Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_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: 7662336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 38
Found at i:2036911 original size:15 final size:15
Alignment explanation
Indices: 2036891--2036919 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2036881 GTTATATGAG
2036891 CTATGTGATAAGAAA
1 CTATGTGATAAGAAA
2036906 CTATGTGATAAGAA
1 CTATGTGATAAGAA
2036920 GCTACGAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.28
Consensus pattern (15 bp):
CTATGTGATAAGAAA
Found at i:2037139 original size:21 final size:21
Alignment explanation
Indices: 2037031--2037139 Score: 65
Period size: 21 Copynumber: 5.1 Consensus size: 21
2037021 AGAGTTCTAC
*
2037031 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTTCGGAACATATAT
** ** *
2037052 GTAATTATTTGGAACATATAT
1 GTGGTCCTTCGGAACATATAT
* * * **
2037073 GCGGTACTTCGGTACACCTAT
1 GTGGTCCTTCGGAACATATAT
* * * *
2037094 TTGGTCCATTTGGAATATGTAT
1 GTGGTCC-TTCGGAACATATAT
*
2037116 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTTCGGAACATATAT
2037137 GTG
1 GTG
2037140 ATATGTGGTC
Statistics
Matches: 59, Mismatches: 28, Indels: 2
0.66 0.31 0.02
Matches are distributed among these distances:
21 44 0.75
22 15 0.25
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.37
Consensus pattern (21 bp):
GTGGTCCTTCGGAACATATAT
Found at i:2037642 original size:65 final size:62
Alignment explanation
Indices: 2037489--2037697 Score: 188
Period size: 65 Copynumber: 3.2 Consensus size: 62
2037479 TTTCAAAGTA
* * * **
2037489 GTGTACCGATGCACCATCTAATGCATCGATGCAC-CCTTGAATAAATTGTATTTCGAATGCATTT
1 GTGTACCGATGCA-CATAT-ATGCATCGATGCACTCC-TGAAT-ATTTGAACATCGAATGCATTT
2037553 T
62 T
2037554 GTGTACCGATGCACA-AGGTATGCATCGATGCACTCCTGAATATTTTTGAACATCGAATGCATTT
1 GTGTACCGATGCACATA--TATGCATCGATGCACTCCTGAATA--TTTGAACATCGAATGCATTT
2037618 T
62 T
* * * * *
2037619 GTGTACCGATGCACATATCATGCACCGTTGCACTCCAGACTCATTTGAAACATCGAATGTATTTT
1 GTGTACCGATGCACATAT-ATGCATCGATGCACTCCTGAAT-ATTTG-AACATCGAATGCATTTT
* * *
2037684 ATGCATCGATGCAC
1 GTGTACCGATGCAC
2037698 CCCTAGTGTA
Statistics
Matches: 122, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
63 1 0.01
64 26 0.21
65 93 0.76
66 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (62 bp):
GTGTACCGATGCACATATATGCATCGATGCACTCCTGAATATTTGAACATCGAATGCATTTT
Found at i:2045495 original size:8 final size:8
Alignment explanation
Indices: 2045478--2045552 Score: 64
Period size: 8 Copynumber: 9.4 Consensus size: 8
2045468 TGTTTTTGGA
2045478 TTGGATGT
1 TTGGATGT
*
2045486 TTGAATGT
1 TTGGATGT
*
2045494 TTGGATAT
1 TTGGATGT
*
2045502 TATGGAT-A
1 T-TGGATGT
2045510 TTGGATGT
1 TTGGATGT
*
2045518 TTGAATGT
1 TTGGATGT
*
2045526 TTGGATAT
1 TTGGATGT
*
2045534 TATGGAT-A
1 T-TGGATGT
2045542 TTGGATGT
1 TTGGATGT
2045550 TTG
1 TTG
2045553 AAATTAATAT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
7 10 0.19
8 33 0.62
9 10 0.19
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (8 bp):
TTGGATGT
Found at i:2045514 original size:32 final size:32
Alignment explanation
Indices: 2045477--2045554 Score: 156
Period size: 32 Copynumber: 2.4 Consensus size: 32
2045467 ATGTTTTTGG
2045477 ATTGGATGTTTGAATGTTTGGATATTATGGAT
1 ATTGGATGTTTGAATGTTTGGATATTATGGAT
2045509 ATTGGATGTTTGAATGTTTGGATATTATGGAT
1 ATTGGATGTTTGAATGTTTGGATATTATGGAT
2045541 ATTGGATGTTTGAA
1 ATTGGATGTTTGAA
2045555 ATTAATATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (32 bp):
ATTGGATGTTTGAATGTTTGGATATTATGGAT
Found at i:2046290 original size:64 final size:64
Alignment explanation
Indices: 2046204--2046347 Score: 159
Period size: 63 Copynumber: 2.3 Consensus size: 64
2046194 GCACCATCTA
* * * * *
2046204 ATGCATCGATGTAC-CCTTGAATAAATTGTATTTAAAATGCATTTTGTGTATCGATGCACA-AGG
1 ATGCATCGATGCACTCCTTGAAT-AATTGAATATAAAATGCATTTTGTGTACCGATGCACAGA-C
2046267 C
64 C
* * ** *
2046268 ATGCATCAATGCACTCC-TGAATATTTGAATATCGAATGCATTTTGTGTACCGATTCACAGACC
1 ATGCATCGATGCACTCCTTGAATAATTGAATATAAAATGCATTTTGTGTACCGATGCACAGACC
2046331 ATGCATCGATGCACTCC
1 ATGCATCGATGCACTCC
2046348 AGGCTCATTT
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
63 47 0.70
64 18 0.27
65 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTCCTTGAATAATTGAATATAAAATGCATTTTGTGTACCGATGCACAGACC
Found at i:2046314 original size:63 final size:65
Alignment explanation
Indices: 2046239--2046390 Score: 184
Period size: 63 Copynumber: 2.4 Consensus size: 65
2046229 TTGTATTTAA
* * *
2046239 AATGCATTTTGTGTATCGATGCACA-AGGCATGCATCAATGCACTCCTGAAT-ATTTG-AATATC
1 AATGCATTTTGTGTATCGATGCACAGA-CCATGCATCAATGCACTCCAGAATCATTTGAAACATC
2046301 G
65 G
* * * **
2046302 AATGCATTTTGTGTACCGATTCACAGACCATGCATCGATGCACTCCAGGCTCATTTGAAACATCG
1 AATGCATTTTGTGTATCGATGCACAGACCATGCATCAATGCACTCCAGAATCATTTGAAACATCG
* *
2046367 AATGCATTTTATGCATCGATGCAC
1 AATGCATTTTGTGTATCGATGCAC
2046391 CCCTAGTGTA
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
63 42 0.57
64 6 0.08
65 26 0.35
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (65 bp):
AATGCATTTTGTGTATCGATGCACAGACCATGCATCAATGCACTCCAGAATCATTTGAAACATCG
Found at i:2046476 original size:54 final size:54
Alignment explanation
Indices: 2046394--2046517 Score: 248
Period size: 54 Copynumber: 2.3 Consensus size: 54
2046384 GATGCACCCC
2046394 TAGTGTACCGATGCACTAAGTCTTCCAACGATCGAAATATTTAAATTTTACACA
1 TAGTGTACCGATGCACTAAGTCTTCCAACGATCGAAATATTTAAATTTTACACA
2046448 TAGTGTACCGATGCACTAAGTCTTCCAACGATCGAAATATTTAAATTTTACACA
1 TAGTGTACCGATGCACTAAGTCTTCCAACGATCGAAATATTTAAATTTTACACA
2046502 TAGTGTACCGATGCAC
1 TAGTGTACCGATGCAC
2046518 CTTGCCTATG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (54 bp):
TAGTGTACCGATGCACTAAGTCTTCCAACGATCGAAATATTTAAATTTTACACA
Found at i:2047333 original size:9 final size:9
Alignment explanation
Indices: 2047321--2047365 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
2047311 AAGAGATATG
2047321 AATGATAAT
1 AATGATAAT
*
2047330 AATGCTAAT
1 AATGATAAT
*
2047339 AATGATAAG
1 AATGATAAT
*
2047348 AATAATAAT
1 AATGATAAT
*
2047357 AAGGATAAT
1 AATGATAAT
2047366 GAGATGATAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.56, C:0.02, G:0.13, T:0.29
Consensus pattern (9 bp):
AATGATAAT
Found at i:2083009 original size:26 final size:24
Alignment explanation
Indices: 2082963--2083015 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 24
2082953 AATAATCCCG
2082963 AATATTTAATTCCAATTAATTAAATA
1 AATATTTAATT-CAATTAATT-AATA
2082989 AATATTTAATT-AATTTAAATTAATA
1 AATATTTAATTCAA-TT-AATTAATA
2083014 AA
1 AA
2083016 AATCCCTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 2 0.08
25 8 0.32
26 15 0.60
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
AATATTTAATTCAATTAATTAATA
Found at i:2087037 original size:2 final size:2
Alignment explanation
Indices: 2086964--2087021 Score: 52
Period size: 2 Copynumber: 30.0 Consensus size: 2
2086954 AAATTATAGG
* *
2086964 AT AT AT AT AT AT A- AT -T AT AT GAT AT -T AT AA AT CCT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT -AT AT AT AT
2087004 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
2087022 TTACAATTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
1 4 0.09
2 39 0.85
3 3 0.07
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2088518 original size:9 final size:9
Alignment explanation
Indices: 2088500--2088650 Score: 57
Period size: 9 Copynumber: 16.8 Consensus size: 9
2088490 GATTATTACC
*
2088500 ATTTTCTTT
1 ATTTTATTT
2088509 ATTTTATTT
1 ATTTTATTT
2088518 A-TTTATTT
1 ATTTTATTT
2088526 A-TTTATTT
1 ATTTTATTT
*
2088534 -TTTCATTT
1 ATTTTATTT
2088542 -TTGTT-TTT
1 ATT-TTATTT
2088550 -TTTTACTTTT
1 ATTTTA--TTT
*
2088560 ATTCCT-TTT
1 ATT-TTATTT
*
2088569 ATTTTCTTT
1 ATTTTATTT
*
2088578 ATCTT-TTT
1 ATTTTATTT
*
2088586 ATCTTCATGTT
1 AT-TTTAT-TT
* *
2088597 ACTTTCTTT
1 ATTTTATTT
**
2088606 ATTTCCTTT
1 ATTTTATTT
*
2088615 ATTTTCTTTT
1 ATTTT-ATTT
*
2088625 ATTTTAGTT
1 ATTTTATTT
2088634 ATTTTCATTT
1 ATTTT-ATTT
*
2088644 TTTTTAT
1 ATTTTAT
2088651 CTAACGTGTT
Statistics
Matches: 110, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
7 2 0.02
8 34 0.31
9 46 0.42
10 22 0.20
11 5 0.05
12 1 0.01
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.74
Consensus pattern (9 bp):
ATTTTATTT
Found at i:2088635 original size:19 final size:19
Alignment explanation
Indices: 2088613--2088649 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2088603 TTTATTTCCT
2088613 TTATTTTC-TTTTATTTTAG
1 TTATTTTCATTTT-TTTTAG
2088632 TTATTTTCATTTTTTTTA
1 TTATTTTCATTTTTTTTA
2088650 TCTAACGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (19 bp):
TTATTTTCATTTTTTTTAG
