATTTAAATACAA
51616 TAA-TTAAATACAA
1 TAATTTAAATACAA
51629 TAATTTAAA
1 TAATTTAAA
51638 GTAACTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (14 bp):
TAATTTAAATACAA
Found at i:53075 original size:16 final size:16
Alignment explanation
Indices: 53051--53096 Score: 62
Period size: 14 Copynumber: 3.1 Consensus size: 16
53041 TTTTTTTAAA
*
53051 TTTAAAATAAATATAT
1 TTTATAATAAATATAT
53067 TTTATAAT-AATAT-T
1 TTTATAATAAATATAT
53081 TTTATAATAAAT-TAT
1 TTTATAATAAATATAT
53096 T
1 T
53097 ATTTTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.37
15 10 0.37
16 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTATAATAAATATAT
Found at i:53118 original size:42 final size:41
Alignment explanation
Indices: 53072--53172 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 41
53062 TATATTTTAT
53072 AATAATATTTTTATAATAAATTATTAT-TTTTTAAACAATTAA
1 AATAATATTTTTATAATAAATTATTATATTTTT-AACAA-TAA
* * * *
53114 AATAATATATTTAT-ATTAATTTTTATATTTTTAATAATAA
1 AATAATATTTTTATAATAAATTATTATATTTTTAACAATAA
* *
53154 AATAAAATTATTTAGAATA
1 AATAATATT-TTTATAATA
53173 TTAAATATTA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
40 10 0.21
41 18 0.38
42 20 0.42
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (41 bp):
AATAATATTTTTATAATAAATTATTATATTTTTAACAATAA
Found at i:60447 original size:15 final size:16
Alignment explanation
Indices: 60421--60451 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
60411 TAATTAGTAA
60421 TAAAAAATAACCTCAC
1 TAAAAAATAACCTCAC
60437 TAAAAAA-AACCTCAC
1 TAAAAAATAACCTCAC
60452 CAAACACTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.58, C:0.26, G:0.00, T:0.16
Consensus pattern (16 bp):
TAAAAAATAACCTCAC
Found at i:62032 original size:17 final size:17
Alignment explanation
Indices: 62000--62049 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
61990 TAATAGTTAA
* *
62000 TTTAATAAACGAACTAG
1 TTTAATGAATGAACTAG
*
62017 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
*
62034 TTTAATTAATGAACTA
1 TTTAATGAATGAACTA
62050 CTTCCCTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:66705 original size:15 final size:15
Alignment explanation
Indices: 66685--66714 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
66675 TAATTAGTAA
*
66685 TAAAAATAACCTCAC
1 TAAAAAAAACCTCAC
66700 TAAAAAAAACCTCAC
1 TAAAAAAAACCTCAC
66715 CAAACACTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.17
Consensus pattern (15 bp):
TAAAAAAAACCTCAC
Found at i:68296 original size:17 final size:17
Alignment explanation
Indices: 68264--68313 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
68254 TAATAGTTAA
* *
68264 TTTAATAAACGAACTAG
1 TTTAATGAATGAACTAG
*
68281 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
*
68298 TTTAATTAATGAACTA
1 TTTAATGAATGAACTA
68314 CTTCCCTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:98105 original size:109 final size:110
Alignment explanation
Indices: 97984--98217 Score: 321
Period size: 111 Copynumber: 2.1 Consensus size: 110
97974 TAAACGTCTA
* * *
97984 CATGG-ACGGCTTGCGGGACCAGTTTGTTGTGAGAAGAAGAAAAAACTGAAGAAGAGACATTC-T
1 CATGGAAC-GCTTGCAGGACCAGTTTGTTGTGAGAAGAAG-AAAAACTGAAGAAGACACATGCTT
* * * * *
98047 T-GTGGTTCCTAAATTTCAACCATTTTTAAGATTAATTTGATGTGTG
64 TAGTGGTTCCAAAAATTCAAACATCTTTAAGATTAATTTGACGTGTG
* *
98093 CATGGAACGCTTGCAGGACCAGTTTGTTGTGAGAAGAAGCAAAATTGAAGAAGACACATGCTTTA
1 CATGGAACGCTTGCAGGACCAGTTTGTTGTGAGAAGAAGAAAAACTGAAGAAGACACATGCTTTA
98158 CGTGGTTCCAAAAATTCAAACATCTTTAAGATTAATTTGACGTGTG
66 -GTGGTTCCAAAAATTCAAACATCTTTAAGATTAATTTGACGTGTG
*
98204 CATGGACCGCTTGC
1 CATGGAACGCTTGC
98218 TGTCATAAAA
Statistics
Matches: 110, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
108 18 0.16
109 37 0.34
110 2 0.02
111 53 0.48
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (110 bp):
CATGGAACGCTTGCAGGACCAGTTTGTTGTGAGAAGAAGAAAAACTGAAGAAGACACATGCTTTA
GTGGTTCCAAAAATTCAAACATCTTTAAGATTAATTTGACGTGTG
Found at i:98464 original size:16 final size:16
Alignment explanation
Indices: 98443--98492 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
98433 TGCTCGTCTA
*
98443 ACTCAGATGGTAGAGC
1 ACTCAGTTGGTAGAGC
98459 ACTCAGTTGGTAGAGC
1 ACTCAGTTGGTAGAGC
98475 ACTCAGTTGGTAGAGC
1 ACTCAGTTGGTAGAGC
98491 AC
1 AC
98493 AAGGCTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (16 bp):
ACTCAGTTGGTAGAGC
Found at i:101079 original size:20 final size:21
Alignment explanation
Indices: 101054--101146 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
101044 TTTTCCCAAT
*
101054 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
101074 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
101095 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
101115 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
101136 TCGCAATGCGA
1 TCGCAATGCGA
101147 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:101160 original size:20 final size:20
Alignment explanation
Indices: 101135--101269 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
101125 AATTGGGAAA
101135 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
101155 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
101176 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATACTGACT
*
101196 TTCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
101216 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
101236 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
101256 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
101270 TTTCAAAGCG
