Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007909.1 Hibiscus syriacus cultivar Beakdansim tig00110303_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: 3382237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 17
Found at i:3261959 original size:16 final size:16
Alignment explanation
Indices: 3261938--3261972 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3261928 ATTTTGAACA
* *
3261938 TAGTTCTAGTTTTAAT
1 TAGTTCTAGGTTGAAT
3261954 TAGTTCTAGGTTGAAT
1 TAGTTCTAGGTTGAAT
3261970 TAG
1 TAG
3261973 ATATCGGGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.20, T:0.49
Consensus pattern (16 bp):
TAGTTCTAGGTTGAAT
Found at i:3263938 original size:13 final size:13
Alignment explanation
Indices: 3263916--3263949 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3263906 AGGGGGAGTA
*
3263916 ATTTTCAAAATTG
1 ATTTTCAAAAATG
3263929 A-TTTCAAAAATG
1 ATTTTCAAAAATG
3263941 ATTTTCAAA
1 ATTTTCAAA
3263950 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:3265214 original size:5 final size:5
Alignment explanation
Indices: 3265210--3265259 Score: 93
Period size: 5 Copynumber: 10.2 Consensus size: 5
3265200 AAAAAGTAAA
3265210 ATAA- ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
3265259 A
1 A
3265260 AAAACGAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.09
5 41 0.91
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:3266545 original size:25 final size:25
Alignment explanation
Indices: 3266516--3266564 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3266506 TTCAAAAATA
3266516 TTTTCAAAACTATATGT-TATATATG
1 TTTTCAAAACTATAT-TATATATATG
3266541 TTTTCAAAACTATATTATATATAT
1 TTTTCAAAACTATATTATATATAT
3266565 ATAAATGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (25 bp):
TTTTCAAAACTATATTATATATATG
Found at i:3266819 original size:37 final size:37
Alignment explanation
Indices: 3266761--3266928 Score: 229
Period size: 37 Copynumber: 4.6 Consensus size: 37
3266751 CATTTCATAT
* *
3266761 TATATA-TATATAT-ATTT-AAAAACGTTTTCAAAAC
1 TATATATTATATATGTTTTCAAAAATGTTTTCAAAAC
* * *
3266795 CATATATTATATATTTTTTCAAAAATATTTTCAAAAC
1 TATATATTATATATGTTTTCAAAAATGTTTTCAAAAC
*
3266832 TATATATTATATATGTTTTC-AAAATATTTTCAAAAC
1 TATATATTATATATGTTTTCAAAAATGTTTTCAAAAC
3266868 TATATATTATATATGTTTTCAAAAATGCTTTT-AAAAC
1 TATATATTATATATGTTTTCAAAAATG-TTTTCAAAAC
*
3266905 TATATATTATATATATTTTCAAAA
1 TATATATTATATATGTTTTCAAAA
3266929 CCTGAATTTA
Statistics
Matches: 121, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
34 5 0.04
35 7 0.06
36 39 0.32
37 66 0.55
38 4 0.03
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.46
Consensus pattern (37 bp):
TATATATTATATATGTTTTCAAAAATGTTTTCAAAAC
Found at i:3266873 original size:73 final size:73
Alignment explanation
Indices: 3266761--3266928 Score: 243
Period size: 73 Copynumber: 2.3 Consensus size: 73
3266751 CATTTCATAT
* ** *
3266761 TATATA-TATATATA-TTTAAAAACGTTTTCAAAACCATATATTATATATTTTTTCAAAAAT-AT
1 TATATATTATATATATTTTCAAAATATTTTCAAAACCATATATTATATATGTTTTCAAAAATGAT
3266823 TTTCAAAAC
66 TTT-AAAAC
* * *
3266832 TATATATTATATATGTTTTCAAAATATTTTCAAAACTATATATTATATATGTTTTCAAAAATGCT
1 TATATATTATATATATTTTCAAAATATTTTCAAAACCATATATTATATATGTTTTCAAAAATGAT
3266897 TTTAAAAC
66 TTTAAAAC
3266905 TATATATTATATATATTTTCAAAA
1 TATATATTATATATATTTTCAAAA
3266929 CCTGAATTTA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
71 6 0.07
72 7 0.08
73 69 0.80
74 4 0.05
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.46
Consensus pattern (73 bp):
TATATATTATATATATTTTCAAAATATTTTCAAAACCATATATTATATATGTTTTCAAAAATGAT
TTTAAAAC
Found at i:3266959 original size:18 final size:18
Alignment explanation
Indices: 3266938--3266977 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3266928 ACCTGAATTT
*
3266938 AAAAA-AAAATTGTTTCCA
1 AAAAAGAAAATTCTTT-CA
3266956 AAAAAGAAAATTCTTTCA
1 AAAAAGAAAATTCTTTCA
3266974 AAAA
1 AAAA
3266978 CTATACTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.60, C:0.10, G:0.05, T:0.25
Consensus pattern (18 bp):
AAAAAGAAAATTCTTTCA
Found at i:3272283 original size:16 final size:16
Alignment explanation
Indices: 3272262--3272299 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3272252 TCCGGAAAAA
3272262 GTCGAGTTCGAAAATT
1 GTCGAGTTCGAAAATT
* *
3272278 GTCGAGTTCGGAAGTT
1 GTCGAGTTCGAAAATT
3272294 GTCGAG
1 GTCGAG
3272300 GACTTTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.13, G:0.34, T:0.29
Consensus pattern (16 bp):
GTCGAGTTCGAAAATT
Found at i:3284300 original size:28 final size:28
Alignment explanation
Indices: 3284256--3284311 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
3284246 TGTACAGTTC
*
3284256 ATCAATCCCATGCCAACTTTCCTTCTTT
1 ATCAATCCCATGACAACTTTCCTTCTTT
3284284 ATCAATCCCATGACAACTTTCCTTCTTT
1 ATCAATCCCATGACAACTTTCCTTCTTT
3284312 CTTTTTAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.34, G:0.04, T:0.39
Consensus pattern (28 bp):
ATCAATCCCATGACAACTTTCCTTCTTT
Found at i:3285996 original size:28 final size:28