Found at i:2092473 original size:95 final size:94
Alignment explanation
Indices: 2092351--2092546 Score: 243
Period size: 95 Copynumber: 2.1 Consensus size: 94
2092341 TATAATATTA
*
2092351 TATATATACAATAAAGCTTAAGTTGTCCCTCT-AGAGCAATTGGCCAATCGCC-CTAACTTTATG
1 TATATATACAATAAAGCTTAAGTTGTCCCTCTAAG-GCAATTGGCCAAACGCCTC-AACTTTATG
** **
2092414 GATATTATTCAGCTAGCCTAATAAAGGTGAT
64 GATAAGATTCAGCTAAACTAATAAAGGTGAT
* ** *
2092445 TATACTATACAATAAAGCTTGAGTTGTCCCTCTAAGGCAATTGGTTAAACGCCTCAGCTTTATGG
1 TATA-TATACAATAAAGCTTAAGTTGTCCCTCTAAGGCAATTGGCCAAACGCCTCAACTTTATGG
* *
2092510 ATAAGATTCAGCTAAACTGATAAAGGTGTT
65 ATAAGATTCAGCTAAACTAATAAAGGTGAT
*
2092540 TACATAT
1 TATATAT
2092547 TTAGTTGTCC
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
94 7 0.08
95 77 0.89
96 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (94 bp):
TATATATACAATAAAGCTTAAGTTGTCCCTCTAAGGCAATTGGCCAAACGCCTCAACTTTATGGA
TAAGATTCAGCTAAACTAATAAAGGTGAT
Found at i:2093994 original size:36 final size:36
Alignment explanation
Indices: 2093936--2094088 Score: 186
Period size: 36 Copynumber: 4.2 Consensus size: 36
2093926 ATATGTTTTC
2093936 CTTGAAACAAATTTTGTCTCTCTTGAGACAGATTA-T
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAG-TTACT
* * *
2093972 -TTGGAACTAAGTTTTGTCTCTCTTAAGACAGTTACT
1 CTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTACT
* * *
2094008 CTTGAAACAAATTTTGTCTCTCTTGAGACTGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTACT
* *
2094044 CTT-AAACAAAGTTTTGTCTCTCTTAAGACAGTTTCT
1 CTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTACT
2094080 CTTGAAACA
1 CTTGAAACA
2094089 CCAATCATTG
Statistics
Matches: 100, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
35 16 0.16
36 73 0.73
37 11 0.11
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTACT
Found at i:2094056 original size:72 final size:72
Alignment explanation
Indices: 2093936--2094088 Score: 227
Period size: 72 Copynumber: 2.1 Consensus size: 72
2093926 ATATGTTTTC
* * *
2093936 CTTGAAACAAATTTTGTCTCTCTTGAGACAGATTATTTGGAACTAAGTTTTGTCTCTCTTAAGAC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGATTACTTGAAACAAAGTTTTGTCTCTCTTAAGAC
2094001 AGTTACT
66 AGTTACT
* * *
2094008 CTTGAAACAAATTTTGTCTCTCTTGAGACTGTTTCCCTT-AAACAAAGTTTTGTCTCTCTTAAGA
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGATT-ACTTGAAACAAAGTTTTGTCTCTCTTAAGA
*
2094072 CAGTTTCT
65 CAGTTACT
2094080 CTTGAAACA
1 CTTGAAACA
2094089 CCAATCATTG
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
72 71 0.97
73 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (72 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACAGATTACTTGAAACAAAGTTTTGTCTCTCTTAAGAC
AGTTACT
Found at i:2094192 original size:67 final size:67
Alignment explanation
Indices: 2094058--2094192 Score: 148
Period size: 67 Copynumber: 2.0 Consensus size: 67
2094048 AACAAAGTTT
* * * * * * *
2094058 TGTCTCTCTTAAGACAGTTTCTCTTGAAACACCAATCATTGAATATGTTTCTCTTGAAAAAATAA
1 TGTCTCTCTTAAGACAGTTTCACTTGAAACACCAAACATTAAAAAAGTTTCCCTTGAAAAAAAAA
2094123 TA
66 TA
* * *
2094125 TGTCTCTCTTGAGACAGTTTCACTTGAAACA-TAAACTTTAAAAAAGTTTCCCTT-AAAACACAA
1 TGTCTCTCTTAAGACAGTTTCACTTGAAACACCAAACATTAAAAAAGTTTCCCTTGAAAA-A-AA
2094188 AATA
64 AATA
2094192 T
1 T
2094193 TTGAATCAGT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
65 4 0.07
66 17 0.30
67 35 0.62
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (67 bp):
TGTCTCTCTTAAGACAGTTTCACTTGAAACACCAAACATTAAAAAAGTTTCCCTTGAAAAAAAAA
TA
Found at i:2094432 original size:31 final size:31
Alignment explanation
Indices: 2094394--2094455 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
2094384 TTTGACAAGA
2094394 ATTCCAAAGTTAGCAGAGGTTTCATCACACC
1 ATTCCAAAGTTAGCAGAGGTTTCATCACACC
2094425 ATTCCAAAGTTAGCAGAGGTTTCATCACACC
1 ATTCCAAAGTTAGCAGAGGTTTCATCACACC
2094456 TTCGGCTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (31 bp):
ATTCCAAAGTTAGCAGAGGTTTCATCACACC
Found at i:2094632 original size:43 final size:43
Alignment explanation
Indices: 2094567--2094649 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
2094557 AGAATATTGT
* * * *
2094567 TCAACTTTTTCTTGATTCCATCACCGAAGGAGTTGGATCAACA
1 TCAACTTTTGCTCGATTCCATCACAGAAGGAGTTGAATCAACA
*
2094610 TCAACTTCTTGCTCGATT-CATCACATAAGGAGTTGAATCA
1 TCAACTT-TTGCTCGATTCCATCACAGAAGGAGTTGAATCA
2094650 GTAACACCTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 26 0.76
44 8 0.24
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (43 bp):
TCAACTTTTGCTCGATTCCATCACAGAAGGAGTTGAATCAACA
Found at i:2095465 original size:2 final size:2
Alignment explanation
Indices: 2095458--2095531 Score: 79
Period size: 2 Copynumber: 39.0 Consensus size: 2
2095448 AAATTATAGC
*
2095458 AT AT AT AT AT A- AT -T A- AT -T AT AT GAT AT -T AT AA AT CAT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT -AT AT
2095496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2095532 TTACAATTTA
Statistics
Matches: 62, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
1 6 0.10
2 52 0.84
3 4 0.06
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2096873 original size:19 final size:18
Alignment explanation
Indices: 2096841--2096881 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
2096831 TTTCTTTTTT
*
2096841 TTTTACTTTATTTATTTA
1 TTTTAATTTATTTATTTA
*
2096859 CTTTTAATTTTTTTATTTA
1 -TTTTAATTTATTTATTTA
2096878 TTTT
1 TTTT
2096882 GATTATTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTAATTTATTTATTTA
Found at i:2096888 original size:32 final size:30
Alignment explanation
Indices: 2096835--2096912 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 30
2096825 ATATGTTTTC
* *
2096835 TTTTTTT-TTTACTTTATTTATTTACTTTTAA
1 TTTTTTTATTTATTTTATTTA-TT-CTCTTAA
*
2096866 TTTTTTTATTTATTTTGA-TTATTCTCTTCA
1 TTTTTTTATTTATTTT-ATTTATTCTCTTAA
2096896 TTTTTTTACTTTATTTT
1 TTTTTTTA-TTTATTTT
2096913 TTACCTTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 13 0.32
31 17 0.41
32 10 0.24
33 1 0.02
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.74
Consensus pattern (30 bp):
TTTTTTTATTTATTTTATTTATTCTCTTAA
Found at i:2096978 original size:4 final size:4
Alignment explanation
Indices: 2096969--2096999 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2096959 TTATTACCAT
2096969 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2097000 TTTCCATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2098208 original size:3 final size:3
Alignment explanation
Indices: 2098200--2098320 Score: 242
Period size: 3 Copynumber: 40.3 Consensus size: 3
2098190 TGCTCGACAC
2098200 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2098248 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2098296 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
2098321 ATCTTGGCCC
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 118 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2100015 original size:18 final size:18
Alignment explanation
Indices: 2099994--2100033 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2099984 GGTTTGAATC
*
2099994 CTCATTCAACATTGAACA
1 CTCATTCAACATTAAACA
2100012 CTCATTCAACATTAAACA
1 CTCATTCAACATTAAACA
2100030 CTCA
1 CTCA
2100034 AACCTCTGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.30, G:0.03, T:0.28
Consensus pattern (18 bp):
CTCATTCAACATTAAACA
Found at i:2101186 original size:22 final size:22
Alignment explanation
Indices: 2101158--2101241 Score: 104
Period size: 22 Copynumber: 4.0 Consensus size: 22
2101148 AAACCACTAC
2101158 GTCCCGAAGGACCACTGTATAT
1 GTCCCGAAGGACCACTGTATAT
* *
2101180 GTCCCGAATGACCACTTTATAT
1 GTCCCGAAGGACCACTGTATAT
*
2101202 GTCTCGAAGGACCAC----TAT
1 GTCCCGAAGGACCACTGTATAT
*
2101220 GTCCCGAATGACCACTGTATAT
1 GTCCCGAAGGACCACTGTATAT
2101242 CCCTCGACTC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
18 16 0.31
22 36 0.69
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGTATAT
Found at i:2101222 original size:18 final size:18
Alignment explanation
Indices: 2101139--2101235 Score: 68
Period size: 22 Copynumber: 4.9 Consensus size: 18
2101129 ACTGAATATT
**
2101139 TGTCCCGAAAAACCACTA
1 TGTCCCGAAGGACCACTA
*
2101157 CGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCAC----TA
*
2101179 TGTCCCGAATGACCACTTTATA
1 TGTCCCGAAGGACCAC----TA
*
2101201 TGTCTCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
2101219 TGTCCCGAATGACCACT
1 TGTCCCGAAGGACCACT
2101236 GTATATCCCT
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
18 30 0.46
22 35 0.54
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2101368 original size:23 final size:23
Alignment explanation