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 64 0.68
21 24 0.26
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:101161 original size:41 final size:41
Alignment explanation
Indices: 101054--101146 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
101044 TTTTCCCAAT
101054 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
101095 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
101136 TCGCAATGCGA
1 TCGCAATGCGA
101147 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:101464 original size:22 final size:22
Alignment explanation
Indices: 101437--101480 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
101427 CACTCTCTCA
101437 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
101459 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
101481 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:101785 original size:20 final size:20
Alignment explanation
Indices: 101725--101778 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
101715 GCGATTTTAG
*
101725 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
101745 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
*
101765 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
101779 TTTCATTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.39
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:103129 original size:18 final size:18
Alignment explanation
Indices: 103108--103152 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
103098 TCCACTTCGG
*
103108 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
103126 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
103144 GAGCCATCA
1 GAGCCATCA
103153 TCTGATTGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:103685 original size:19 final size:20
Alignment explanation
Indices: 103631--103697 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
103621 TAGTTTACTT
* *
103631 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
103651 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
103671 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
103690 TCGCAACG
1 TCGCAACG
103698 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:103705 original size:14 final size:14
Alignment explanation
Indices: 103686--103743 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
103676 ATGCGAAATG
*
103686 AAAATCGCAACGAC
1 AAAATCGCAACGAA
103700 AAAATCGCAATACGAA
1 AAAATCGC-A-ACGAA
103716 ATGAAATCGCAACGAA
1 A--AAATCGCAACGAA
103732 AAAATCGCAACG
1 AAAATCGCAACG
103744 CGAAATGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 19 0.49
15 1 0.03
16 11 0.28
17 1 0.03
18 7 0.18
ACGTcount: A:0.52, C:0.22, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:103728 original size:32 final size:33
Alignment explanation
Indices: 103670--103760 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
103660 GGAAATGGCT
*
103670 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
103703 ATCGCAATACGAAATG-AAATCGCAACGAAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
103735 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
103761 TGCGATTTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.55
33 24 0.45
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
Found at i:103855 original size:20 final size:19
Alignment explanation
Indices: 103821--103873 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
103811 TTGCGATTTT
*
103821 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
103840 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
103860 CATTTTCGCGTTGC
1 CA-TTTCGCGTTGC
103874 AATTTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 5 0.17
20 22 0.73
21 3 0.10
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:106597 original size:65 final size:65
Alignment explanation
Indices: 106439--106597 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 65
106429 GTTTAAGGTG
* * * **
106439 CATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTTAT
1 CATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTTAT
*
106502 G
65 A
*
106503 CATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTATA
1 CATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTATA
*
106567 CATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 CATCGATGCATAAG-G-AGTGCATCGATGCAT
106598 ACCTTTATTA
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 59 0.71
65 22 0.27
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (65 bp):
CATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTATA
Found at i:107109 original size:18 final size:18
Alignment explanation
Indices: 107086--107120 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
107076 CTAGGAGATT
107086 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
107104 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
107121 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:108202 original size:103 final size:103
Alignment explanation
Indices: 108023--108235 Score: 374
Period size: 103 Copynumber: 2.1 Consensus size: 103
108013 GGGTATACGC
* **
108023 GGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATATATGAT
1 GGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATATATGAT
108088 CCCTAGCATATGTATATGATTCTTAAGGAATTCTATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATTCTATGT
*
108126 GGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATACT-TGA
1 GGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATA-TATGA