Alignment explanation
Indices: 3285965--3286033 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
3285955 TACTTTCAAA
*
3285965 AAATATATTGTATTGTTATATTAA-TTT
1 AAATATATTGTATTCTTATATTAACTTT
*
3285992 GAAATATATTATATTCTTATATTAACTTT
1 -AAATATATTGTATTCTTATATTAACTTT
*
3286021 AAAAATA-TGTATT
1 AAATATATTGTATT
3286034 TTTTTATCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 5 0.14
28 28 0.78
29 3 0.08
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.51
Consensus pattern (28 bp):
AAATATATTGTATTCTTATATTAACTTT
Found at i:3293445 original size:43 final size:40
Alignment explanation
Indices: 3293362--3293445 Score: 98
Period size: 43 Copynumber: 2.0 Consensus size: 40
3293352 CTTCCTTTTT
*
3293362 TTTATTATTTTTTCTTATCTTATCTTATCTTATTTGTTTA
1 TTTATTATTTTTTCTTATCTTATCTTATCTTATTTCTTTA
* *
3293402 TTTATTTATTATTTTCTTCTCTTTATCTTAT-TTGTTTTCTTTA
1 TTTA-TTATT-TTTTCTTATC-TTATCTTATCTT-ATTTCTTTA
3293445 T
1 T
3293446 CTTGTTTCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
40 4 0.11
41 5 0.14
42 11 0.30
43 17 0.46
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.71
Consensus pattern (40 bp):
TTTATTATTTTTTCTTATCTTATCTTATCTTATTTCTTTA
Found at i:3303811 original size:11 final size:11
Alignment explanation
Indices: 3303795--3303819 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3303785 CTAAATTAAA
3303795 AAAAGAAAAAG
1 AAAAGAAAAAG
3303806 AAAAGAAAAAG
1 AAAAGAAAAAG
3303817 AAA
1 AAA
3303820 GAACAAAAAG
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:3304689 original size:105 final size:105
Alignment explanation
Indices: 3304507--3305249 Score: 1202
Period size: 105 Copynumber: 7.1 Consensus size: 105
3304497 TAGCCATAGT
* * * * * * *
3304507 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGTTAAACTTTACGATGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
3304572 GGACCGCTGGTTGTCAACAACAACGTCCCAATTTTAGAGC
66 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGC
* *
3304612 CAATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCGACTTCACGACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
3304677 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGC
* * *
3304717 CAATTTCAACTTCATAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCGACTTCATGACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
3304782 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGC
** **
3304822 CAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTTGACTTCACGACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
3304887 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGC
* * * *
3304927 CAATTTCAACTTCACAGCGAAGGATATTGGGCTCCAGATAACGCAAGTTTAACTTCACGAAGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
3304992 GGACCGCTGGTTGTCAACAATAACTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGC
*
3305032 CAATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
3305097 GGA-CGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGC
* * *
3305136 CAATTTTAACTTCA-AGCGAAGGATATTAGACTCTAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
**
3305200 GGACCGCTGGTTGTCAACGAACATTTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGC
3305241 CAATTTCAA
1 CAATTTCAA
3305250 AGGATATTGG
Statistics
Matches: 600, Mismatches: 36, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
103 52 0.09
104 62 0.10
105 486 0.81
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGC
Found at i:3306676 original size:20 final size:20
Alignment explanation
Indices: 3306651--3306690 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3306641 TGTGTTTAGC
*
3306651 CACCGATGAACGGCGGCCGG
1 CACCGATCAACGGCGGCCGG
3306671 CACCGATCAACGGCGGCCGG
1 CACCGATCAACGGCGGCCGG
3306691 TGAGGTGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.38, G:0.38, T:0.05
Consensus pattern (20 bp):
CACCGATCAACGGCGGCCGG
Found at i:3308959 original size:20 final size:20
Alignment explanation
Indices: 3308918--3308959 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3308908 ATCCAGAAAG
*
3308918 CACTTGCAAACATTAGCCAA
1 CACTTGCAAACATTAGCAAA
*
3308938 CACTTGCAAACATTTGCAAA
1 CACTTGCAAACATTAGCAAA
3308958 CA
1 CA
3308960 TTCATCCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.29, G:0.10, T:0.21
Consensus pattern (20 bp):
CACTTGCAAACATTAGCAAA
Found at i:3308960 original size:10 final size:10
Alignment explanation
Indices: 3308921--3308961 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
3308911 CAGAAAGCAC
3308921 TTGCAAACAT
1 TTGCAAACAT
* * *
3308931 TAGCCAACAC
1 TTGCAAACAT
3308941 TTGCAAACAT
1 TTGCAAACAT
3308951 TTGCAAACAT
1 TTGCAAACAT
3308961 T
1 T
3308962 CATCCCCACA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (10 bp):
TTGCAAACAT
Found at i:3310081 original size:26 final size:26
Alignment explanation
Indices: 3310045--3310103 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
3310035 GTTTTCTTTT
*
3310045 GTTGTGTTTTAGGTGAAGCGCTTATC
1 GTTGTATTTTAGGTGAAGCGCTTATC
3310071 GTTGTATTTTAGGTGAAGCGCTTATC
1 GTTGTATTTTAGGTGAAGCGCTTATC