Indices: 2101338--2101389 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
2101328 ATCTTTTTCA
2101338 TCACTTTTCATATAAACACATAT
1 TCACTTTTCATATAAACACATAT
*
2101361 TCACTTTTCATATAAGCACATAT
1 TCACTTTTCATATAAACACATAT
2101384 TCACTT
1 TCACTT
2101390 CACATGTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (23 bp):
TCACTTTTCATATAAACACATAT
Found at i:2101401 original size:21 final size:22
Alignment explanation
Indices: 2101346--2101404 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
2101336 CATCACTTTT
**
2101346 CATATAAACACATATTCACTTTT
1 CATAT-AACACATATTCACTTCA
2101369 CATATAAGCACATATTCACTTCA
1 CATATAA-CACATATTCACTTCA
*
2101392 CATGT-ACACATAT
1 CATATAACACATAT
2101405 GATCATTTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 7 0.22
22 3 0.09
23 22 0.69
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (22 bp):
CATATAACACATATTCACTTCA
Found at i:2101707 original size:18 final size:18
Alignment explanation
Indices: 2101681--2101721 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2101671 TCCTTCGATT
*
2101681 GTTCCGGAACAGGATTAC
1 GTTCTGGAACAGGATTAC
2101699 GTTCTGGAACAGGATTAC
1 GTTCTGGAACAGGATTAC
*
2101717 ATTCT
1 GTTCT
2101722 ATATCTACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (18 bp):
GTTCTGGAACAGGATTAC
Found at i:2108192 original size:18 final size:18
Alignment explanation
Indices: 2108165--2108236 Score: 90
Period size: 18 Copynumber: 3.8 Consensus size: 18
2108155 GAATATTTAC
2108165 CCCGAAGGACCACTATGT
1 CCCGAAGGACCACTATGT
* *
2108183 CTCAAAGGACCACTGTATATGT
1 CCCGAAGGACCAC----TATGT
2108205 CCCGAAGGACCACTATGT
1 CCCGAAGGACCACTATGT
2108223 CCCGAAGGACCACT
1 CCCGAAGGACCACT
2108237 GTATATCCCT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 30 0.65
22 16 0.35
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.18
Consensus pattern (18 bp):
CCCGAAGGACCACTATGT
Found at i:2108209 original size:40 final size:40
Alignment explanation
Indices: 2108165--2108242 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
2108155 GAATATTTAC
*
2108165 CCCGAAGGACCACTATGTCTCAAAGGACCACTGTATATGT
1 CCCGAAGGACCACTATGTCCCAAAGGACCACTGTATATGT
*
2108205 CCCGAAGGACCACTATGTCCCGAAGGACCACTGTATAT
1 CCCGAAGGACCACTATGTCCCAAAGGACCACTGTATAT
2108243 CCCTCGACTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (40 bp):
CCCGAAGGACCACTATGTCCCAAAGGACCACTGTATATGT
Found at i:2108212 original size:22 final size:22
Alignment explanation
Indices: 2108178--2108242 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
2108168 GAAGGACCAC
* *
2108178 TATGTCTCAAAGGACCACTGTA
1 TATGTCCCGAAGGACCACTGTA
2108200 TATGTCCCGAAGGACCAC----
1 TATGTCCCGAAGGACCACTGTA
2108218 TATGTCCCGAAGGACCACTGTA
1 TATGTCCCGAAGGACCACTGTA
2108240 TAT
1 TAT
2108243 CCCTCGACTC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 18 0.49
22 19 0.51
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (22 bp):
TATGTCCCGAAGGACCACTGTA
Found at i:2112859 original size:235 final size:235
Alignment explanation
Indices: 2112448--2112914 Score: 790
Period size: 235 Copynumber: 2.0 Consensus size: 235
2112438 TCGTTTCCCG
* * * *
2112448 AGTGTCAAACAAAGGCATAAGTCTTGTGGAATATTACCTTATAACATTCTTATGCTTATCACATA
1 AGTGTCAAACAAAGGCATAAGTCTTATGGAATATTACCTTATAACATTCTTATACTTATCAAACA
*
2112513 ATCATTAGGGGTTTTCACTTGTAAGCTTTTATTTTTAAGGTTATTGACCCTTAAACCCCTCACTC
66 ATCATTAGGGGTTTTCACTTGTAAGCTTTCATTTTTAAGGTTATTGACCCTTAAACCCCTCACTC
2112578 AAACCTCAAGGCTAAACTGGTTCTAGCCTATTTTTAATCATGATGGTACCAATACTCACCCATGT
131 AAACCTCAAGGCTAAACTGGTTCTAGCCTATTTTTAATCATGATGGTACCAATACTCACCCATGT
* *
2112643 GGTATCGATACAACTTACTCACGGTATCGATACTACCCCA
196 GGTATCGATACAACTCACTCACGATATCGATACTACCCCA
* ** * *
2112683 AGTGTCAAACAAGGGCATAAGTCTTATGGAATATTACCTTATAATGTTCTTATATTTATTAAACA
1 AGTGTCAAACAAAGGCATAAGTCTTATGGAATATTACCTTATAACATTCTTATACTTATCAAACA
*
2112748 ATCATTAGGGGTTTTCACTTGTAAGCTTTCATTTTTAAGGTTATTGATCCTTAAACCCCTCACTC
66 ATCATTAGGGGTTTTCACTTGTAAGCTTTCATTTTTAAGGTTATTGACCCTTAAACCCCTCACTC
* * *
2112813 GAACCTCAAGGCTAAACTGGTTCTAGCCTATTTTTAATTATGATGGTATCAATACTCACCCATGT
131 AAACCTCAAGGCTAAACTGGTTCTAGCCTATTTTTAATCATGATGGTACCAATACTCACCCATGT
2112878 GGTATCGATACAACTCACTCACGATATCGATACTACC
196 GGTATCGATACAACTCACTCACGATATCGATACTACC
2112915 TTGAGTATCG
Statistics
Matches: 216, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
235 216 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.34
Consensus pattern (235 bp):
AGTGTCAAACAAAGGCATAAGTCTTATGGAATATTACCTTATAACATTCTTATACTTATCAAACA
ATCATTAGGGGTTTTCACTTGTAAGCTTTCATTTTTAAGGTTATTGACCCTTAAACCCCTCACTC
AAACCTCAAGGCTAAACTGGTTCTAGCCTATTTTTAATCATGATGGTACCAATACTCACCCATGT
GGTATCGATACAACTCACTCACGATATCGATACTACCCCA
Found at i:2114246 original size:20 final size:21
Alignment explanation
Indices: 2114217--2114261 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2114207 AGGAGTATCA
2114217 ATACCATAAG-AAAGGAATCG
1 ATACCATAAGTAAAGGAATCG
* * *
2114237 ATACCCTAAGTAAGGGTATCG
1 ATACCATAAGTAAAGGAATCG
2114258 ATAC
1 ATAC
2114262 TGAATTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (21 bp):
ATACCATAAGTAAAGGAATCG
Found at i:2114259 original size:21 final size:20
Alignment explanation
Indices: 2114211--2114261 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2114201 ACTCATAGGA
*
2114211 GTATCAATACCATAAGAAAG
1 GTATCGATACCATAAGAAAG
* * *
2114231 GAATCGATACCCTAAGTAAGG
1 GTATCGATACCATAAG-AAAG
2114252 GTATCGATAC
1 GTATCGATAC
2114262 TGAATTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22
Consensus pattern (20 bp):
GTATCGATACCATAAGAAAG
Found at i:2121672 original size:3 final size:3
Alignment explanation
Indices: 2121664--2121705 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2121654 AAGCTAACCC
2121664 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2121706 CCTTTTATGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2123232 original size:24 final size:25
Alignment explanation
Indices: 2123204--2123257 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
2123194 CAAAGGTTTG
* *
2123204 ATTTGGTTTTAGAAAACATA-GTTC
1 ATTTGGTTTTAAAAAAAATAGGTTC
2123228 ATTTGGTTTTAAAAAAAATATGGTTC
1 ATTTGGTTTTAAAAAAAATA-GGTTC
2123254 ATTT
1 ATTT
2123258 TTATTTCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 18 0.69
26 8 0.31
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (25 bp):
ATTTGGTTTTAAAAAAAATAGGTTC
Found at i:2123549 original size:29 final size:30
Alignment explanation
Indices: 2123510--2123570 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
2123500 GTTTTTATTT
*
2123510 TAGTTATTAAACTTTTAA-AACTTTCATTA
1 TAGTTACTAAACTTTTAATAACTTTCATTA
*
2123539 TAGTTACTAAACTTTTAATTCACTTTCATTA
1 TAGTTACTAAACTTTTAA-TAACTTTCATTA
2123570 T
1 T
2123571 TGTCACTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.61
31 11 0.39
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.49
Consensus pattern (30 bp):
TAGTTACTAAACTTTTAATAACTTTCATTA
Found at i:2126667 original size:20 final size:21
Alignment explanation
Indices: 2126638--2126677 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2126628 AAAATATAAA
2126638 AAATACATTC-TAAAATTATG
1 AAATACATTCGTAAAATTATG
* *
2126658 AAATATATTCGTAATATTAT
1 AAATACATTCGTAAAATTAT
2126678 ATTTCAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (21 bp):
AAATACATTCGTAAAATTATG
Found at i:2127199 original size:149 final size:148
Alignment explanation
Indices: 2126847--2127360 Score: 454
Period size: 149 Copynumber: 3.4 Consensus size: 148
2126837 AAAAAAGTAA
* * * ** * * *
2126847 GAATTGAAGTTACATAGGTATCCTATTATGGTATATGAGCATGT-AGTTCAAATTTGACAAAAAC
1 GAATTGAAATTACATATGTATACTACGATGGTTTAGGAGCATGTGA-TTCAAATTTGATAAAAAC
* *
2126911 GAATATAAAAT-AAGAATGAATTGAAAAAAAATAAAGAAATTATGAAAAT-TTGAGGGACTAAAT
65 GAAT-TAAAATAAAGGATGAATTG--AAAAAATAAGGAAATTAT-AAAATATTGAGGGACTAAAT
* *
2126974 TGAAAAATAGAAAATTTGTTATAAAAAA
126 TG-AAAA-A-AAAA-TTATTA-AAAAAG
* * * * ** * *
2127002 G-A-GGAATTTATATATGTATTCTACGATGGTTTAGGAAAATGTGGTTCAAATTTGGTAAAAACG
1 GAATTGAAATTACATATGTATACTACGATGGTTTAGGAGCATGTGATTCAAATTTGATAAAAAC-
* *
2127065 GACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATTATAAAATATTGA-GGACTAAATTGAA
65 GAATTAAAATAAAGGATGAATTGAAAAAATAAGGAAATTATAAAATATTGAGGGACTAAATTGAA
2127129 AAAAAAATTATTAGAAAAAG
130 AAAAAAATTATTA-AAAAAG
* * * * *
2127149 GAATTGAAAGTACGTATGTATACTACGATAGTTTAGGAGCATGTGATTCAAATTAGGTAAAAAAA
1 GAATTGAAATTACATATGTATACTACGATGGTTTAGGAGCATGTGATTCAAATT---TGATAAAA
* * * *
2127214 AAGAGTCAAAATAAAGGATGAATTGAATAAATAAGGAAATTAT-AAATA-TGAGGGACTAAATTG
63 ACGAATTAAAATAAAGGATGAATTGAAAAAATAAGGAAATTATAAAATATTGAGGGACTAAATTG
**** *
2127277 -AAAATTTGTTATCAAAAAGAG
128 AAAAAAAAATTATTAAAAA-AG
* * *