108190 TCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGT
65 TCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGT
108229 GGTCCTT
1 GGTCCTT
108236 ATGGACATTA
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
103 104 0.99
104 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATATATGAT
CCCTAGCATATGTATATGATTCTTAAGGAATTCTATGT
Found at i:111801 original size:63 final size:64
Alignment explanation
Indices: 111662--111821 Score: 209
Period size: 64 Copynumber: 2.5 Consensus size: 64
111652 TTGTTTAAGG
* * * *
111662 TGCATCGATGCACATGCAGTGCATCGATGCATGAATTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCAATTTAAATAGAAAACATCGAATAGGATTTA
* *
111726 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCA-TTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CAATTTAAATAGAAAACATCGAATAGGATTTA
*
111789 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
111822 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
62 1 0.01
63 33 0.38
64 51 0.59
65 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCAATTTAAATAGAAAACATCGAATAGGATTTA
Found at i:113407 original size:149 final size:149
Alignment explanation
Indices: 113234--113548 Score: 535
Period size: 149 Copynumber: 2.1 Consensus size: 149
113224 GAGTCGAGGG
* **
113234 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
113299 A-TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 ACT-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATAGACATCATT
*
113363 ATATGGCACTACGGTGCAAT
130 AAATGGCACTACGGTGCAAT
*
113383 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
113448 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATAGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATAGACATCATTA
113513 AATGGCACTACGGTGCAAT
131 AATGGCACTACGGTGCAAT
113532 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
113549 TGTAATTATA
Statistics
Matches: 157, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
148 1 0.01
149 155 0.99
150 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATAGACATCATTA
AATGGCACTACGGTGCAAT
Found at i:113549 original size:23 final size:23
Alignment explanation
Indices: 113516--113560 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
113506 ATTATTAAAT
*
113516 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
113539 GGCACTTCGGTGTAATTATACG
1 GGCACTACGGTGCAATTATACG
113561 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:114318 original size:14 final size:14
Alignment explanation
Indices: 114299--114334 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
114289 ATTGTTTAAT
114299 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
114313 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
114327 TGATTTGT
1 TGATTTGT
114335 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:114457 original size:14 final size:14
Alignment explanation
Indices: 114438--114491 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
114428 CGAAATGGCT
114438 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
114452 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
114471 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
114485 ATCGCAA
1 ATCGCAA
114492 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:114509 original size:33 final size:33
Alignment explanation
Indices: 114419--114496 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
114409 CAAACAGACT
* ***
114419 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
114452 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
114485 ATCGCAATGCGA
1 ATCGCAATGCGA
114497 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:114540 original size:20 final size:20
Alignment explanation
Indices: 114515--114572 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
114505 TCGCATTGCG
*
114515 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
114535 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
114555 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
114573 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:115634 original size:24 final size:24
Alignment explanation
Indices: 115607--115653 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
115597 GTATTCAAAA
* *
115607 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
115631 TTTGATATTGGTCAATACACGGA
1 TTTGATATTGGTCAATACACGGA
115654 TTTTTATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:115852 original size:12 final size:12
Alignment explanation
Indices: 115835--115859 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
115825 ATATAATCCT
115835 GAAGAAGAAAAA
1 GAAGAAGAAAAA
115847 GAAGAAGAAAAA
1 GAAGAAGAAAAA
115859 G
1 G
115860 TCCCTGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:118176 original size:19 final size:19
Alignment explanation
Indices: 118134--118283 Score: 89
Period size: 19 Copynumber: 8.7 Consensus size: 19
118124 CTTCATGTCT
* **
118134 ATCGCAATGCGGAAATTACT
1 ATCGCAATGC-GAAATGAAA
118154 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
118173 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
118187 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
118206 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
118220 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
118239 ATCGCAA--CG--A-G-GG
1 ATCGCAATGCGAAATGAAA
118252 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
118271 ATCGCAACGCGAA
1 ATCGCAATGCGAA
118284 TTAAATTCGC
Statistics
Matches: 98, Mismatches: 16, Indels: 33