3310097 GTTGTAT
1 GTTGTAT
3310104 CTGATTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.17, C:0.10, G:0.29, T:0.44
Consensus pattern (26 bp):
GTTGTATTTTAGGTGAAGCGCTTATC
Found at i:3310731 original size:2 final size:2
Alignment explanation
Indices: 3310724--3310752 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3310714 ATAAGATGAG
3310724 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3310753 ATAAAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3313527 original size:105 final size:106
Alignment explanation
Indices: 3313404--3313623 Score: 354
Period size: 105 Copynumber: 2.1 Consensus size: 106
3313394 GTGACAGAGT
* * *
3313404 TATTGATAATAGTGTCGAACATTTGGTCTCTAAAAAACACTTAGTGTGACAATATTGGTGGTCAC
1 TATTGATAATAGTATCGAACATTTGGTCACTAAAAAACACTTAGTGTGACAATATTGATGGTCAC
* *
3313469 AAAATATACTTTCAGTGTTAAACAAATTTATCACAATTT-C
66 AAAATATACTTTCAGTGTCAAACAAATTCATCACAATTTAC
*
3313509 TATTGATAATAGTATCGAACATTTGGTCACTAAAAAATACTTAGTGTGACAATATTGATGGTCAC
1 TATTGATAATAGTATCGAACATTTGGTCACTAAAAAACACTTAGTGTGACAATATTGATGGTCAC
* *
3313574 AAAATATATTTTTAGTGTCAAACAAATTCATCACAATTTAC
66 AAAATATACTTTCAGTGTCAAACAAATTCATCACAATTTAC
3313615 -ATTGATAAT
1 TATTGATAAT
3313624 TTTGTCGAAT
Statistics
Matches: 106, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
105 105 0.99
106 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (106 bp):
TATTGATAATAGTATCGAACATTTGGTCACTAAAAAACACTTAGTGTGACAATATTGATGGTCAC
AAAATATACTTTCAGTGTCAAACAAATTCATCACAATTTAC
Found at i:3313649 original size:105 final size:105
Alignment explanation
Indices: 3313435--3313649 Score: 279
Period size: 105 Copynumber: 2.0 Consensus size: 105
3313425 TTTGGTCTCT
* * *
3313435 AAAAAACACTTAGTGTGACAATATTGGTGGTCACAAAATATACTTTCAGTGTTAAACAAATTTAT
1 AAAAAACACTTAGTGTGACAATATTGATGGTCACAAAATATACTTTCAGTGTCAAACAAATTCAT
** * **
3313500 CACAATTTCTATTGATAATAGTATCGAACATTTGGTCACT
66 CACAATTTCTATTGATAATAGTATCGAACAGATGATCAAA
* * *
3313540 AAAAAATACTTAGTGTGACAATATTGATGGTCACAAAATATATTTTTAGTGTCAAACAAATTCAT
1 AAAAAACACTTAGTGTGACAATATTGATGGTCACAAAATATACTTTCAGTGTCAAACAAATTCAT
** * *
3313605 CACAATTTAC-ATTGATAATTTTGTCGAATAGATGATCAAA
66 CACAATTT-CTATTGATAATAGTATCGAACAGATGATCAAA
3313645 AAAAA
1 AAAAA
3313650 TGAACAATTG
Statistics
Matches: 94, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
105 93 0.99
106 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (105 bp):
AAAAAACACTTAGTGTGACAATATTGATGGTCACAAAATATACTTTCAGTGTCAAACAAATTCAT
CACAATTTCTATTGATAATAGTATCGAACAGATGATCAAA
Found at i:3313662 original size:105 final size:105
Alignment explanation
Indices: 3313404--3313650 Score: 273
Period size: 105 Copynumber: 2.4 Consensus size: 105
3313394 GTGACAGAGT
* ** * * * * * *
3313404 TATTGATAATAGTGTCGAACATTTGGTCTCTAAAAAACACTTAGTGTGACAATATTGGTGGTCAC
1 TATTGATAATAGTATCGAACAGATGATCACAAAAAAATACTAAGTGTGACAATATTGATGGTCAC
* *
3313469 AAAATATACTTTCAGTGTTAAACAAATTTATCACAATTTC
66 AAAATATACTTTCAGTGTCAAACAAATTCATCACAATTTC
** * * *
3313509 TATTGATAATAGTATCGAACATTTGGTCACTAAAAAATACTTAGTGTGACAATATTGATGGTCAC
1 TATTGATAATAGTATCGAACAGATGATCACAAAAAAATACTAAGTGTGACAATATTGATGGTCAC
* *
3313574 AAAATATATTTTTAGTGTCAAACAAATTCATCACAATTTAC
66 AAAATATACTTTCAGTGTCAAACAAATTCATCACAATTT-C
** * *
3313615 -ATTGATAATTTTGTCGAATAGATGATCA-AAAAAAAT
1 TATTGATAATAGTATCGAACAGATGATCACAAAAAAAT
3313651 GAACAATTGT
Statistics
Matches: 125, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
104 7 0.06
105 117 0.94
106 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (105 bp):
TATTGATAATAGTATCGAACAGATGATCACAAAAAAATACTAAGTGTGACAATATTGATGGTCAC
AAAATATACTTTCAGTGTCAAACAAATTCATCACAATTTC
Found at i:3314191 original size:19 final size:19
Alignment explanation
Indices: 3314169--3314210 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
3314159 ATAATTTGAG
3314169 TTGACTCGAATAACTCAAC
1 TTGACTCGAATAACTCAAC
*
3314188 TTGACTCGAATAACTCGAC
1 TTGACTCGAATAACTCAAC
3314207 TTGA
1 TTGA
3314211 ATAACTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (19 bp):
TTGACTCGAATAACTCAAC
Found at i:3314499 original size:28 final size:28
Alignment explanation
Indices: 3314459--3314547 Score: 160
Period size: 28 Copynumber: 3.2 Consensus size: 28
3314449 GATAATTTTG
3314459 TATTCAATTTAATAAAAACCTAAAATAA
1 TATTCAATTTAATAAAAACCTAAAATAA
3314487 TATTCAATTTAATAAAAACCTAAAATAA
1 TATTCAATTTAATAAAAACCTAAAATAA
* *
3314515 TATTAAATTTAATAAAAACCTAAACTAA
1 TATTCAATTTAATAAAAACCTAAAATAA
3314543 TATTC
1 TATTC
3314548 TGAATTACAC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TATTCAATTTAATAAAAACCTAAAATAA
Found at i:3322514 original size:13 final size:13
Alignment explanation
Indices: 3322496--3322521 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3322486 AAATTACTTC
3322496 CCCTTACTATATT
1 CCCTTACTATATT
3322509 CCCTTACTATATT
1 CCCTTACTATATT
3322522 ATTCTCCCCC
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:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (13 bp):
CCCTTACTATATT