2127298 GAATTTAAATTACACATGTATTA-TACGATGGTTTAGGAGCATGTAATTCAAATTTGATAAAAA
1 GAATTGAAATTACATATGTA-TACTACGATGGTTTAGGAGCATGTGATTCAAATTTGATAAAAA
2127361 AAATAAATTT
Statistics
Matches: 296, Mismatches: 51, Indels: 33
0.78 0.13 0.09
Matches are distributed among these distances:
146 7 0.02
147 11 0.04
148 9 0.03
149 100 0.34
150 22 0.07
151 54 0.18
152 26 0.09
153 51 0.17
154 15 0.05
155 1 0.00
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (148 bp):
GAATTGAAATTACATATGTATACTACGATGGTTTAGGAGCATGTGATTCAAATTTGATAAAAACG
AATTAAAATAAAGGATGAATTGAAAAAATAAGGAAATTATAAAATATTGAGGGACTAAATTGAAA
AAAAAATTATTAAAAAAG
Found at i:2127832 original size:45 final size:45
Alignment explanation
Indices: 2127768--2127903 Score: 254
Period size: 45 Copynumber: 3.0 Consensus size: 45
2127758 AAAAGTCAAG
*
2127768 ATCAATTCTTTGAATTTAAGGTAATCTCTCTCATATATCTGGTAA
1 ATCAATTCTTTGAATTTAAGGTAATCTCTCTCATTTATCTGGTAA
*
2127813 ATCAATTCTTTGAATTTAAGGTAATCTCTCTCATTTATCTGGCAA
1 ATCAATTCTTTGAATTTAAGGTAATCTCTCTCATTTATCTGGTAA
2127858 ATCAATTCTTTGAATTTAAGGTAATCTCTCTCATTTATCTGGTAA
1 ATCAATTCTTTGAATTTAAGGTAATCTCTCTCATTTATCTGGTAA
2127903 A
1 A
2127904 CTGATTTTTT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 88 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (45 bp):
ATCAATTCTTTGAATTTAAGGTAATCTCTCTCATTTATCTGGTAA
Found at i:2133515 original size:68 final size:68
Alignment explanation
Indices: 2133443--2133575 Score: 257
Period size: 68 Copynumber: 2.0 Consensus size: 68
2133433 TGAAATCTAA
*
2133443 CTAAAAGTGGAGGCTCTATTTAACCTATTTAATTATGTCAATATTAAAACTCTAATTGAAATTTG
1 CTAAAAGTGGAGGCTCTATTTAACCTATTTAATTATGCCAATATTAAAACTCTAATTGAAATTTG
2133508 TAG
66 TAG
2133511 CTAAAAGTGGAGGCTCTATTTAACCTATTTAATTATGCCAATATTAAAACTCTAATTGAAATTTG
1 CTAAAAGTGGAGGCTCTATTTAACCTATTTAATTATGCCAATATTAAAACTCTAATTGAAATTTG
2133576 GGGACTAAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (68 bp):
CTAAAAGTGGAGGCTCTATTTAACCTATTTAATTATGCCAATATTAAAACTCTAATTGAAATTTG
TAG
Found at i:2133941 original size:13 final size:14
Alignment explanation
Indices: 2133923--2133960 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
2133913 TAATAAACCT
2133923 AATAAAAATAAT-A
1 AATAAAAATAATAA
2133936 AATAAAAA-ACATAA
1 AATAAAAATA-ATAA
2133950 AATAAAAATAA
1 AATAAAAATAA
2133961 ACATAAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.05
13 10 0.45
14 10 0.45
15 1 0.05
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (14 bp):
AATAAAAATAATAA
Found at i:2133959 original size:6 final size:6
Alignment explanation
Indices: 2133923--2133974 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
2133913 TAATAAACCT
* * *
2133923 AATAAA AATAATA AATAAAA AACATAA AATAAA AATAAA CATAAA CATAAA
1 AATAAA AATAA-A AAT-AAA AATA-AA AATAAA AATAAA AATAAA AATAAA
2133974 A
1 A
2133975 TAAGGACCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 25 0.64
7 12 0.31
8 2 0.05
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:2133972 original size:23 final size:21
Alignment explanation
Indices: 2133927--2133977 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 21
2133917 AAACCTAATA
2133927 AAAATAATAAATAAAAAACAT
1 AAAATAATAAATAAAAAACAT
2133948 AAAATAA-AAATAAACATAAACAT
1 AAAATAATAAAT-AA-A-AAACAT
2133971 AAAATAA
1 AAAATAA
2133978 GGACCTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.15
21 9 0.33
22 1 0.04
23 13 0.48
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (21 bp):
AAAATAATAAATAAAAAACAT
Found at i:2133977 original size:17 final size:17
Alignment explanation
Indices: 2133932--2133974 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
2133922 TAATAAAAAT
*
2133932 AATAAATAAAAAACATAA
1 AATAAA-AATAAACATAA
2133950 AATAAAAATAAACATAA
1 AATAAAAATAAACATAA
2133967 ACATAAAA
1 A-ATAAAA
2133975 TAAGGACCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (17 bp):
AATAAAAATAAACATAA
Found at i:2134029 original size:20 final size:21
Alignment explanation
Indices: 2134006--2134050 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2133996 GTGAAATTAC
2134006 TAAAC-TAAATGAGAAC-AAAT
1 TAAACATAAAT-AGAACTAAAT
*
2134026 TAAACATAAATAGGACTAAAT
1 TAAACATAAATAGAACTAAAT
2134047 TAAA
1 TAAA
2134051 ACAAATTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.22
Consensus pattern (21 bp):
TAAACATAAATAGAACTAAAT
Found at i:2134823 original size:2 final size:2
Alignment explanation
Indices: 2134818--2134905 Score: 176
Period size: 2 Copynumber: 44.0 Consensus size: 2
2134808 AGAGAATCAC
2134818 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2134860 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2134902 TA TA
1 TA TA
2134906 CGAAATAGAA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2135861 original size:59 final size:59
Alignment explanation
Indices: 2135798--2135909 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 59
2135788 ATTCGACGTG
* * *
2135798 TTGTGAATTGAGCAATAGGAAATGTTAACCCTTCTGG-GGGGCATTGCTGATTCAAAGCA
1 TTGTGAATTGAG-AAAAGAAAATGTTAACCCCTCTGGTGGGGCATTGCTGATTCAAAGCA
* *
2135857 TTGTGAATTGAGAAAAGAAAATGTTAACCCCTCTGGTGGGGCGTTTCTGATTC
1 TTGTGAATTGAGAAAAGAAAATGTTAACCCCTCTGGTGGGGCATTGCTGATTC
2135910 GAAGTATCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
58 21 0.45
59 26 0.55
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (59 bp):
TTGTGAATTGAGAAAAGAAAATGTTAACCCCTCTGGTGGGGCATTGCTGATTCAAAGCA
Found at i:2135923 original size:59 final size:59
Alignment explanation
Indices: 2135801--2135940 Score: 149
Period size: 59 Copynumber: 2.4 Consensus size: 59
2135791 CGACGTGTTG
* * * **
2135801 TGAATTGAGCAATAGGAAATGTTAACCCTTCTGGGGGGCATTGCTGATTCAAAGCATTG
1 TGAATTGAGCAAAAGAAAATGTTAACCCCTCTGGGGGGCATTGCTGATTCAAAGCATCA
* * * *
2135860 TGAATTGAG-AAAAGAAAATGTTAACCCCTCTGGTGGGGCGTTTCTGATTCGAAGTATCA
1 TGAATTGAGCAAAAGAAAATGTTAACCCCTCTGG-GGGGCATTGCTGATTCAAAGCATCA
** *
2135919 TGAATCAAGC-AACGAAAATGTT
1 TGAATTGAGCAAAAGAAAATGTT
2135941 GAAAACATCC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
58 21 0.31
59 46 0.69
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (59 bp):
TGAATTGAGCAAAAGAAAATGTTAACCCCTCTGGGGGGCATTGCTGATTCAAAGCATCA
Found at i:2136070 original size:42 final size:42
Alignment explanation
Indices: 2135962--2136070 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 42
2135952 GCCCAAAGGT
* * * *
2135962 CTTATGGATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGA
* *
2136003 CTTATAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGA
*
2136045 CTTACT-GATGACCCGAAGAACTTAAG
1 CTTA-TAGATGACCCGAAGGACTTAAG
2136071 TTGATTCGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 19 0.33
42 37 0.65
43 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (42 bp):
CTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGA
Found at i:2136272 original size:228 final size:226
Alignment explanation
Indices: 2135875--2136381 Score: 755
Period size: 228 Copynumber: 2.2 Consensus size: 226
2135865 TGAGAAAAGA
* * * *
2135875 AAATGTTAACCCCTCTGGTGGGGCGTT-TCTGATTCGAAGTATCATGAATCAAGCAACGAAAATG
1 AAATGTTAACCCCTCTGGT-GGGCATTGT-TGATTCGAAGTGTTATGAATCGAGCAACGAAAATG
2135939 TTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGAC
64 TTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGAC
* * * *
2136004 TTATAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGAACTTA
129 TAATAGATGACCCAAAGGATTTAAGAATCATGCTCGAAAGACTTACTAAAGACCCGAAGAACTTA
* * *
2136069 AGTTGATTCGAAGTGTTGTGAATCGAGCCATAGG
194 AGCTGATTCAAAGTGTT-TGAATCAAGCCATAGG
**
2136103 AAATGTTAACCCCTCTGGTGGAGCATTGTTGATTTTAAGTGTTATGAATCGAGCAACGAAAATGT
1 AAATGTTAACCCCTCTGGTGG-GCATTGTTGATTCGAAGTGTTATGAATCGAGCAACGAAAATGT
* *
2136168 TGAAAACATCCTGCCCCAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGACT
65 TGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACT
* * * *
2136233 AATAGATGACCCAAAGGATTTAAGAATCATGCTCGAAAGATTTACTAAAGGCCCGAAGGATTTAA
130 AATAGATGACCCAAAGGATTTAAGAATCATGCTCGAAAGACTTACTAAAGACCCGAAGAACTTAA
* *
2136298 GCTGATTTAAAGTGTTTGAATCAAGCCATATG
195 GCTGATTCAAAGTGTTTGAATCAAGCCATAGG
* *
2136330 AAATGTTAACCCCTCTGGTAGGGCATTGCTGATTCGAAGTGTTGTGAATCGA
1 AAATGTTAACCCCTCTGGT-GGGCATTGTTGATTCGAAGTGTTATGAATCGA
2136382 TTAAAGGAAA
Statistics
Matches: 251, Mismatches: 25, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
227 61 0.24
228 189 0.75
229 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (226 bp):
AAATGTTAACCCCTCTGGTGGGCATTGTTGATTCGAAGTGTTATGAATCGAGCAACGAAAATGTT
GAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTA
ATAGATGACCCAAAGGATTTAAGAATCATGCTCGAAAGACTTACTAAAGACCCGAAGAACTTAAG
CTGATTCAAAGTGTTTGAATCAAGCCATAGG
Found at i:2136371 original size:59 final size:59