0.67 0.11 0.22
Matches are distributed among these distances:
13 7 0.07
14 19 0.19
15 5 0.05
16 4 0.04
17 7 0.07
18 3 0.03
19 43 0.44
20 10 0.10
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:118196 original size:33 final size:33
Alignment explanation
Indices: 118154--118279 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
118144 GGAAATTACT
118154 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
118187 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
118219 TTTCGCAATGCGAAATGAAAATCGCAACGAG-GG
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
118252 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
118280 CGAATTAAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
32 28 0.33
33 56 0.67
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:118280 original size:65 final size:66
Alignment explanation
Indices: 118155--118285 Score: 237
Period size: 65 Copynumber: 2.0 Consensus size: 66
118145 GAAATTACTA
*
118155 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
118220 T
66 T
*
118221 TCGCAATGCGAAATGAAAATCGCAACGAG-GGATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
118285 T
66 T
118286 AAATTCGCGT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 34 0.54
66 29 0.46
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:118334 original size:19 final size:19
Alignment explanation
Indices: 118289--118353 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
118279 GCGAATTAAA
118289 TTCGCGTTGCGATTCTC--
1 TTCGCGTTGCGATTCTCAT
* *
118306 -T--CGTTACGATTTTCAT
1 TTCGCGTTGCGATTCTCAT
118322 TTCGCGTTGCGATTCTCAT
1 TTCGCGTTGCGATTCTCAT
*
118341 TTCGCATTGCGAT
1 TTCGCGTTGCGAT
118354 AGTACTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
14 11 0.29
16 1 0.03
17 1 0.03
19 25 0.66
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTCTCAT
Found at i:119881 original size:21 final size:21
Alignment explanation
Indices: 119852--119932 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
119842 GAATGGTGGG
*
119852 AGGGACCTCTTCAACGATGAT
1 AGGGGCCTCTTCAACGATGAT
* * * **
119873 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTCAACGATGAT
* * *
119894 AGGGGACTC-TCGAGGAATGAT
1 AGGGGCCTCTTCAACG-ATGAT
119915 AGGGGCCTCTTCAACGAT
1 AGGGGCCTCTTCAACGAT
119933 AGGAGTGGAC
Statistics
Matches: 41, Mismatches: 17, Indels: 4
0.66 0.27 0.06
Matches are distributed among these distances:
20 3 0.07
21 34 0.83
22 4 0.10
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.22
Consensus pattern (21 bp):
AGGGGCCTCTTCAACGATGAT
Found at i:119914 original size:42 final size:41
Alignment explanation
Indices: 119837--119955 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 41
119827 GTGAATCGGG
* * * *
119837 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGATAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
119879 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
119921 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGA
119956 CAGGCGAGTC
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
41 4 0.06
42 55 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:122039 original size:33 final size:33
Alignment explanation
Indices: 121982--122078 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 33
121972 ACGAGATAAT
*
121982 GAGAATCGTAACGCAGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
122016 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
122049 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
122079 TGCGATTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 45 0.78
34 13 0.22
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:122074 original size:19 final size:19
Alignment explanation
Indices: 121957--122083 Score: 76
Period size: 20 Copynumber: 7.1 Consensus size: 19
121947 TCTTTTGGTT
* *
121957 GAAATGAAAATCGCAACGA
1 GAAATGAGAATCGCAACGC
*
121976 GATAATGAGAATCGTAACGC
1 GA-AATGAGAATCGCAACGC
**
121996 AGAAATGACTATCGCAA--C
1 -GAAATGAGAATCGCAACGC
122014 G--A-GAGAATCGCAACGC
1 GAAATGAGAATCGCAACGC
** *
122030 GAAATGACTATCGCGA--C
1 GAAATGAGAATCGCAACGC
122047 G--A-GAGAATCGCAACGC
1 GAAATGAGAATCGCAACGC
* *
122063 GAAATGAAAATCGCAATGC
1 GAAATGAGAATCGCAACGC
122082 GA
1 GA
122084 TTTTTGTTTC
Statistics
Matches: 80, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
14 17 0.21
15 2 0.03
16 4 0.05
17 3 0.04
18 3 0.04
19 24 0.30
20 25 0.31
21 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAGAATCGCAACGC
Found at i:122679 original size:20 final size:20
Alignment explanation
Indices: 122654--122707 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
122644 GGCGCTATGT
122654 AAATCGCGTTGCGAAAGTCA
1 AAATCGCGTTGCGAAAGTCA
122674 AAATCGCGTTGCGAAAGTCA
1 AAATCGCGTTGCGAAAGTCA
** *
122694 GTATCTCGTTGCGA
1 AAATCGCGTTGCGA
122708 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (20 bp):
AAATCGCGTTGCGAAAGTCA
Found at i:122741 original size:20 final size:20
Alignment explanation
Indices: 122716--122769 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
122706 GATTTTGTAT
122716 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
122736 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
122756 TATCGCATTGCGAT
1 TATCGCATTGCGAT
122770 TTTTCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:122788 original size:61 final size:61
Alignment explanation
Indices: 122651--122790 Score: 153
Period size: 61 Copynumber: 2.3 Consensus size: 61
122641 AATGGCGCTA