Found at i:3324784 original size:19 final size:20
Alignment explanation
Indices: 3324762--3324839 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 20
3324752 AAAACCCGAT
*
3324762 GGGGGTATCGATACCCTT-A
1 GGGGGTATCGATACCATTAA
*
3324781 GGGGGTATTGATACACATTCAAA
1 GGGGGTATCGATAC-CATT--AA
*
3324804 GGGGGTATCGATACC-TGGCAA
1 GGGGGTATCGATACCAT--TAA
3324825 GGGGGTATCGATACC
1 GGGGGTATCGATACC
3324840 TGGTGCACAG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
19 13 0.27
20 3 0.06
21 18 0.37
22 1 0.02
23 14 0.29
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.23
Consensus pattern (20 bp):
GGGGGTATCGATACCATTAA
Found at i:3324828 original size:21 final size:21
Alignment explanation
Indices: 3324802--3324842 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3324792 TACACATTCA
3324802 AAGGGGGTATCGATACCTGGC
1 AAGGGGGTATCGATACCTGGC
3324823 AAGGGGGTATCGATACCTGG
1 AAGGGGGTATCGATACCTGG
3324843 TGCACAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.39, T:0.20
Consensus pattern (21 bp):
AAGGGGGTATCGATACCTGGC
Found at i:3330626 original size:74 final size:74
Alignment explanation
Indices: 3330498--3330635 Score: 172
Period size: 74 Copynumber: 1.9 Consensus size: 74
3330488 GTTATATGAC
* * * * *
3330498 TAGGGGTATCGATACCTCTAAGGGGGTATCGGTACCCATATGACATTCTGTTTTTCTCGGAGCCA
1 TAGGGGTATCGATACCTCTAAGGGGGTATCGATACCCATAGGACAATCTATTTTTCTCGAAGCCA
3330563 AATCTTGCA
66 AATCTTGCA
* * *
3330572 TAGGGGTATCGGTACC-CTAAGAGGGGTATCGATATCCACT-GGGCAATCTATTTTTCTCGAAGC
1 TAGGGGTATCGATACCTCTAAG-GGGGTATCGATACCCA-TAGGACAATCTATTTTTCTCGAAGC
3330635 C
64 C
3330636 CTTCTATTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
73 5 0.09
74 48 0.89
75 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (74 bp):
TAGGGGTATCGATACCTCTAAGGGGGTATCGATACCCATAGGACAATCTATTTTTCTCGAAGCCA
AATCTTGCA
Found at i:3333795 original size:36 final size:36
Alignment explanation
Indices: 3333748--3333821 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
3333738 GTGGGTGACC
*
3333748 TTGAAAATGAAATTCGTGGATTAACTCTTTAGTCGT
1 TTGAAAATGAAATTCGTGGATTAACTCTTTAGCCGT
3333784 TTGAAAATGAAATTCGTGGATTAACTCTTTAGCCGT
1 TTGAAAATGAAATTCGTGGATTAACTCTTTAGCCGT
3333820 TT
1 TT
3333822 CCGTACAAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (36 bp):
TTGAAAATGAAATTCGTGGATTAACTCTTTAGCCGT
Found at i:3333904 original size:24 final size:24
Alignment explanation
Indices: 3333875--3333937 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
3333865 GATTATAACC
3333875 TTTTAAAGTTTCAAATTATACTAA
1 TTTTAAAGTTTCAAATTATACTAA
3333899 TTTTAAAGTTTCAAATTATACTAA
1 TTTTAAAGTTTCAAATTATACTAA
3333923 TTTTAAAGTTTCAAA
1 TTTTAAAGTTTCAAA
3333938 CATCAAAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (24 bp):
TTTTAAAGTTTCAAATTATACTAA
Found at i:3334799 original size:20 final size:20
Alignment explanation
Indices: 3334774--3334818 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
3334764 TGGAGGATGT
3334774 TCGTCTTGGTCGGTGGTTGA
1 TCGTCTTGGTCGGTGGTTGA
*
3334794 TCGTCTTGGTCGGTGGTTGG
1 TCGTCTTGGTCGGTGGTTGA
3334814 TCGTC
1 TCGTC
3334819 AGTTTAGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.02, C:0.18, G:0.40, T:0.40
Consensus pattern (20 bp):
TCGTCTTGGTCGGTGGTTGA
Found at i:3335078 original size:5 final size:5
Alignment explanation
Indices: 3335068--3335092 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3335058 CGGTCAAAGT
3335068 AGAAG AGAAG AGAAG AGAAG AGAAG
1 AGAAG AGAAG AGAAG AGAAG AGAAG
3335093 GGAGTTGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:3335858 original size:32 final size:32
Alignment explanation
Indices: 3335822--3335991 Score: 137
Period size: 35 Copynumber: 4.9 Consensus size: 32
3335812 TTTTCTAACT
*
3335822 TACTAACATTCTAACTTTTAATTTATTGTTCA
1 TACTAACATTCTAACTTTTATTTTATTGTTCA
*
3335854 TACTAACTTTCTAACTTTTTTATTTTTATTGTTCTTACTGA
1 TACTAACATTCTAAC--TTTTA-TTTTATTG---TT-C--A
3335895 TTACTAACATTCTAACTTTTATTTTATTGTTCA
1 -TACTAACATTCTAACTTTTATTTTATTGTTCA
* *
3335928 TACTAACATACTGACATTTTTATTTTTATTGTTC-
1 TACTAACATTCT-A-ACTTTTA-TTTTATTGTTCA
*
3335962 TCACTAAC-TCACTAACATTTTATTTTATTG
1 T-ACTAACAT-TCTAAC-TTTTATTTTATTG
3335992 CACAAACTAA
Statistics
Matches: 116, Mismatches: 6, Indels: 31
0.76 0.04 0.20
Matches are distributed among these distances:
32 25 0.22
33 11 0.09
34 19 0.16
35 28 0.24
36 2 0.02
38 2 0.02
39 9 0.08
40 5 0.04
41 1 0.01
42 14 0.12
ACGTcount: A:0.27, C:0.16, G:0.04, T:0.53
Consensus pattern (32 bp):
TACTAACATTCTAACTTTTATTTTATTGTTCA
Found at i:3335908 original size:42 final size:39
Alignment explanation
Indices: 3335854--3335931 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 39
3335844 TTATTGTTCA
* *
3335854 TACTAACTTTCTAACTTTTTTATTTTTATTGTTCTTACTGAT
1 TACTAACATTCTAAC--TTTTA-TTTTATTGTTCATACTGAT
3335896 TACTAACATTCTAACTTTTATTTTATTGTTCATACT
1 TACTAACATTCTAACTTTTATTTTATTGTTCATACT
3335932 AACATACTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 15 0.44
40 5 0.15
42 14 0.41
ACGTcount: A:0.24, C:0.15, G:0.04, T:0.56