Alignment explanation
Indices: 2136298--2136431 Score: 153
Period size: 59 Copynumber: 2.3 Consensus size: 59
2136288 AAGGATTTAA
** * *
2136298 GCTGATTTAAAGTGTT-TGAATCAAGCCATATGAAATGTTAACCCCTCTGGTAGGGCATT
1 GCTGATTCGAAGTGTTGTGAATCAA-CCAAAGGAAATGTTAACCCCTCTGGTAGGGCATT
* ** * **
2136357 GCTGATTCGAAGTGTTGTGAATCGATTAAAGGAAATGTTAACCCCTCTGGTGGGGTGTT
1 GCTGATTCGAAGTGTTGTGAATCAACCAAAGGAAATGTTAACCCCTCTGGTAGGGCATT
*
2136416 GTTGATTCGAAGTGTT
1 GCTGATTCGAAGTGTT
2136432 ATAAATCGAG
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 56 0.89
60 7 0.11
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (59 bp):
GCTGATTCGAAGTGTTGTGAATCAACCAAAGGAAATGTTAACCCCTCTGGTAGGGCATT
Found at i:2136439 original size:59 final size:59
Alignment explanation
Indices: 2136329--2136440 Score: 170
Period size: 59 Copynumber: 1.9 Consensus size: 59
2136319 CAAGCCATAT
* *
2136329 GAAATGTTAACCCCTCTGGTAGGGCATTGCTGATTCGAAGTGTTGTGAATCGATTAAAG
1 GAAATGTTAACCCCTCTGGTAGGGCATTGCTGATTCGAAGTGTTATAAATCGATTAAAG
* ** *
2136388 GAAATGTTAACCCCTCTGGTGGGGTGTTGTTGATTCGAAGTGTTATAAATCGA
1 GAAATGTTAACCCCTCTGGTAGGGCATTGCTGATTCGAAGTGTTATAAATCGA
2136441 GCAATGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 47 1.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (59 bp):
GAAATGTTAACCCCTCTGGTAGGGCATTGCTGATTCGAAGTGTTATAAATCGATTAAAG
Found at i:2136452 original size:59 final size:59
Alignment explanation
Indices: 2136330--2136454 Score: 160
Period size: 59 Copynumber: 2.1 Consensus size: 59
2136320 AAGCCATATG
* * ** *
2136330 AAATGTTAACCCCTCTGGTAGGGCATTGCTGATTCGAAGTGTTGTGAATCGATTAAAGG
1 AAATGTTAACCCCTCTGGTAGGGCATTGCTGATTCGAAGTGTTATAAATCGAGCAAAGA
* ** * *
2136389 AAATGTTAACCCCTCTGGTGGGGTGTTGTTGATTCGAAGTGTTATAAATCGAGCAATGA
1 AAATGTTAACCCCTCTGGTAGGGCATTGCTGATTCGAAGTGTTATAAATCGAGCAAAGA
2136448 AAATGTT
1 AAATGTT
2136455 GAAAACATCA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (59 bp):
AAATGTTAACCCCTCTGGTAGGGCATTGCTGATTCGAAGTGTTATAAATCGAGCAAAGA
Found at i:2136642 original size:56 final size:57
Alignment explanation
Indices: 2136558--2136770 Score: 226
Period size: 56 Copynumber: 3.8 Consensus size: 57
2136548 ATTTTCAGTT
* *
2136558 ATCATCAAGAAACTCCT-AAACATTAGGCTTAGTTTCTTT-AAAATTCTTTGGAAATA
1 ATCATCAAGAAACCCCTGAAA-ATTAGGCTTAGTTTCTTTAAAAATTCATTGGAAATA
* *
2136614 ATCATCAAGAAACCCCTGAAAATCAGGCTTAG-TT-TTTAAAAACTCAATT-G-AA-A
1 ATCATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTTAAAAATTC-ATTGGAAATA
* * * * *
2136667 A-CATCAGGAAACCCCTAAAAATTAGGCTTAGATTCTTTTAAAAATTCATTGAAAATC
1 ATCATCAAGAAACCCCTGAAAATTAGGCTTAGTTTC-TTTAAAAATTCATTGGAAATA
* * * *
2136724 ATCATCAATAAACTCCTGAAAATAAGACTTAGTTTCTTTAAAAATTC
1 ATCATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTTAAAAATTC
2136771 TTTTGAAAAC
Statistics
Matches: 130, Mismatches: 17, Indels: 19
0.78 0.10 0.11
Matches are distributed among these distances:
52 27 0.21
53 4 0.03
54 8 0.06
55 19 0.15
56 30 0.23
57 15 0.12
58 27 0.21
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (57 bp):
ATCATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTTAAAAATTCATTGGAAATA
Found at i:2150933 original size:21 final size:21
Alignment explanation
Indices: 2150890--2150933 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2150880 AAATGGGTGA
* *
2150890 TTTTAATAAAATATTTTATTT
1 TTTTAATAAAATATTTAAGTT
2150911 TTTTAATCAAAATA-TTAAGTT
1 TTTTAAT-AAAATATTTAAGTT
2150932 TT
1 TT
2150934 AGGGTCTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTAATAAAATATTTAAGTT
Found at i:2151501 original size:12 final size:12
Alignment explanation
Indices: 2151484--2151510 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2151474 TCCCTATTTG
2151484 ATTTTTAAACCA
1 ATTTTTAAACCA
2151496 ATTTTTAAACCA
1 ATTTTTAAACCA
2151508 ATT
1 ATT
2151511 ACGTGAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTTTTAAACCA
Found at i:2153461 original size:3 final size:3
Alignment explanation
Indices: 2153453--2153499 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
2153443 TATTGGCTTG
*
2153453 TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2153500 TAGGGTAGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2155805 original size:15 final size:15
Alignment explanation
Indices: 2155785--2155817 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2155775 TGGTTGTATT
*
2155785 GGGGGATGACGGTGA
1 GGGGGATAACGGTGA
2155800 GGGGGATAACGGTGA
1 GGGGGATAACGGTGA
2155815 GGG
1 GGG
2155818 AAAACAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.61, T:0.12
Consensus pattern (15 bp):
GGGGGATAACGGTGA
Found at i:2155924 original size:21 final size:21
Alignment explanation
Indices: 2155900--2155943 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2155890 AAGACAATCA
2155900 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
2155921 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
2155942 AG
1 AG
2155944 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:2157211 original size:4 final size:4
Alignment explanation
Indices: 2157202--2157226 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2157192 TAAGAGATTG
2157202 GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT G
2157227 AAAGGACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:2158620 original size:400 final size:401
Alignment explanation
Indices: 2158118--2159034 Score: 1491
Period size: 400 Copynumber: 2.3 Consensus size: 401
2158108 ACATATGCAT
*
2158118 CCATAATTATAATGTCATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGATTTTATGAGA
1 CCATAATTATAATGTAATAGGTAAA-TTTCAATGTAACCGGTATAAATATACCGATTTTATGAGA
*
2158183 GAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
65 GAATAGGTCTACAACATGTATCTACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
* *
2158248 ATGCAAAAAAGGATGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCACAGCAACAT
130 ATGCAAAAAAGGATGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCAATCACAGAAACAT
* * * ** **
2158313 ATG-TATCCATAAGTATAATGTAATAGGTAAATTTTTAATGTAACCGGTATAAATATACCGGTTT
195 -CGAAACCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCAATTT
* *
2158377 TATGAGAGAATAGGTCTACAACATGTATCGATA-TTTTTTAATTTTGTGTCGATACTTTTGGTCC
259 TATGAGAGAATAGGTCTACAACATGTATCGACACATTTTTAATTTTGTGTCGATACTTTTGGTCC
*
2158441 AGAATGGATG-CAGAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCA
324 AGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCA
* * *
2158505 GAAATATTGAAAC
389 AAAACATCGAAAC
* * *
2158518 CCATAATTATAAAGTAATAGGTATATTTACAATGTAACCGGTATAAATATAACGATTTTATGAGA
1 CCATAATTATAATGTAATAGGTAAATTT-CAATGTAACCGGTATAAATATACCGATTTTATGAGA
*
2158583 GAATAGGTGTACAACATGTATCTACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
65 GAATAGGTCTACAACATGTATCTACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
* * *
2158648 ATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCAATCCCAGAAACAT
130 ATGCAAAAAAGGATGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCAATCACAGAAACAT
* *
2158713 CGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATATCAATTTT
195 CGAAACCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCAATTTT
*
2158778 ATGAGAGAATAGGTCTATAACATGTATCGACACATTTTTAATTTTGTGTCGATACTTTTGGTCCA
260 ATGAGAGAATAGGTCTACAACATGTATCGACACATTTTTAATTTTGTGTCGATACTTTTGGTCCA
2158843 GAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAA
325 GAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAA
2158908 AAACATCGAAAC
390 AAACATCGAAAC
* *
2158920 CCATAATTATAATGTAATAGGTAAAGTTTTAATGTAACCGGTATAAATATACCGGTTTTATGAGA
1 CCATAATTATAATGTAATAGGTAAA-TTTCAATGTAACCGGTATAAATATACCGATTTTATGAGA
*
2158985 GAATAGGTCTATAACATGTAT-TGACACTTTTTTAATTTTGTGTCGATACT
65 GAATAGGTCTACAACATGTATCT-ACACTTTTTTAATTTTGTGTCGATACT
2159035 AATTTAAATC
Statistics
Matches: 477, Mismatches: 34, Indels: 10
0.92 0.07 0.02
Matches are distributed among these distances:
399 4 0.01
400 264 0.55
401 41 0.09
402 165 0.35
403 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33
Consensus pattern (401 bp):
CCATAATTATAATGTAATAGGTAAATTTCAATGTAACCGGTATAAATATACCGATTTTATGAGAG
AATAGGTCTACAACATGTATCTACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGGA
TGCAAAAAAGGATGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCAATCACAGAAACATC
GAAACCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCAATTTTA
TGAGAGAATAGGTCTACAACATGTATCGACACATTTTTAATTTTGTGTCGATACTTTTGGTCCAG
AATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAA
AACATCGAAAC
Found at i:2158721 original size:201 final size:201
Alignment explanation
Indices: 2158118--2159034 Score: 1500
Period size: 201 Copynumber: 4.6 Consensus size: 201