* * * *
122651 TGTAA-ATCGCGTTGCGAAAGTCAAAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTT
1 TGTAATATCGCGTTGCGATAGTCAAAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
* * * *
122711 TGTATTATCGCATTGCGATAGT-AAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTT
1 TGTAATATCGCGTTGCGATAGTCAA-AATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
122772 T-TCCAAT-TCGCGTTGCGAT
1 TGT--AATATCGCGTTGCGAT
122791 TTACTTATTC
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
60 7 0.11
61 57 0.86
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
TGTAATATCGCGTTGCGATAGTCAAAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
Found at i:124280 original size:388 final size:388
Alignment explanation
Indices: 123564--124493 Score: 1554
Period size: 388 Copynumber: 2.4 Consensus size: 388
123554 AGCATTTCCT
* *
123564 TTGGCTAAGCTATACTTATTAACCTGGGAAGTCGAAAACAAGAGATCCAAGTATAATCCTAAAAG
1 TTGGCTAAGCTATACTTGTTAACCTGGGAAGTCGAAAACAAGAGATCCAAGTATATTCCTAAAAG
* * *
123629 TTGAGTGATGGGGCAAAAACAACACCTATAACCCTTCCACTCCTACACTAACTCTGCCACCAAAG
66 TAGAGTGATGGGACAAAAACAACACCTATAAGCCTTCCACTCCTACACTAACTCTGCCACCAAAG
*
123694 ACTACACAACCTACGAGTAGTCAACGATTTTCTGACAGAAATTGCAACGATACTGTTGAAGAATT
131 ACTACACAACCTACGAGTAGTCAACGATTCTCTGACAGAAATTGCAACGATACTGTTGAAGAATT
*
123759 TAATAAACTAACTCAGGGAGGTTCAGTGGAGGATTATCATGAAAAATTTGAGGAATTGTAATCAT
196 TAATAAACTAACTCAGGGAGGTTCAGTGGAGGACTATCATGAAAAATTTGAGGAATTGTAATCAT
* * *
123824 TTATGCTTCGGTGCAATCTATTGTTAGATGAGGGTTTCTTTGTTTCAAGTTTTTTGAGCGGATTG
261 TTATGCTTCAGTGCAATCTATTGTTAGATGAGGGTTACTTTGTATCAAGTTTTTTGAGCGGATTG
* * ** *
123889 AAGGAGGAAGTTAAGCACAGAGTCAAATCTCATGAACCACAAACATTGGTTGTTGCCTTCAAG
326 AAGGAGAAAGTTAAGCACAGAGTCAAATCTCATGAACCACAAACATTGGCTACTACCTTCAAG
123952 TTGGCTAAGCTATACTTGTTAACCTGGGAAGTCGAAAACAAGAGATCCAAGTATATTCCTAAAAG
1 TTGGCTAAGCTATACTTGTTAACCTGGGAAGTCGAAAACAAGAGATCCAAGTATATTCCTAAAAG
* * *
124017 TGGAGTGATAGGACAAAAACAACACTTATAAGCCTTCCACTCCTACACTAACTCTGCCACCAAAG
66 TAGAGTGATGGGACAAAAACAACACCTATAAGCCTTCCACTCCTACACTAACTCTGCCACCAAAG
* *
124082 ACTACACAACCTACGAGTAGTCAACGATTCTCTGACAGGAATTGCAATGATACTGTTGAAGAATT
131 ACTACACAACCTACGAGTAGTCAACGATTCTCTGACAGAAATTGCAACGATACTGTTGAAGAATT
*
124147 TAATAAACTTACTCAGGGAGGTTCAGTGGAGGACTATCATGAAAAATTTGAGGAATTGTAATCAT
196 TAATAAACTAACTCAGGGAGGTTCAGTGGAGGACTATCATGAAAAATTTGAGGAATTGTAATCAT
* * *
124212 TTATGCTTCATTGTAATCTATTGTTATATGAGGGTTACTTTGTATCAAGTTTTTTGAGCGGATTG
261 TTATGCTTCAGTGCAATCTATTGTTAGATGAGGGTTACTTTGTATCAAGTTTTTTGAGCGGATTG
* *
124277 AAGGAGAAAGTTAAGCACATAGTCAAATCTCATGAACCACAAACATTGGCTACTACCTTGAAG
326 AAGGAGAAAGTTAAGCACAGAGTCAAATCTCATGAACCACAAACATTGGCTACTACCTTCAAG
124340 TTGGCTAAGCTATACTTGTTAACCTGGGAAGTCGAAAACAAGAGATCCAAGTATATTCCTAAAAG
1 TTGGCTAAGCTATACTTGTTAACCTGGGAAGTCGAAAACAAGAGATCCAAGTATATTCCTAAAAG
* * * * ** *
124405 TAGAGTGATGGGACAAAAACGACACCTATAAGCATTCCACTCCAACACTGACTCTTTCACCATAG
66 TAGAGTGATGGGACAAAAACAACACCTATAAGCCTTCCACTCCTACACTAACTCTGCCACCAAAG
*
124470 AATACACAACCTACGAGTAGTCAA
131 ACTACACAACCTACGAGTAGTCAA
124494 ACTAAACAGC
Statistics
Matches: 506, Mismatches: 36, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
388 506 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (388 bp):
TTGGCTAAGCTATACTTGTTAACCTGGGAAGTCGAAAACAAGAGATCCAAGTATATTCCTAAAAG
TAGAGTGATGGGACAAAAACAACACCTATAAGCCTTCCACTCCTACACTAACTCTGCCACCAAAG
ACTACACAACCTACGAGTAGTCAACGATTCTCTGACAGAAATTGCAACGATACTGTTGAAGAATT
TAATAAACTAACTCAGGGAGGTTCAGTGGAGGACTATCATGAAAAATTTGAGGAATTGTAATCAT
TTATGCTTCAGTGCAATCTATTGTTAGATGAGGGTTACTTTGTATCAAGTTTTTTGAGCGGATTG
AAGGAGAAAGTTAAGCACAGAGTCAAATCTCATGAACCACAAACATTGGCTACTACCTTCAAG
Found at i:128790 original size:13 final size:13
Alignment explanation
Indices: 128772--128797 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
128762 ATGAGGTTTA
128772 GGTTATGAAAAAT
1 GGTTATGAAAAAT
128785 GGTTATGAAAAAT
1 GGTTATGAAAAAT
128798 AGTGATTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (13 bp):
GGTTATGAAAAAT
Found at i:129022 original size:20 final size:20
Alignment explanation
Indices: 128997--129069 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
128987 CTATCGCAAA
*
128997 TTCGCGTTGCGATCTTCCAT
1 TTCGCGTTGCGATTTTCCAT
129017 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
*
129037 TTCGCGTTGCAATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
129057 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
129070 AGTCTACAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.11, C:0.26, G:0.21, T:0.42
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCCAT
Found at i:129108 original size:19 final size:19
Alignment explanation
Indices: 129084--129150 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
129074 TACAATGTCA
129084 TTGCGATTTTCCAAATTCG
1 TTGCGATTTTCCAAATTCG
* * ** *
129103 TTGCGATAGTCTACAGTTGTCA
1 TTGCGAT--TTTCCAAAT-TCG
129125 TTGCGATTTTCCAAATTCG
1 TTGCGATTTTCCAAATTCG
*
129144 TTACGAT
1 TTGCGAT
129151 AGTCTACAGT
Statistics
Matches: 34, Mismatches: 11, Indels: 6
0.67 0.22 0.12
Matches are distributed among these distances:
19 15 0.44
20 5 0.15
21 5 0.15
22 9 0.26
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Consensus pattern (19 bp):
TTGCGATTTTCCAAATTCG
Found at i:129131 original size:22 final size:22
Alignment explanation
Indices: 129100--129194 Score: 97
Period size: 22 Copynumber: 4.5 Consensus size: 22
129090 TTTTCCAAAT
129100 TCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
* * * **