Consensus pattern (39 bp):
TACTAACATTCTAACTTTTATTTTATTGTTCATACTGAT
Found at i:3335909 original size:74 final size:75
Alignment explanation
Indices: 3335816--3335980 Score: 251
Period size: 74 Copynumber: 2.2 Consensus size: 75
3335806 GTTAACTTTT
* * *
3335816 CTAACTTACTAACATTCTAACTTTTAATTTATTGTTCATACTAACTTTCTAACTTTTTTATTTTT
1 CTAACTTACTAACATTCTAACTTTTAATTTATTGTTCATACTAACATACTAACATTTTTATTTTT
*
3335881 ATTGTTCTTA
66 ATTGTTCTCA
* * *
3335891 CTGA-TTACTAACATTCTAACTTTTATTTTATTGTTCATACTAACATACTGACATTTTTATTTTT
1 CTAACTTACTAACATTCTAACTTTTAATTTATTGTTCATACTAACATACTAACATTTTTATTTTT
3335955 ATTGTTCTCA
66 ATTGTTCTCA
*
3335965 CTAACTCACTAACATT
1 CTAACTTACTAACATT
3335981 TTATTTTATT
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
74 67 0.84
75 13 0.16
ACGTcount: A:0.28, C:0.18, G:0.04, T:0.51
Consensus pattern (75 bp):
CTAACTTACTAACATTCTAACTTTTAATTTATTGTTCATACTAACATACTAACATTTTTATTTTT
ATTGTTCTCA
Found at i:3336659 original size:23 final size:23
Alignment explanation
Indices: 3336646--3336704 Score: 100
Period size: 23 Copynumber: 2.5 Consensus size: 23
3336636 TATTTTTTGT
3336646 TTTATTTTTATCTTATTATTATA
1 TTTATTTTTATCTTATTATTATA
*
3336669 TTTATTTTTATCTTATTATTCTA
1 TTTATTTTTATCTTATTATTATA
3336692 TTTATTTTATATC
1 TTTATTTT-TATC
3336705 ATTCTATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 30 0.88
24 4 0.12
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTATTTTTATCTTATTATTATA
Found at i:3337804 original size:27 final size:27
Alignment explanation
Indices: 3337770--3337826 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
3337760 AGTGTTGTCT
3337770 TTTGTCATGTTTTCAAAGGATTGTGAG
1 TTTGTCATGTTTTCAAAGGATTGTGAG
3337797 TTTGTCATGTTTTCAAAGGATTGTGAG
1 TTTGTCATGTTTTCAAAGGATTGTGAG
3337824 TTT
1 TTT
3337827 CTCCTCACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.47
Consensus pattern (27 bp):
TTTGTCATGTTTTCAAAGGATTGTGAG
Found at i:3344892 original size:70 final size:66
Alignment explanation
Indices: 3344801--3344960 Score: 175
Period size: 66 Copynumber: 2.4 Consensus size: 66
3344791 ATGAATAAAG
* *
3344801 TTTCATCTCGTTTGAGACAATTTTTCTTGAAACA-AATTGATCTCACTT-A-ATTG-TTTTCTCT
1 TTTCGTCTCGCTTGAGACAATTTTTCTTGAAACATAA---A--TC-CTTAAGATTGTTTTTCT-T
*
3344862 GAAAATAAA
59 G-AAACAAA
* *
3344871 TTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAATCCTTAAGATTGTTTTTCTTGAAACAA
1 TTTCGTCTCGCTTGAGACAATTTTTCTTGAAACATAAATCCTTAAGATTGTTTTTCTTGAAACAA
3344936 A
66 A
3344937 TTTCGTCTCGCTTGAGACAATTTT
1 TTTCGTCTCGCTTGAGACAATTTT
3344961 CTCCAAATTT
Statistics
Matches: 79, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
65 3 0.04
66 31 0.39
67 6 0.08
68 7 0.09
70 30 0.38
71 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (66 bp):
TTTCGTCTCGCTTGAGACAATTTTTCTTGAAACATAAATCCTTAAGATTGTTTTTCTTGAAACAA
A
Found at i:3345535 original size:25 final size:25
Alignment explanation
Indices: 3345507--3345562 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
3345497 CGATCAGATC
3345507 TCCTCAACGCGCATGAGCATCATCA
1 TCCTCAACGCGCATGAGCATCATCA
3345532 TCCTCAACGCGCATGAGCATCATCA
1 TCCTCAACGCGCATGAGCATCATCA
3345557 TCCTCA
1 TCCTCA
3345563 GGCAATCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.27, C:0.38, G:0.14, T:0.21
Consensus pattern (25 bp):
TCCTCAACGCGCATGAGCATCATCA
Found at i:3345701 original size:164 final size:164
Alignment explanation
Indices: 3345394--3345701 Score: 386
Period size: 164 Copynumber: 1.9 Consensus size: 164
3345384 CATGTTATCA
* * * * * * *
3345394 TCAGGTAATCAGACTTTCTCATCACGTAAGAATCGTGTTGTCTCCAAATTATCCCCCTAAAGACG
1 TCAGGCAATCAAACTTCCTCATCACATAAGAACCGTGTTGTCTCCAAATTAT-CCCATAAAGAAG
* * * *
3345459 GCTAGACGTCCTCATCACATTGGAACAATGTCATCCACCGATCAGATCTCCTCAACGCGCATGAG
65 GCTAGACGTCCTCA-CACATAGGAACAATGCCATCCACCGACCAGATCTCCTCAACGCGCAGGAG
*
3345524 CATCATCATCCTCAACGCGCATGAGCATCATCATCC
129 CAACATCATCCTCAACGCGCATGAGCATCATCATCC
*
3345560 TCAGGCAATCAAACTTCCTCATCACATAGGAACCGTGTTGTCTCCAAATTAT-CCATAAAGAAGG
1 TCAGGCAATCAAACTTCCTCATCACATAAGAACCGTGTTGTCTCCAAATTATCCCATAAAGAAGG
* * * * *
3345624 CTAGATGTCCTCA-ACATGAAGGAACAATGCCGTCCATCGGCCAGATCTCCTCAACGCGTAGGAG
66 CTAGACGTCCTCACACAT--AGGAACAATGCCATCCACCGACCAGATCTCCTCAACGCGCAGGAG
* *
3345688 CAACGTTATCCTCA
129 CAACATCATCCTCA
3345702 TGCAATCAGG
Statistics
Matches: 120, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
162 4 0.03
164 70 0.58
166 46 0.38
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (164 bp):
TCAGGCAATCAAACTTCCTCATCACATAAGAACCGTGTTGTCTCCAAATTATCCCATAAAGAAGG
CTAGACGTCCTCACACATAGGAACAATGCCATCCACCGACCAGATCTCCTCAACGCGCAGGAGCA
ACATCATCCTCAACGCGCATGAGCATCATCATCC
Found at i:3345786 original size:139 final size:139
Alignment explanation
Indices: 3345532--3345858 Score: 366
Period size: 139 Copynumber: 2.4 Consensus size: 139
3345522 AGCATCATCA
* * * * * *
3345532 TCCTCAACGCGCATGAGCATCATCATCCTCAGGCAATCAAACTTCCTCATCACATAGGAACCGTG
1 TCCTCAACGCGTAGGAGCAACGTCATCCTCATGCAATCAGACTTCCTCATCACATAGGAACCGTG
* * * * *