2158108 ACATATGCAT
* *
2158118 CCATAATTATAATGTCATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGATTTTATGAGA
1 CCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGA
2158183 GAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
66 GAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
* * * *
2158248 ATGCAAAAAAGGATGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCACAGCAACAT
131 ATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAGAAACAT
* * *
2158313 ATG-TAT
196 -CGAAAC
* ** *
2158319 CCATAAGTATAATGTAATAGGTAAATTTTTAATGTAACCGGTATAAATATACCGGTTTTATGAGA
1 CCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGA
*
2158384 GAATAGGTCTACAACATGTATCGATA-TTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
66 GAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
* *
2158448 ATG-CAGAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAGAAATAT
131 ATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAGAAACAT
*
2158512 TGAAAC
196 CGAAAC
* * *
2158518 CCATAATTATAAAGTAATAGGTATATTTACAATGTAACCGGTATAAATATAACGATTTTATGAGA
1 CCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGA
* *
2158583 GAATAGGTGTACAACATGTATCTACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
66 GAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
*
2158648 ATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCAATCCCAGAAACAT
131 ATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAGAAACAT
2158713 CGAAAC
196 CGAAAC
* *
2158719 CCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATATCAATTTTATGAGA
1 CCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGA
* *
2158784 GAATAGGTCTATAACATGTATCGACACATTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
66 GAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
*
2158849 ATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACAT
131 ATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAGAAACAT
2158914 CGAAAC
196 CGAAAC
* *
2158920 CCATAATTATAATGTAATAGGTAAAGTTT-TAATGTAACCGGTATAAATATACCGGTTTTATGAG
1 CCATAATTATAATGTAATAGGTAAA-TTTACAATGTAACCGGTATAAATATACCGATTTTATGAG
* *
2158984 AGAATAGGTCTATAACATGTATTGACACTTTTTTAATTTTGTGTCGATACT
65 AGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACT
2159035 AATTTAAATC
Statistics
Matches: 669, Mismatches: 43, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
198 2 0.00
199 137 0.20
200 82 0.12
201 445 0.67
202 3 0.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33
Consensus pattern (201 bp):
CCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGA
GAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
ATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAGAAACAT
CGAAAC
Found at i:2160539 original size:3 final size:3
Alignment explanation
Indices: 2160502--2160554 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
2160492 CAAGCGGTCA
* * * * *
2160502 ATG AAG ATG AAG ATG ACG ATG AAG ATG ACG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
2160550 ATG AT
1 ATG AT
2160555 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.40, C:0.04, G:0.32, T:0.25
Consensus pattern (3 bp):
ATG
Found at i:2160554 original size:12 final size:12
Alignment explanation
Indices: 2160502--2160553 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
2160492 CAAGCGGTCA
*
2160502 ATGAAGATGAAG
1 ATGACGATGAAG
2160514 ATGACGATGAAG
1 ATGACGATGAAG
*
2160526 ATGACGATGATG
1 ATGACGATGAAG
* *
2160538 ATGATGATGATG
1 ATGACGATGAAG
2160550 ATGA
1 ATGA
2160554 TCCAAACAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.40, C:0.04, G:0.33, T:0.23
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:2162265 original size:251 final size:251
Alignment explanation
Indices: 2161821--2162564 Score: 1152
Period size: 251 Copynumber: 3.0 Consensus size: 251
2161811 TAAAGTTTCC
* * * **
2161821 CATAAAGTGTCGATCCATATATAAAAAGTAACGA-CCCAAAAAACATCGAAACCCATAATTATAA
1 CATAAAGTGTCGATACATTTATTAAAAGTGTCGATCCC-AAAAACATCGAAACCCATAATTATAA
* * * * *
2161885 TGTAATGGGTAATTATTCAATATAACCGGTATAAATATACCAGTTTTATAAGAGAATAGGTCTAT
65 TGTAATAGGTAATTATTTAATATAACCGGTATACATATACCGGTTTTATGAGAGAATAGGTCTAT
* *
2161950 AACATTTATCGACACTTATTAGTATTGTGTCGATACTTTTTCTCTAGAATGGATGCCAAAAAGGG
130 AACATGTATCGACACTTATTAGTATTGTGTCGATACTTTTTCTCCAGAATGGATGCCAAAAAGGG
*
2162015 TGAACCTACAAAGTGTCGATACATTTTCATAGAGTGTCGATCCAAAAGGGTTTCACGA
195 TGAACCTACAAAGTGTCGATACATTTTCATAGAGTGTCGATCCAAAAGGGTTGCAC-A
*
2162073 -ATAAAGTGTCTATACATTTATTAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAAT
1 CATAAAGTGTCGATACATTTATTAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAAT
* * *
2162137 GTAATAGGTAATTGTTTAATATAACCGGTATACATATACCGGTTTTATGAGAGAATATGTCTACA
66 GTAATAGGTAATTATTTAATATAACCGGTATACATATACCGGTTTTATGAGAGAATAGGTCTATA
*
2162202 ACATGTATCGACACTTATTAGTATTGTGTCGATACTTTTTTTCCAGAATGGATGCCAAAAAGGGT
131 ACATGTATCGACACTTATTAGTATTGTGTCGATACTTTTTCTCCAGAATGGATGCCAAAAAGGGT
*
2162267 GAACCTACAAAGTGTCGATACATTTTCATAGAGTGTCGATCTAAAAGGGTTGCACA
196 GAACCTACAAAGTGTCGATACATTTTCATAGAGTGTCGATCCAAAAGGGTTGCACA
2162323 CATAAAGTGTCGATACATTTATTAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAAT
1 CATAAAGTGTCGATACATTTATTAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAAT
* *
2162388 GTAATAGGTAATTTTTTAATATAACCGGTATACTTATACCGGTTTTATGAGAGAATAGGTCTATA
66 GTAATAGGTAATTATTTAATATAACCGGTATACATATACCGGTTTTATGAGAGAATAGGTCTATA
* * * * * *
2162453 ATATGTATTGACACTTATTAATATTGTGTCGATAATTTTTGTCCATAATGGATGCCAAAAAGGGT
131 ACATGTATCGACACTTATTAGTATTGTGTCGATACTTTTTCTCCAGAATGGATGCCAAAAAGGGT
* * * *
2162518 GAACGC-ATAAAGTGTCGATACATTTTCAAAAAGTGTCAATCACAAAA
196 GAAC-CTACAAAGTGTCGATACATTTTCATAGAGTGTCGATC-CAAAA
2162565 ACATCGAAAC
Statistics
Matches: 453, Mismatches: 35, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
250 1 0.00
251 444 0.98
252 8 0.02
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (251 bp):
CATAAAGTGTCGATACATTTATTAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAAT
GTAATAGGTAATTATTTAATATAACCGGTATACATATACCGGTTTTATGAGAGAATAGGTCTATA
ACATGTATCGACACTTATTAGTATTGTGTCGATACTTTTTCTCCAGAATGGATGCCAAAAAGGGT
GAACCTACAAAGTGTCGATACATTTTCATAGAGTGTCGATCCAAAAGGGTTGCACA
Found at i:2164229 original size:45 final size:47
Alignment explanation
Indices: 2164116--2164243 Score: 136
Period size: 48 Copynumber: 2.8 Consensus size: 47
2164106 ATATAAATTT
* *
2164116 CTTACC-TTTTATCCCATAAGCTCATAAGCTTATTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTACCAAAATA
* * ** *
2164162 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTTTTTTTTTCAATATA
1 CTTACCATTT-AATTCCATAAGCTCATAAGCTTATTTTTACCAAAATA
* * *
2164210 CTTGCCA-TT-ATTCCGTAAGCTCATAAGATTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
2164244 GCATGGTTAC
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
45 21 0.31
46 6 0.09
47 5 0.07
48 36 0.53
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (47 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTACCAAAATA
Found at i:2164391 original size:40 final size:40
Alignment explanation
Indices: 2164347--2164468 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
2164337 ACCGTAGTGC
2164347 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2164387 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2164427 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2164467 TA
1 TA
2164469 TAAACCTGCA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2171387 original size:40 final size:40
Alignment explanation
Indices: 2171343--2171424 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
2171333 ACCGTAGTGC
2171343 TACACATAACGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAACGTCGTGCCCACCATATACACCGAAGTGTAT
**
2171383 TACACATATGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAACGTCGTGCCCACCATATACACCGAAGTGTAT
2171423 TA
1 TA
2171425 TAAACCTGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAACGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2175692 original size:200 final size:196
Alignment explanation
Indices: 2175289--2175997 Score: 721
Period size: 200 Copynumber: 3.5 Consensus size: 196
2175279 ACCTAAATAT
* *
2175289 GTGTCGATACATTTTATACAAGTATCGA-CCTAAAAAACATC-AAACCCAATAATTATAATGTAA
1 GTGTCGATACA-TTTATAAAAGTATCGATCC-AAAAAACATCGAAA-CCGATAATTATAATGTAA
* * * * * *
2175352 TAGGTAAATTAACAATGTAACTGGTATAAATATACCA-ATTAATTAGAAAACAGGTCAACATAAT
63 TAGGTAAATTTACAATGTAACCGGTATAAATATACCAGTTTTATGAGAAAATAGGTCAA-ATAAT
* * * * * *
2175416 GTTTCGAAACTTGTGTAATTTGTGTCGATACTTATTGTTCAGGATGAAT-GCACAAACGAGGTGC
127 GTATCGACACTTGT-TAATTTGTGTCGATACTT-TTGTCCAGAATGAATACCA-AAAAG-GGTGC
2175480 -ACGCATAAA