129122 TCATTGCGAT--TTTCCAAAT-
1 TCGTTGCGATAGTCTACAGTTG
*
129141 TCGTTACGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
* *
129163 TTGTTGCGAAAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
129185 TCGTTGCGAT
1 TCGTTGCGAT
129195 TTTCCAAATT
Statistics
Matches: 54, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
19 8 0.15
20 5 0.09
21 5 0.09
22 36 0.67
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (22 bp):
TCGTTGCGATAGTCTACAGTTG
Found at i:129171 original size:41 final size:41
Alignment explanation
Indices: 129061--129163 Score: 181
Period size: 41 Copynumber: 2.5 Consensus size: 41
129051 TTCCATTTCG
*
129061 CGTTGCGATAGTCTACA-ATGTCATTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCATTGCGATTTTCCAAATT
129101 CGTTGCGATAGTCTACAGTTGTCATTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCATTGCGATTTTCCAAATT
*
129142 CGTTACGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
129164 TGTTGCGAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
40 17 0.28
41 43 0.72
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCATTGCGATTTTCCAAATT
Found at i:129846 original size:5 final size:5
Alignment explanation
Indices: 129838--129871 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
129828 CTCGTCTCAT
*
129838 GTCGG GTCGG GTCGG GTAGG GTCGG GTCGG GTCG
1 GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG GTCG
129872 ATTCGGGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.03, C:0.18, G:0.59, T:0.21
Consensus pattern (5 bp):
GTCGG
Found at i:130019 original size:22 final size:22
Alignment explanation
Indices: 129992--130085 Score: 113
Period size: 22 Copynumber: 4.4 Consensus size: 22
129982 AATTTGGAAA
129992 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
130014 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
130036 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
130055 ATCGCAATGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
130077 ATCGCAACG
1 ATCGCAACG
130086 CGAACTGGAA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 12 0.21
20 2 0.04
21 2 0.04
22 41 0.72
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:130068 original size:41 final size:41
Alignment explanation
Indices: 130014--130104 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 41
130004 ACTGTAGACT
*
130014 ATCGCAACAACAACTGTAGACTATCGCAA-CGAATTTGGAAA
1 ATCGCAACAACAACTGTAGACTATCGCAACCGAA-CTGGAAA
**
130055 ATCGCAATGACAACTGTAGACTATCGCAACGCGAACTGGAAA
1 ATCGCAACAACAACTGTAGACTATCGCAAC-CGAACTGGAAA
130097 ATCGCAAC
1 ATCGCAAC
130105 GCGAAATGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 27 0.61
42 13 0.30
43 4 0.09
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.18
Consensus pattern (41 bp):
ATCGCAACAACAACTGTAGACTATCGCAACCGAACTGGAAA
Found at i:130102 original size:20 final size:20
Alignment explanation
Indices: 130077--130128 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
130067 ACTGTAGACT
*
130077 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
130097 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
130117 ATCGCAACGCGA
1 ATCGCAACGCGA
130129 TTTTCAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.25, G:0.25, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:130143 original size:21 final size:21
Alignment explanation
Indices: 130117--130170 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
130107 GAAATGGAAA
130117 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* *
130138 ATCGCAACGTGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
130159 ATCGCAACGCGA
1 ATCGCAACGCGA
130171 AATGCAACGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:130858 original size:136 final size:135
Alignment explanation
Indices: 130617--130956 Score: 451
Period size: 136 Copynumber: 2.5 Consensus size: 135
130607 AGGAACAATT
* *
130617 TCTTCTCATTATGAAC-T-TTCT-CCT-T-TAAGATGAGTTTCTTCTCATTATGAACTCT--TCT
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAG-TTCTTCTCATTATGAACTCTCCACT
* ** * * *
130675 GAAACGTTGATCCCTCAAGAAAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGATAGGTCGA
65 AAAATATTGATCCCTCAAGAAAGGCGTCACTGATTCGAAATGCCATGAATCGAGCGATAGGTCGA
130740 ACAAGC
130 ACAAGC
*
130746 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCACTC
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCACT-
* ** * *
130811 AAAATATTGATCCCTCGAGCGAGGCGTCGCTGATTCGAAATGCCATGAATCGAGCGATAGGTTGA
65 AAAATATTGATCCCTCAAGAAAGGCGTCACTGATTCGAAATGCCATGAATCGAGCGATAGGTCGA
130876 ACAAGC
130 ACAAGC
* * *
130882 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATAAGTTCTTCCCATTATGAACTCTCCATTA
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCACTA
130947 GAAATATTGA
66 -AAATATTGA
130957 CTGATTTATT
Statistics
Matches: 184, Mismatches: 18, Indels: 11
0.86 0.08 0.05
Matches are distributed among these distances:
129 16 0.09
130 1 0.01
131 4 0.02
132 3 0.02
133 21 0.11
134 7 0.04
135 3 0.02
136 129 0.70
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (135 bp):
TCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCACTA
AAATATTGATCCCTCAAGAAAGGCGTCACTGATTCGAAATGCCATGAATCGAGCGATAGGTCGAA
CAAGC
Found at i:131963 original size:19 final size:20
Alignment explanation
Indices: 131936--132010 Score: 73
Period size: 19 Copynumber: 3.8 Consensus size: 20
131926 ATCATGCTCA
131936 AAAGACTTACTGATGGCCCG
1 AAAGACTTACTGATGGCCCG
* * * *
131956 -AGGACTTACTCATCATGCTCG
1 AAAGACTTACTGAT--GGCCCG
131977 AAAGACTTACTGATGGCCCG