3345597 TTGTCTCCAAATTATCCATAAAGAAGGCTAGATGTCCTCAACATGAAGGAACAATGCCGTCCATC
66 TTGTCTACAAAGTATCCATAAAGAAGGCTAGACGTCCTCAACACGAAGGAACAATGCCGTCCACC
* * *
3345662 GGCCAGATC
131 GACAAAATC
* * * * *
3345671 TCCTCAACGCGTAGGAGCAACGTTATCCTCATGCAATCAGGCTTCCTCGTCACGTATGAACCGTG
1 TCCTCAACGCGTAGGAGCAACGTCATCCTCATGCAATCAGACTTCCTCATCACATAGGAACCGTG
* * * * * * **
3345736 TTGTCTATAAAGTATCCCTAAAGATGGCTAGACGTCTTCATCACGTAGGAACAATTTCGTCCACC
66 TTGTCTACAAAGTATCCATAAAGAAGGCTAGACGTCCTCAACACGAAGGAACAATGCCGTCCACC
3345801 GACAAAATC
131 GACAAAATC
* * * * *
3345810 TCCTTAATGCGTAGGAGCAATGTCATCCTTATACAATCAGACTTCCTCA
1 TCCTCAACGCGTAGGAGCAACGTCATCCTCATGCAATCAGACTTCCTCA
3345859 ACGAGAAGGA
Statistics
Matches: 153, Mismatches: 35, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
139 153 1.00
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.25
Consensus pattern (139 bp):
TCCTCAACGCGTAGGAGCAACGTCATCCTCATGCAATCAGACTTCCTCATCACATAGGAACCGTG
TTGTCTACAAAGTATCCATAAAGAAGGCTAGACGTCCTCAACACGAAGGAACAATGCCGTCCACC
GACAAAATC
Found at i:3347639 original size:31 final size:33
Alignment explanation
Indices: 3347600--3347683 Score: 88
Period size: 35 Copynumber: 2.6 Consensus size: 33
3347590 CTATAACAAT
3347600 CTAA-CTTTTATTTTA-TG-TCATT-CTAACATA
1 CTAACCTTTTATTTTATTGTTC-TTACTAACATA
*
3347630 CTAACCTTTTTATTTTTATTGTTCTTACTAACTTA
1 CTAACC-TTTTA-TTTTATTGTTCTTACTAACATA
*
3347665 CTAACATTTTA-TTTATTGT
1 CTAACCTTTTATTTTATTGT
3347684 ACAAACTAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
30 4 0.09
31 1 0.02
32 13 0.28
33 5 0.11
34 9 0.20
35 14 0.30
ACGTcount: A:0.26, C:0.15, G:0.04, T:0.55
Consensus pattern (33 bp):
CTAACCTTTTATTTTATTGTTCTTACTAACATA
Found at i:3347658 original size:75 final size:76
Alignment explanation
Indices: 3347508--3347667 Score: 211
Period size: 75 Copynumber: 2.1 Consensus size: 76
3347498 GCTAACTTTT
* * *
3347508 CTAACTTA-T-TAACATTCTAAATTTTATTTTATTGTTCATAATAACATTCTATCTTTTTATTTT
1 CTAACTTACTATAACAATCTAAATTTTATTTTATTGTTCATAATAACATACTACCTTTTTATTTT
*
3347571 TTTTGTTATTA
66 TATTGTTATTA
* **
3347582 CTAACTTACTATAACAATCTAACTTTTATTTTA-TG-TCATTCTAACATACTAACCTTTTTATTT
1 CTAACTTACTATAACAATCTAAATTTTATTTTATTGTTCATAATAACATACT-ACCTTTTTATTT
*
3347645 TTATTGTTCTTA
65 TTATTGTTATTA
3347657 CTAACTTACTA
1 CTAACTTACTA
3347668 ACATTTTATT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
74 20 0.27
75 35 0.47
76 20 0.27
ACGTcount: A:0.29, C:0.15, G:0.03, T:0.53
Consensus pattern (76 bp):
CTAACTTACTATAACAATCTAAATTTTATTTTATTGTTCATAATAACATACTACCTTTTTATTTT
TATTGTTATTA
Found at i:3347813 original size:4 final size:4
Alignment explanation
Indices: 3347794--3347847 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
3347784 TAACTTTTAA
*
3347794 ATTT ATGT ATTTT ATTT A-TT A-TT ATTT ATTT ATTT A-TT -TTT ATTTT
1 ATTT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT
3347840 ATTT ATTT
1 ATTT ATTT
3347848 TTTCGCACTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
3 10 0.23
4 26 0.60
5 7 0.16
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:3347827 original size:18 final size:19
Alignment explanation
Indices: 3347804--3347847 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
3347794 ATTTATGTAT
3347804 TTTATTTATTATTA-TTTA
1 TTTATTTATTATTATTTTA
*
3347822 TTTATTTATTTTTATTTTA
1 TTTATTTATTATTATTTTA
3347841 TTTATTT
1 TTTATTT
3347848 TTTCGCACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTATTTATTATTATTTTA
Found at i:3347827 original size:23 final size:23
Alignment explanation
Indices: 3347794--3347847 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
3347784 TAACTTTTAA
*
3347794 ATTTATGTATTT-TATTTATTATT
1 ATTTATTTATTTATATTTATT-TT
*
3347817 ATTTATTTATTTATTTTTATTTT
1 ATTTATTTATTTATATTTATTTT
3347840 ATTTATTT
1 ATTTATTT
3347848 TTTCGCACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 21 0.75
24 7 0.25
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (23 bp):
ATTTATTTATTTATATTTATTTT
Found at i:3347847 original size:15 final size:14
Alignment explanation
Indices: 3347794--3347849 Score: 71
Period size: 15 Copynumber: 4.0 Consensus size: 14
3347784 TAACTTTTAA
*
3347794 ATTTATGTA-TTTT
1 ATTTATTTATTTTT
3347807 ATTTA-TTATTATTT
1 ATTTATTTATT-TTT
3347821 ATTTATTTATTTTT
1 ATTTATTTATTTTT
3347835 ATTTTATTTATTTTT
1 A-TTTATTTATTTTT
3347850 TCGCACTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
12 2 0.05
13 6 0.16
14 12 0.32
15 18 0.47
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (14 bp):
ATTTATTTATTTTT
Found at i:3351740 original size:23 final size:22
Alignment explanation
Indices: 3351713--3351756 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
3351703 TATCAAAATC
3351713 ATGACCA-GTAGATTATTGTAAAA
1 ATGACCATGTAG-TTATT-TAAAA
*
3351736 ATGACTATGTAGTTATTTAAA
1 ATGACCATGTAGTTATTTAAA
3351757 TCACATGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (22 bp):
ATGACCATGTAGTTATTTAAAA
Found at i:3354583 original size:43 final size:44
Alignment explanation
Indices: 3354533--3355063 Score: 428