1 AAAGACTTACTGATGGCCCG
*
131997 AATGACTTA-TGATG
1 AAAGACTTACTGATG
132011 ATTCAAAGTG
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
19 16 0.37
20 12 0.28
21 4 0.09
22 11 0.26
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (20 bp):
AAAGACTTACTGATGGCCCG
Found at i:131986 original size:22 final size:22
Alignment explanation
Indices: 131925--131987 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 22
131915 AGGATTTAAG
*
131925 CATCATGCTCAAAAGACTTACT
1 CATCATGCTCGAAAGACTTACT
* * * *
131947 GAT--GGCCCG-AGGACTTACT
1 CATCATGCTCGAAAGACTTACT
131966 CATCATGCTCGAAAGACTTACT
1 CATCATGCTCGAAAGACTTACT
131988 GATGGCCCGA
Statistics
Matches: 29, Mismatches: 9, Indels: 6
0.66 0.20 0.14
Matches are distributed among these distances:
19 11 0.38
20 3 0.10
21 4 0.14
22 11 0.38
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (22 bp):
CATCATGCTCGAAAGACTTACT
Found at i:132186 original size:42 final size:42
Alignment explanation
Indices: 132140--132241 Score: 152
Period size: 42 Copynumber: 2.4 Consensus size: 42
132130 ATGGATGACA
132140 CGAAGGACTTACACATCATGCTCGAAAGACCTACTGATGGCC
1 CGAAGGACTTACACATCATGCTCGAAAGACCTACTGATGGCC
* * *
132182 CGAAGGATTTA-AGCATCATGTTCGAAAGACTTACTGATGGCC
1 CGAAGGACTTACA-CATCATGCTCGAAAGACCTACTGATGGCC
*
132224 CGAAGGACTTACTCATCA
1 CGAAGGACTTACACATCA
132242 AGAAACCCTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
41 1 0.02
42 52 0.98
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (42 bp):
CGAAGGACTTACACATCATGCTCGAAAGACCTACTGATGGCC
Found at i:132407 original size:52 final size:53
Alignment explanation
Indices: 132290--132530 Score: 249
Period size: 52 Copynumber: 4.5 Consensus size: 53
132280 AAGGAACCCT
132290 TAAAAATTAGGCTTAGTTTCCTTTTAAAAACTCA-TTGAAAACCATCATCAAGAAATCCC
1 TAAAAATTAGGCTTAGTTT-C--TTAAAAACTCATTTG-AAA--A-CATCAAGAAATCCC
* *
132349 TGAAAATTAGGCTTAGTTTC-TAAAAACTCATTTGAAAACATCAAGATATCCC
1 TAAAAATTAGGCTTAGTTTCTTAAAAACTCATTTGAAAACATCAAGAAATCCC
* ** * * *
132401 TAAAAATTAGGCTTAATTTCTTTGAAATTCATTTGAAAACATTAAGAAACCCC
1 TAAAAATTAGGCTTAGTTTCTTAAAAACTCATTTGAAAACATCAAGAAATCCC
* ** * *
132454 T-AAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCGAGAAA-CCC
1 TAAAAATTAGGCTTAGTTTCTTAAAAACTCATTTGAAAACATCAAGAAATCCC
* *
132505 TGAAAATCAGGCTTAGTTTC-TAAAAA
1 TAAAAATTAGGCTTAGTTTCTTAAAAA
132531 TCTTTTGTTT
Statistics
Matches: 160, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
51 8 0.05
52 89 0.56
53 28 0.17
55 13 0.08
56 3 0.02
58 1 0.01
59 18 0.11
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (53 bp):
TAAAAATTAGGCTTAGTTTCTTAAAAACTCATTTGAAAACATCAAGAAATCCC
Found at i:132489 original size:105 final size:107
Alignment explanation
Indices: 132284--132525 Score: 278
Period size: 104 Copynumber: 2.2 Consensus size: 107
132274 GTTGTAAAGG
*
132284 AACCCTTAAAAATTAGGCTTAGTTTCCTTTTAAAAACTCATTGAAAACCATCATCAAGAAATCCC
1 AACCC-TAAAAATTAGGCTTAGTTT-C-TTTAAAAACTCATTGAAAACCAT-ATCAAGAAACCCC
*
132349 TGAAAATTAGGCTTAGTTTCTAAAAACTCATTTGAAAACATCAAGA
62 TGAAAATTAGGCTTAGCTTCTAAAAACTCATTTGAAAACATCAAGA
* * * *
132395 TATCCCTAAAAATTAGGCTTAATTTCTTT-GAAATTCATTTGAAAA-CAT-T-AAGAAACCCCT-
1 -AACCCTAAAAATTAGGCTTAGTTTCTTTAAAAACTCA-TTGAAAACCATATCAAGAAACCCCTG
** * *
132455 AAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCGAGA
64 AAAATTAGGCTTAGCTTC-TAAAAACTCATTTGAAAACATCAAGA
* *
132500 AACCCTGAAAATCAGGCTTAGTTTCT
1 AACCCTAAAAATTAGGCTTAGTTTCT
132526 AAAAATCTTT
Statistics
Matches: 114, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
104 39 0.34
105 32 0.28
106 1 0.01
108 9 0.08
109 10 0.09
110 1 0.01
111 18 0.16
112 4 0.04
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (107 bp):
AACCCTAAAAATTAGGCTTAGTTTCTTTAAAAACTCATTGAAAACCATATCAAGAAACCCCTGAA
AATTAGGCTTAGCTTCTAAAAACTCATTTGAAAACATCAAGA
Found at i:132587 original size:39 final size:39
Alignment explanation
Indices: 132527--132684 Score: 205
Period size: 39 Copynumber: 4.1 Consensus size: 39
132517 TTAGTTTCTA
* * * *
132527 AAAATCTTTTGTTTTGGGCGAAACTATCTCAAGTGAGAT
1 AAAATCTTATGTTTCGAGCGAAACTATCTCAAGCGAGAT
*
132566 AAAATCTTATGTTTCGAGCGAAACTATCTCAAGGGAGAT
1 AAAATCTTATGTTTCGAGCGAAACTATCTCAAGCGAGAT
* *
132605 AAAATCTTATGTTCCGAGTGAAACTATCTCAAGCGAGAT
1 AAAATCTTATGTTTCGAGCGAAACTATCTCAAGCGAGAT
* * *
132644 AAAAT-TCA--TTTCAAGGGAAACTATCTCAAGCGAGAT
1 AAAATCTTATGTTTCGAGCGAAACTATCTCAAGCGAGAT
132680 AAAAT
1 AAAAT
132685 TCGTTTGAAG
Statistics
Matches: 108, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
36 30 0.28
38 2 0.02
39 76 0.70
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (39 bp):
AAAATCTTATGTTTCGAGCGAAACTATCTCAAGCGAGAT
Found at i:132671 original size:36 final size:36
Alignment explanation
Indices: 132546--132806 Score: 211
Period size: 36 Copynumber: 7.1 Consensus size: 36
132536 TGTTTTGGGC
* * * *
132546 GAAACTATCTCAAGTGAGATAAAATCTTATGTTTCGAGC
1 GAAACTATCTCAAGGGAGATAAAAT-TCA--TTTCAAGG
* * *
132585 GAAACTATCTCAAGGGAGATAAAATCTTATGTTCCGAGT
1 GAAACTATCTCAAGGGAGATAAAAT-TCAT-TT-CAAGG
*
132624 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGGGAGATAAAATTCATTTCAAGG
* * * *
132660 GAAACTATCTCAAGCGAGATAAAATTCGTTTGAAGA
1 GAAACTATCTCAAGGGAGATAAAATTCATTTCAAGG
* ** * * *
132696 GAAACTGTCTCAAGGGAGACGAGATGT-GTTTCAAGA
1 GAAACTATCTCAAGGGAGATAAAAT-TCATTTCAAGG
* * * ** *
132732 GAAACTATCTCAAGAGAGACAAATTTTGTTTAAAGG
1 GAAACTATCTCAAGGGAGATAAAATTCATTTCAAGG
* *
132768 GAAACTGTCTCAAGGGAGA-CAAATTCATTTCAAGG
1 GAAACTATCTCAAGGGAGATAAAATTCATTTCAAGG
132803 GAAA
1 GAAA
132807 TGATGTTAAA
Statistics
Matches: 189, Mismatches: 29, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
35 16 0.08
36 108 0.57
37 4 0.02
38 5 0.03
39 56 0.30
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.26
Consensus pattern (36 bp):
GAAACTATCTCAAGGGAGATAAAATTCATTTCAAGG
Found at i:133019 original size:34 final size:34
Alignment explanation
Indices: 132952--133019 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
132942 GTGAGATCAA
* * * *
132952 TTTTGGGAGAATGTCTCAAGTAAGACTATATTTG
1 TTTTGAGAGAATGTCTCAAGCAAGACAAAATTTG
* *
132986 TTTTGAGAGAATGTTTCAAGCGAGACAAAATTTG
1 TTTTGAGAGAATGTCTCAAGCAAGACAAAATTTG
133020 GTTCAAGTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (34 bp):
TTTTGAGAGAATGTCTCAAGCAAGACAAAATTTG
Found at i:133092 original size:97 final size:96
Alignment explanation
Indices: 132961--133190 Score: 252
Period size: 100 Copynumber: 2.4 Consensus size: 96
132951 ATTTTGGGAG
* * * *
132961 AATGTCTCAAGT-AAGACTATATTTGTTTTGAGAGAATGTTTCAAGCGAGACAAAA-TTTGGTTC
1 AATGTCTCAAGTGAA-AC-AAATTTGTTTTAAGAGAATGTCTCAAGCGAGACAAAATTTTAGTTC
*
133024 AAGTAAAATAACTTTGAAATTGTGCTCCGAAGGA
64 AAG-AAAACAACTTTGAAATTGTGCTCCGAAGGA
* * * *
133058 AATGTCTCAAGTGAAACGAAATTTATTTTAAGAGAAAAATGTCTCAAGTGATACAAAATTTTATT
1 AATGTCTCAAGTGAAAC-AAATTTGTTTTAAGAG---AATGTCTCAAGCGAGACAAAATTTTAGT
* * *
133123 TTAAGAAAACAACTTTGAAATTGTGTTTCGAAGGA
62 TCAAGAAAACAACTTTGAAATTGTGCTCCGAAGGA
*
133158 AATGGCTCAAGTGAAA-AAA-TTGTTTTAAGAGAA
1 AATGTCTCAAGTGAAACAAATTTGTTTTAAGAGAA
133191 AATATGACTC
Statistics
Matches: 113, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
94 2 0.02
97 38 0.34
98 5 0.04
100 60 0.53
101 8 0.07
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (96 bp):
AATGTCTCAAGTGAAACAAATTTGTTTTAAGAGAATGTCTCAAGCGAGACAAAATTTTAGTTCAA
GAAAACAACTTTGAAATTGTGCTCCGAAGGA
Found at i:133099 original size:37 final size:38
Alignment explanation
Indices: 133057--133128 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 38
133047 GCTCCGAAGG
*
133057 AAATGTCTCAAGTGAAACGAAA-TTTATTTTAAGAGAA
1 AAATGTCTCAAGTGAAACAAAATTTTATTTTAAGAGAA
*
133094 AAATGTCTCAAGTGATACAAAATTTTATTTTAAGA
1 AAATGTCTCAAGTGAAACAAAATTTTATTTTAAGA
133129 AAACAACTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 20 0.62
38 12 0.38
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.33
Consensus pattern (38 bp):
AAATGTCTCAAGTGAAACAAAATTTTATTTTAAGAGAA
Found at i:133231 original size:100 final size:99
Alignment explanation
Indices: 133001--133226 Score: 280
Period size: 100 Copynumber: 2.3 Consensus size: 99
132991 AGAGAATGTT
* ** * * *
133001 TCAAGCGAGACAAAA-TTTGGTTCAAGTAAAATAACTTTGAAATTGTGCTCCGAAGGAAATGTCT
1 TCAAGTGAGACAAAATTTTATTTTAAG-AAAACAACTTTGAAATTGTGCTCCGAAGGAAATGGCT
*
133065 CAAGTGAAACGAAATTTATTTTAAGAGAAAAATGTC
65 CAAGTGAAAC-AAATTTATTTTAAGAGAAAAATGAC
* * *
133101 TCAAGTGATACAAAATTTTATTTTAAGAAAACAACTTTGAAATTGTGTTTCGAAGGAAATGGCTC
1 TCAAGTGAGACAAAATTTTATTTTAAGAAAACAACTTTGAAATTGTGCTCCGAAGGAAATGGCTC
*
133166 AAGTGAAA-AAA-TTGTTTTAAGAGAAAATATGAC
66 AAGTGAAACAAATTTATTTTAAGAGAAAA-ATGAC
*
133199 TCAAGTTAGACAAAATTTGT-TTTTAAGA
1 TCAAGTGAGACAAAATTT-TATTTTAAGA
133227 GAAAAATGTC
Statistics
Matches: 110, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
97 15 0.14
98 31 0.28
99 1 0.01
100 55 0.50
101 8 0.07
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.31
Consensus pattern (99 bp):
TCAAGTGAGACAAAATTTTATTTTAAGAAAACAACTTTGAAATTGTGCTCCGAAGGAAATGGCTC
AAGTGAAACAAATTTATTTTAAGAGAAAAATGAC
Found at i:133268 original size:38 final size:38
Alignment explanation
Indices: 133163--133246 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 38
133153 AAGGAAATGG
133163 CTCAAGTGA-A-AAAA-TTGTTTTAAGAGAAAATATGA
1 CTCAAGTGAGACAAAATTTGTTTTAAGAGAAAATATGA
* *
133198 CTCAAGTTAGACAAAATTTGTTTTTAAGAGAAAA-ATGT
1 CTCAAGTGAGACAAAATTTG-TTTTAAGAGAAAATATGA
133236 CTCAAGTGAGA
1 CTCAAGTGAGA
133247 TGACATTTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
35 8 0.19
36 1 0.02
37 4 0.10
38 16 0.38
39 13 0.31
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (38 bp):
CTCAAGTGAGACAAAATTTGTTTTAAGAGAAAATATGA
Found at i:136831 original size:34 final size:30
Alignment explanation
Indices: 136793--136861 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
136783 TTGATATAAC
136793 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
136827 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
136856 AATTTA
1 AATTTA
136862 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:136872 original size:29 final size:30
Alignment explanation
Indices: 136802--136861 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
136792 CAATTTAAGG
136802 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
136833 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
136862 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:143384 original size:36 final size:37
Alignment explanation
Indices: 143310--143384 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 37
143300 AAATATATGC
* * *
143310 ATATGTTTTCTAAATATGATATTAAATATAGAACATA
1 ATATGTATTCTAAATATGATATGAAATATAAAACATA
*
143347 ATATGTATTCTAAA-AT-ATAATGAAATATAAAATATA
1 ATATGTATTCTAAATATGAT-ATGAAATATAAAACATA
143383 AT
1 AT
143385 TTTACCATGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 2 0.06
36 18 0.55
37 13 0.39
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.39
Consensus pattern (37 bp):
ATATGTATTCTAAATATGATATGAAATATAAAACATA
Done.