Period size: 44 Copynumber: 12.2 Consensus size: 44
3354523 GGGCCTGCAA
* * * *
3354533 AAACGGTAAGGTTTTACCCTTGCACATAGAAAAAGAGCAT-GGG
1 AAACTGTAAGGTCTTACCCTTGCACATAGAAAAGGAGCCTGGGG
* *** ***
3354576 AAACGGTAAGGTCTTATTATTGCACATAGAAAAGGAGCCTAGTAA
1 AAACTGTAAGGTCTTACCCTTGCACATAGAAAAGGAGCCT-GGGG
* * * *
3354621 AAACTATAAGG-CTTACCCTTACACATAGCAGAGGAGCCT-GGG
1 AAACTGTAAGGTCTTACCCTTGCACATAGAAAAGGAGCCTGGGG
* * * *
3354663 AAACTGTAAGG-CTTACCCTTGTACACA-ACAAATGAACCTGGGG
1 AAACTGTAAGGTCTTACCCTTGCACATAGA-AAAGGAGCCTGGGG
* * *
3354706 AAACTGTAAGGTCTTACCCTTGCACACAGCAAAGGAACCTGGGG
1 AAACTGTAAGGTCTTACCCTTGCACATAGAAAAGGAGCCTGGGG
* * * * *
3354750 AAACTGTAAGGTCTTACCCTTGTACACAGCAAATGAACCTGGGG
1 AAACTGTAAGGTCTTACCCTTGCACATAGAAAAGGAGCCTGGGG
* * * * *
3354794 AAACTATAAGG-CTTACCCTTACACACA-ACAAAAGAACCTGGGG
1 AAACTGTAAGGTCTTACCCTTGCACATAGA-AAAGGAGCCTGGGG
* *
3354837 AAAACTGTAAGG-CTTACCCTTGCACACA-ACAAAGGAACCTGGGG
1 -AAACTGTAAGGTCTTACCCTTGCACATAGA-AAAGGAGCCTGGGG
* * *
3354881 AAAACTGTAAGG-CTTACACTTGCACACA-ACAAAGGAACCTGGGG
1 -AAACTGTAAGGTCTTACCCTTGCACATAGA-AAAGGAGCCTGGGG
* *
3354925 AAAACTGTAAGG-CTTACCTTTGCACATAGCAAAGGAGCCTGGGG
1 -AAACTGTAAGGTCTTACCCTTGCACATAGAAAAGGAGCCTGGGG
** *
3354969 AAACTGTAAGG-CTTACCCTTGCACGCA-ACAAAGGAACCTGGGG
1 AAACTGTAAGGTCTTACCCTTGCACATAGA-AAAGGAGCCTGGGG
* * * * * *
3355012 AATCTATAA-GACTTACCCTTGCTCACA-ACAAAGGACCCTGGGG
1 AAACTGTAAGGTCTTACCCTTGCACATAGA-AAAGGAGCCTGGGG
3355055 AAACTGTAA
1 AAACTGTAA
3355064 TTAATCCATT
Statistics
Matches: 418, Mismatches: 59, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
42 31 0.07
43 155 0.37
44 223 0.53
45 9 0.02
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (44 bp):
AAACTGTAAGGTCTTACCCTTGCACATAGAAAAGGAGCCTGGGG
Found at i:3354656 original size:44 final size:43
Alignment explanation
Indices: 3354621--3355063 Score: 582
Period size: 44 Copynumber: 10.2 Consensus size: 43
3354611 AGCCTAGTAA
* * * * *
3354621 AAACTATAAGGCTTACCCTTACACATAGCAGAGGAGCCT-GGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
* * *
3354663 AAACTGTAAGGCTTACCCTTGTACACAACAAATGAACCTGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
3354706 AAACTGTAAGGTCTTACCCTTGCACACAGCAAAGGAACCTGGGG
1 AAACTGTAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGGGG
* *
3354750 AAACTGTAAGGTCTTACCCTTGTACACAGCAAATGAACCTGGGG
1 AAACTGTAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGGGG
* * * *
3354794 AAACTATAAGGCTTACCCTTACACACAACAAAAGAACCTGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
*
3354837 AAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGG
1 -AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
* *
3354881 AAAACTGTAAGGCTTACACTTGCACACAACAAAGGAACCTGGGG
1 -AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
* * *
3354925 AAAACTGTAAGGCTTACCTTTGCACATAGCAAAGGAGCCTGGGG
1 -AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
* *
3354969 AAACTGTAAGGCTTACCCTTGCACGCAACAAAGGAACCTGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
* * * * * *
3355012 AATCTATAAGACTTACCCTTGCTCACAACAAAGGACCCTGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
3355055 AAACTGTAA
1 AAACTGTAA
3355064 TTAATCCATT
Statistics
Matches: 358, Mismatches: 40, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
42 31 0.09
43 124 0.35
44 203 0.57
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (43 bp):
AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
Found at i:3354839 original size:131 final size:129
Alignment explanation
Indices: 3354621--3355063 Score: 600
Period size: 131 Copynumber: 3.4 Consensus size: 129
3354611 AGCCTAGTAA
* * * * * *
3354621 AAACTATAAGGCTTACCCTTACACATAGCAGAGGAGCCT-GGGAAACTGTAAGGCTTACCCTTGT
1 AAACTATAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGC
* *
3354685 ACACAACAAATGAACCTGGGGAAACTGTAAGGTCTTACCCTTGCACACAGCAAAGGAACCTGGGG
66 ACACAACAAAAGAACCTGGGGAAACTGTAAGG-CTTACCCTTGCACACAACAAAGGAACCTGGGG
* * * * * *
3354750 AAACTGTAAGGTCTTACCCTTGTACACAGCAAATGAACCTGGGGAAACTATAAGGCTTACCCTTA
1 AAACTATAAGG-CTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTG
3354815 CACACAACAAAAGAACCTGGGGAAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
65 CACACAACAAAAGAACCTGGGG-AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
3354880 G
129 G
* * *
3354881 AAAACTGTAAGGCTTACACTTGCACACAACAAAGGAACCTGGGGAAAACTGTAAGGCTTACCTTT
1 -AAACTATAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGG-AAACTGTAAGGCTTACCCTT
* * * * *
3354946 GCACATAGCAAAGGAGCCTGGGGAAACTGTAAGGCTTACCCTTGCACGCAACAAAGGAACCTGGG
64 GCACACAACAAAAGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
3355011 G
129 G
* * * *
3355012 AATCTATAAGACTTACCCTTGCTCACAACAAAGGACCCTGGGGAAACTGTAA
1 AAACTATAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAA
3355064 TTAATCCATT
Statistics
Matches: 279, Mismatches: 30, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
129 19 0.07
130 59 0.21
131 143 0.51
132 58 0.21
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (129 bp):
AAACTATAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGC
ACACAACAAAAGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGG
Found at i:3354905 original size:175 final size:174
Alignment explanation
Indices: 3354621--3355063 Score: 640
Period size: 175 Copynumber: 2.5 Consensus size: 174
3354611 AGCCTAGTAA
* * * * *
3354621 AAACTATAAGGCTTACCCTTACACATAGCAGAGGAGCCT-GGGAAACTGTAAGGCTTACCCTTGT
1 AAACTATAAGGCTTACCCTTACACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGC
* * *
3354685 ACACAACAAATGAACCTGGGGAAACTGTAAGGTCTTACCCTTGCACACAGCAAAGGAACCTGGGG
66 ACACAACAAAGGAACCTGGGGAAACTGTAAGGTCTTACACTTGCACACAACAAAGGAACCTGGGG
* *
3354750 -AAACTGTAAGGTCTTACCCTTGTACACAGCAAATGAACCTGGGG
131 AAAACTGTAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGGGG
*
3354794 AAACTATAAGGCTTACCCTTACACACAACAAAAGAACCTGGGGAAAACTGTAAGGCTTACCCTTG
1 AAACTATAAGGCTTACCCTTACACACAACAAAGGAACCTGGGG-AAACTGTAAGGCTTACCCTTG
3354859 CACACAACAAAGGAACCTGGGGAAAACTGTAAGG-CTTACACTTGCACACAACAAAGGAACCTGG
65 CACACAACAAAGGAACCTGGGG-AAACTGTAAGGTCTTACACTTGCACACAACAAAGGAACCTGG
* * *
3354923 GGAAAACTGTAAGGCTTACCTTTGCACATAGCAAAGGAGCCTGGGG
129 GGAAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
* * * * * *
3354969 AAACTGTAAGGCTTACCCTTGCACGCAACAAAGGAACCTGGGGAATCTATAAGACTTACCCTTGC
1 AAACTATAAGGCTTACCCTTACACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGC
* *
3355034 TCACAACAAAGGACCCTGGGGAAACTGTAA
66 ACACAACAAAGGAACCTGGGGAAACTGTAA
3355064 TTAATCCATT
Statistics
Matches: 243, Mismatches: 23, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
173 43 0.18
174 41 0.17
175 137 0.56
176 22 0.09
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (174 bp):
AAACTATAAGGCTTACCCTTACACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGC
ACACAACAAAGGAACCTGGGGAAACTGTAAGGTCTTACACTTGCACACAACAAAGGAACCTGGGG
AAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
Found at i:3356372 original size:28 final size:27
Alignment explanation
Indices: 3356340--3356401 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
3356330 AATTCTAGGG
*
3356340 TTTAGGGATACTTTAGGTCATTTTACAC
1 TTTAGGGACA-TTTAGGTCATTTTACAC
* *
3356368 TTTAGGGGCATTTTGGTCATTTTACAC
1 TTTAGGGACATTTAGGTCATTTTACAC
3356395 TTTAGGG
1 TTTAGGG
3356402 GTATTTCTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 23 0.74
28 8 0.26
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.44
Consensus pattern (27 bp):
TTTAGGGACATTTAGGTCATTTTACAC
Found at i:3356388 original size:27 final size:27
Alignment explanation
Indices: 3356355--3356407 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
3356345 GGATACTTTA
3356355 GGTCATTTTACACTTTAGGGGCATTTT
1 GGTCATTTTACACTTTAGGGGCATTTT
*
3356382 GGTCATTTTACACTTTAGGGGTATTT
1 GGTCATTTTACACTTTAGGGGCATTT
3356408 CTATAATTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.13, G:0.23, T:0.45
Consensus pattern (27 bp):
GGTCATTTTACACTTTAGGGGCATTTT
Found at i:3360438 original size:15 final size:15
Alignment explanation
Indices: 3360418--3360447 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3360408 TATCACAATC
3360418 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
3360433 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
3360448 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:3365406 original size:15 final size:15
Alignment explanation
Indices: 3365386--3365415 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3365376 TATCACAATC
3365386 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
3365401 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
3365416 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:3376742 original size:17 final size:17
Alignment explanation
Indices: 3376722--3376770 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
3376712 TTTAGGGAAG
3376722 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* **
3376739 TAGTTCATTCACCAAAC
1 TAGTTCATTAATTAAAC
*
3376756 TAGTTCATTTATTAA
1 TAGTTCATTAATTAA
3376771 CTAACACTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:3378462 original size:17 final size:17
Alignment explanation
Indices: 3378440--3378483 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
3378430 TAGTTTAATA
3378440 GAACTAGTTTGATGAGT
1 GAACTAGTTTGATGAGT
3378457 GAACTAGTTTGATGAGT
1 GAACTAGTTTGATGAGT
3378474 GAACTAGTTT
1 GAACTAGTTT
3378484 AGTTAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (17 bp):
GAACTAGTTTGATGAGT
Found at i:3378493 original size:17 final size:18
Alignment explanation
Indices: 3378429--3378496 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 18
3378419 AAACAAAGAG
*
3378429 TTAGTTTAATAGAACTAGT
1 TTAGATTAAT-GAACTAGT
* *
3378448 TT-GATGAGTGAACTAGT
1 TTAGATTAATGAACTAGT
* *
3378465 TT-GATGAGTGAACTAGT
1 TTAGATTAATGAACTAGT
3378482 TTAG-TTAATGAACTA
1 TTAGATTAATGAACTA
3378497 ACTTTATTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
17 36 0.84
18 5 0.12
19 2 0.05
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (18 bp):
TTAGATTAATGAACTAGT
Done.