188 AAC-CATAAA
* * * *
2175489 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAATATCGAAACTGATAATTATAATGTATTA
1 GTGTCGATACATTTA-TAAAAGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * *
2175554 GATAAATTTACAATGTAACCGATATAAATATACCAGTTTTATGATAAAATAGGTCAGTATAAAGT
65 GGTAAATTTACAATGTAACCGGTATAAATATACCAGTTTTATGAGAAAATAGGTCA-AATAATGT
*
2175619 ATCGACACTTGATAAATTTGTGTCGATACTTTTGGTCCAGAATGAATACCAAAAAGGGTGCAACC
129 ATCGACACTTG-TTAATTTGTGTCGATACTTTT-GTCCAGAATGAATACCAAAAAGGGTGCAACC
*
2175684 ACAAA
192 ATAAA
* * * * *
2175689 GTGTCGATACATTTATAAGAAGTATCGATCCCAGAAACATCGAAACCCATCAGTATAATGTAATA
1 GTGTCGATACATTTATAA-AAGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATA
* * * *
2175754 GGTAAATTTTCAATGTAACCGTTATAAATATACCGGTTTTATGAGAGAATAGGTACAAATAATGT
65 GGTAAATTTACAATGTAACCGGTATAAATATACCAGTTTTATGAGAAAATAGGT-CAAATAATGT
* * **
2175819 ATCGACACGTTGTTAGTTTGTGTCGATACTTTTTTCCAGAATGAAATATGAATGTCCAACTA-GG
129 ATCGACAC-TTGTTAATTTGTGTCGATACTTTTGTCCAGAATG--A-AT--A---CCAAAAAGGG
*
2175883 TGCAAGCATAAA
185 TGCAACCATAAA
* * * *
2175895 GTGTCGATACATTTA-AAATTGTATCGATCTAAAAAACATCGTAACCGATAATAATAATGTAATA
1 GTGTCGATACATTTATAAA-AGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATA
** * *
2175959 GGTAAATTTGTAATGTTACCGGTATAAATATACCGGTTT
65 GGTAAATTTACAATGTAACCGGTATAAATATACCAGTTT
2175998 ACTTCGAAAA
Statistics
Matches: 428, Mismatches: 60, Indels: 37
0.82 0.11 0.07
Matches are distributed among these distances:
199 16 0.04
200 225 0.53
201 75 0.18
202 5 0.01
204 2 0.00
205 73 0.17
206 27 0.06
207 5 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (196 bp):
GTGTCGATACATTTATAAAAGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATAG
GTAAATTTACAATGTAACCGGTATAAATATACCAGTTTTATGAGAAAATAGGTCAAATAATGTAT
CGACACTTGTTAATTTGTGTCGATACTTTTGTCCAGAATGAATACCAAAAAGGGTGCAACCATAA
A
Found at i:2176116 original size:87 final size:87
Alignment explanation
Indices: 2176015--2176177 Score: 308
Period size: 87 Copynumber: 1.9 Consensus size: 87
2176005 AAATAAGTCA
*
2176015 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTAATAATATTT
2176080 CCGGTTAAATGTCTATTTTATT
66 CCGGTTAAATGTCTATTTTATT
*
2176102 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTAATAATATTT
2176167 CCGGTTAAATG
66 CCGGTTAAATG
2176178 ATATAACATT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTAATAATATTT
CCGGTTAAATGTCTATTTTATT
Found at i:2176149 original size:23 final size:23
Alignment explanation
Indices: 2176099--2176143 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2176089 TGTCTATTTT
*
2176099 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
2176122 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
2176144 TGTTATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:2177785 original size:14 final size:14
Alignment explanation
Indices: 2177766--2177804 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2177756 TAATGGGGAG
2177766 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
2177780 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
2177794 GAATCTCTGCA
1 TAATCCCTGCA
2177805 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:2182630 original size:12 final size:11
Alignment explanation
Indices: 2182615--2182678 Score: 71
Period size: 11 Copynumber: 5.8 Consensus size: 11
2182605 AAAAACACAC
2182615 AAAAAGAAAGTA
1 AAAAAGAAAG-A
2182627 AAAACAGAAAG-
1 AAAA-AGAAAGA
2182638 AAAAA-AAAGA
1 AAAAAGAAAGA
2182648 AAAAA-AAAGA
1 AAAAAGAAAGA
2182658 GAAAAAGAAAGA
1 -AAAAAGAAAGA
*
2182670 AGAAAGAAA
1 AAAAAGAAA
2182679 ACCGATCAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
9 4 0.09
10 11 0.23
11 17 0.36
12 9 0.19
13 6 0.13
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:2182637 original size:13 final size:12
Alignment explanation
Indices: 2182615--2182679 Score: 62
Period size: 13 Copynumber: 5.2 Consensus size: 12
2182605 AAAAACACAC
2182615 AAAAAGAAAGTAA
1 AAAAAGAAAG-AA
*
2182628 AAACAGAAAGAAA
1 AAAAAGAAAG-AA
2182641 AAAAAGAAA-AA
1 AAAAAGAAAGAA
2182652 AAAAGAGAAA-AA
1 AAAA-AGAAAGAA
2182664 GAAAGAAGAAAGAA
1 -AAA-AAGAAAGAA
2182678 AA
1 AA
2182680 CCGATCAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
11 6 0.13
12 7 0.16
13 29 0.64
14 3 0.07
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAGAA
Found at i:2182643 original size:25 final size:25
Alignment explanation
Indices: 2182615--2182679 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
2182605 AAAAACACAC
2182615 AAAAAGAAAGTAAAAACAGAAAGAAA-
1 AAAAAGAAAG-AAAAACAGAAA-AAAG
2182641 AAAAAGAAA-AAAAA-AGAGAAAAAG
1 AAAAAGAAAGAAAAACAGA-AAAAAG
2182665 AAAGAAGAAAGAAAA
1 AAA-AAGAAAGAAAA
2182680 CCGATCAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
23 6 0.17
24 10 0.29
25 6 0.17
26 13 0.37
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (25 bp):
AAAAAGAAAGAAAAACAGAAAAAAG
Found at i:2184578 original size:55 final size:54
Alignment explanation
Indices: 2184519--2184903 Score: 486
Period size: 55 Copynumber: 7.0 Consensus size: 54
2184509 GTTTTTTAGG
* * *
2184519 AACTAAGTCTGATTTTTAGAAGTTTCTTGACAATTTGTAATTGAGTTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTT-TAAATGAGTTTTTAAAGA
* * *
2184574 AACTAGGTATGATTTTCAGAAGTTTCTTGACAATTTTTAAATGAGTTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGA-TTTTAAATGAGTTTTTAAAGA
* * *
2184629 AACTAAGTCTGATTTATCAGAAGTTTCTTGACG--TTCAAATGAGATTTTAAATA
1 AACTAAGTCTGATTT-TCAGAAGTTTCTTGACGATTTTAAATGAGTTTTTAAAGA
* * *
2184682 AACTAATTCTGATTTTGAGAAGTTTCTTTACGATTTTTAAATGAGTTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGA-TTTTAAATGAGTTTTTAAAGA
* *
2184737 AACTAAGTCTGATTTTCAGAACTTTCTTGATGATTTTCAAATGAGTTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTT-AAATGAGTTTTTAAAGA
* * ** *
2184792 AACTAAGTCTGATTTTCAGAAGTTTCCTGATGATTTTAAATCTGTTTTTTTTAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTAAA--TGAGTTTTTAAAGA
* * *
2184848 AATTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGACTTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTT-AAATGAGTTTTTAAAGA
2184903 A
1 A
2184904 GTTATGCCTA
Statistics
Matches: 290, Mismatches: 31, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
52 15 0.05
53 31 0.11
54 7 0.02
55 169 0.58
56 65 0.22
57 3 0.01
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (54 bp):
AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTAAATGAGTTTTTAAAGA
Found at i:2184796 original size:163 final size:164
Alignment explanation
Indices: 2184519--2184903 Score: 504
Period size: 163 Copynumber: 2.3 Consensus size: 164
2184509 GTTTTTTAGG
* * * * *
2184519 AACTAAGTCTGATTTTTAGAAGTTTCTTGACAATTTGTAATTGAGTTTTTAAAGAAACTAGGTAT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGTTTTTAAAGAAACTAAGTAT
* *
2184584 GATTTTCAGAAGTTTCTTGACAATTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTATCAG
66 GATTTTCAGAACTTTCTTGACAATTTTCAAATGAGTTTTTAAAGAAACTAAGTCTGATTT-TCAG
* *
2184649 AAGTTTCTTGACG-TTCAAA-TGAGATTTTAAATA
130 AAGTTTCCTGACGATTCAAACTGAGATTTTAAAGA
* * * *
2184682 AACTAATTCTGATTTTGAGAAGTTTCTTTACGATTTTTAAATGAGTTTTTAAAGAAACTAAGTCT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGTTTTTAAAGAAACTAAGTAT
**
2184747 GATTTTCAGAACTTTCTTGATGATTTTCAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGA
66 GATTTTCAGAACTTTCTTGACAATTTTCAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGA
* * *** *
2184812 AGTTTCCTGATGATTTTAAATCTGTTTTTTTTAAGA
131 AGTTTCCTGACGA-TTCAAA-CTGAGATTTTAAAGA
* * * *
2184848 AATTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGACTTTTTAAAGAA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGTTTTTAAAGAA
2184904 GTTATGCCTA
Statistics
Matches: 191, Mismatches: 27, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
162 15 0.08
163 113 0.59
164 5 0.03
166 58 0.30
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (164 bp):
AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGTTTTTAAAGAAACTAAGTAT
GATTTTCAGAACTTTCTTGACAATTTTCAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGA
AGTTTCCTGACGATTCAAACTGAGATTTTAAAGA
Found at i:2185038 original size:105 final size:108
Alignment explanation
Indices: 2184732--2185144 Score: 290
Period size: 111 Copynumber: 3.8 Consensus size: 108
2184722 ATGAGTTTTT
* * ** *
2184732 AAAGAAACTAAGTCTGATTTTCAGAACTTTCTTGATGATTTTCAAATGAGTTTTTAAAGAA-ACT
1 AAAGAAATTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGACATATTAAAGAAGA-T
* * * ** * * * *** *
2184796 AAGTCTGATTTTCAGAAGTTTCCTGATGA-TTTTAAATCTGTTTTTTT
65 AAGCCTAATTTTTAGGGGTTGCTTGAT-ACTTTCAAA--T-AAATTTG
* * * *
2184843 TAAGAAATTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGACTTTTTAAAGAAGTTA
1 AAAGAAATTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGACATATTAAAGAAGATA
* **
2184908 TGCCTAATTTTTAGGGGTTTTTTGATACTTTCAAATAAATTTG
66 AGCCTAATTTTTAGGGGTTGCTTGATACTTTCAAATAAATTTG
* *
2184951 AAAGAAATTAAGTCAT-ATTTTC-GAAAGTTTCTTGATTA-TTT-AAATGA-ATATTAAATAAGA
1 AAAGAAATTAAGTC-TGATTTTCAG-AAGTTTCTTGATGATTTTCAAATGACATATTAAAGAAGA
** *
2185011 TAAGCCTAATTTTTAGGGGTTGCTTGATGTTTTCAAATGAATTTG
64 TAAGCCTAATTTTTAGGGGTTGCTTGATACTTTCAAATAAATTTG
** * * * * * * * *
2185056 AAAGAAGCTAAGCCTGTTTTTCAG-GGATTTCTTGATTA-TTTCCAATG-GAT-TTAAAAAAAGC
1 AAAGAAATTAAGTCTGATTTTCAGAAG-TTTCTTGATGATTTTCAAATGACATATT-AAAGAAGA
* * *
2185117 TAAGCCTGATTTTCAGGGGTTTCTTGAT
64 TAAGCCTAATTTTTAGGGGTTGCTTGAT
2185145 GTTTTAAATG
Statistics
Matches: 251, Mismatches: 41, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
104 2 0.01
105 80 0.32
106 44 0.18
107 4 0.02
108 35 0.14
109 2 0.01
110 1 0.00
111 83 0.33
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (108 bp):
AAAGAAATTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGACATATTAAAGAAGATA
AGCCTAATTTTTAGGGGTTGCTTGATACTTTCAAATAAATTTG
Found at i:2185068 original size:53 final size:53
Alignment explanation
Indices: 2184869--2185198 Score: 271
Period size: 53 Copynumber: 6.2 Consensus size: 53
2184859 ATTTTCAGAA
* * * *
2184869 GTTTCTTGATGATTTTCAAATGACTTTTTAAAGAAGTTATGCCTAATTTTTAGGG
1 GTTTCTTGATG-TTTTCAAATGA-ATTTGAAAGAAGCTAAGCCTAATTTTTAGGG
* ** * ** * * **
2184924 GTTTTTTGATACTTTCAAATAAATTTGAAAGAAATTAAG--TCATATTTTCGAAA
1 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCTAAT-TTTTAG-GG
* *
2184977 GTTTCTTGAT-TATTT-AAATGAATATT-AAATAAGATAAGCCTAATTTTTAGGG
1 GTTTCTTGATGT-TTTCAAATGAAT-TTGAAAGAAGCTAAGCCTAATTTTTAGGG
* *
2185029 GTTGCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCT-GTTTTTCAGGG
1 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCTAATTTTT-AGGG
* * * * * * *
2185082 ATTTCTTGAT-TATTTCCAATGGATTTAAAAAAAGCTAAGCCTGATTTTCAGGG
1 GTTTCTTGATGT-TTTCAAATGAATTTGAAAGAAGCTAAGCCTAATTTTTAGGG
* * *
2185135 GTTTCTTGATGTTTT-AAATGAATTTTTACAGAAGCTAAGCCTAATTTTTAGTG
1 GTTTCTTGATGTTTTCAAATGAA-TTTGAAAGAAGCTAAGCCTAATTTTTAGGG
2185188 GTTTCTTGATG
1 GTTTCTTGATG
2185199 AAAACTAAGA
Statistics
Matches: 218, Mismatches: 43, Indels: 30
0.75 0.15 0.10
Matches are distributed among these distances:
51 3 0.01
52 46 0.21
53 143 0.66
54 17 0.08
55 9 0.04
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (53 bp):
GTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCTAATTTTTAGGG
Found at i:2185282 original size:42 final size:42
Alignment explanation
Indices: 2185236--2185349 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 42
2185226 AAGGGTTTCT
*
2185236 TGATGAGCAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCA
1 TGATGAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCA
* * * *
2185278 TGATGTGTAAGGCATTCGGGCCATCTATAAGTCTTTCGAGCA
1 TGATGAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCA
* ** *
2185320 AGATGA-TAAGTCCTTCATGCCATCCATAAG
1 TGATGAGTAAGTCCTTCGGGCCATCAATAAG
2185350 ACCTTTGGGT
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
41 19 0.32
42 41 0.68
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (42 bp):
TGATGAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCA
Found at i:2185315 original size:20 final size:20
Alignment explanation
Indices: 2185244--2185315 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
2185234 CTTGATGAGC
* *
2185244 AAGTCCTTCGGGCCATCAAT
1 AAGTCTTTCGGGCCATCTAT
* * * *
2185264 AAGTCTTTCGAGCATGATGTGT
1 AAGTCTTTCGGGC--CATCTAT
* *
2185286 AAGGCATTCGGGCCATCTAT
1 AAGTCTTTCGGGCCATCTAT
2185306 AAGTCTTTCG
1 AAGTCTTTCG
2185316 AGCAAGATGA
Statistics
Matches: 36, Mismatches: 14, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
20 23 0.64
22 13 0.36
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (20 bp):
AAGTCTTTCGGGCCATCTAT
Found at i:2185430 original size:86 final size:86
Alignment explanation
Indices: 2185326--2185579 Score: 359
Period size: 85 Copynumber: 3.0 Consensus size: 86
2185316 AGCAAGATGA
** *
2185326 TAAGTCCTTCATGCCATCCATAAGACCTTTGGGTAGGATGTTTTCAACATTTCCTATTGCTCGAT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTTGGGAAGGATGTTTTCAACATTTCCT-TTGCTCGAT
*
2185391 TCATAACACTTCGAATCAGT-T
65 TCATAACACTTCGAATCAATCT
* * * * * *
2185412 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAATATTTCCTTCGCTAGACT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTTGGGAAGGATGTTTTCAACATTTCCTTTGCTCGATT
2185477 CATAACACTTCGAAT-AATCT
66 CATAACACTTCGAATCAATCT
* * *
2185497 TAAGTCTTTCGGGCCATCCATAAGACCTTTGGGAAGGACGTTTTCAACGTTTCCTTTGCTCGATT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTTGGGAAGGATGTTTTCAACATTTCCTTTGCTCGATT
*
2185562 CACAACACTTCGAATCAA
66 CATAACACTTCGAATCAA
2185580 CAATGCCCCA
Statistics
Matches: 147, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
84 2 0.01
85 93 0.63
86 52 0.35
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.33
Consensus pattern (86 bp):
TAAGTCCTTCGGGCCATCCATAAGACCTTTGGGAAGGATGTTTTCAACATTTCCTTTGCTCGATT
CATAACACTTCGAATCAATCT
Found at i:2185696 original size:60 final size:59
Alignment explanation
Indices: 2185546--2185699 Score: 218
Period size: 59 Copynumber: 2.6 Consensus size: 59
2185536 GTTTTCAACG
* * * *
2185546 TTTCCTTTGCTCGATTCACAACACTTCGAATCAACAATGCCCCACCAGAGGGGTTAACA
1 TTTCCTTTGCTCGATTCACAACACATCGAATCAGCAACGCCCAACCAGAGGGGTTAACA
* * * *
2185605 TTTCTTTTGCTCGATTCACAATACCTCGAATCAGCAACGCTCAACCAGAGGGGTTAACA
1 TTTCCTTTGCTCGATTCACAACACATCGAATCAGCAACGCCCAACCAGAGGGGTTAACA
*
2185664 TTTCCTATTGCTTGATTCACAACACATCGAATCAGC
1 TTTCCT-TTGCTCGATTCACAACACATCGAATCAGC
2185700 TTAAGTCATT
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 57 0.69
60 26 0.31
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (59 bp):
TTTCCTTTGCTCGATTCACAACACATCGAATCAGCAACGCCCAACCAGAGGGGTTAACA
Found at i:2185904 original size:42 final size:42
Alignment explanation
Indices: 2185858--2185967 Score: 134
Period size: 42 Copynumber: 2.6 Consensus size: 42
2185848 TCCTTCGGGC
* **
2185858 CATCAGTAGGTCTTTCGAGTTTGATGTGTAAGTCATTCGGAA
1 CATCAGTAAGTCTTTCGAGCATGATGTGTAAGTCATTCGGAA
* *
2185900 CATCAGTAAGTCTTTCGAGCATGATGTGTAAGTCCTTCGG-G
1 CATCAGTAAGTCTTTCGAGCATGATGTGTAAGTCATTCGGAA
*
2185941 CAATCTA-TAAGTCTTTCGAGCAAGATG
1 C-ATC-AGTAAGTCTTTCGAGCATGATG
2185968 ATAAGTCCTT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
41 1 0.02
42 58 0.97
43 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATGATGTGTAAGTCATTCGGAA
Found at i:2185931 original size:22 final size:22
Alignment explanation
Indices: 2185867--2185982 Score: 73
Period size: 20 Copynumber: 5.5 Consensus size: 22
2185857 CCATCAGTAG
**
2185867 GTCTTTCGAGTTTGATGTGTAA
1 GTCTTTCGAGCATGATGTGTAA
* * *
2185889 GTCATTCGGAACATCA---GTAA
1 GTCTTTC-GAGCATGATGTGTAA
2185909 GTCTTTCGAGCATGATGTGTAA
1 GTCTTTCGAGCATGATGTGTAA
* * * *
2185931 GTCCTTCGGGCA--ATCTATAA
1 GTCTTTCGAGCATGATGTGTAA
* *
2185951 GTCTTTCGAGCAAGATG-ATAA
1 GTCTTTCGAGCATGATGTGTAA
*
2185972 GTCCTTCGAGC
1 GTCTTTCGAGC
2185983 CATCCATAAG
Statistics
Matches: 72, Mismatches: 16, Indels: 13
0.71 0.16 0.13
Matches are distributed among these distances:
19 6 0.08
20 26 0.36
21 14 0.19
22 22 0.31
23 4 0.06
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (22 bp):
GTCTTTCGAGCATGATGTGTAA
Found at i:2185953 original size:20 final size:21
Alignment explanation
Indices: 2185906--2185982 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 21
2185896 GGAACATCAG
* * *
2185906 TAAGTCTTTCGAGCATGATGTG
1 TAAGTCCTTCGAGCAAGATG-A
* **
2185928 TAAGTCCTTCGGGCAATCT-A
1 TAAGTCCTTCGAGCAAGATGA
*
2185948 TAAGTCTTTCGAGCAAGATGA
1 TAAGTCCTTCGAGCAAGATGA
2185969 TAAGTCCTTCGAGC
1 TAAGTCCTTCGAGC
2185983 CATCCATAAG
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
20 15 0.35
21 14 0.33
22 14 0.33
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (21 bp):
TAAGTCCTTCGAGCAAGATGA
Found at i:2185992 original size:41 final size:42
Alignment explanation
Indices: 2185906--2185992 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 42
2185896 GGAACATCAG
* * * *
2185906 TAAGTCTTTCGAGCATGATGTGTAAGTCCTTCGGGCAATCTA
1 TAAGTCTTTCGAGCAAGATGTATAAGTCCTTCGAGCAATCCA
*
2185948 TAAGTCTTTCGAGCAAGATG-ATAAGTCCTTCGAGCCATCCA
1 TAAGTCTTTCGAGCAAGATGTATAAGTCCTTCGAGCAATCCA
2185989 TAAG
1 TAAG
2185993 ATTTTCAGGG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 21 0.52
42 19 0.47
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (42 bp):
TAAGTCTTTCGAGCAAGATGTATAAGTCCTTCGAGCAATCCA
Found at i:2187099 original size:20 final size:19
Alignment explanation
Indices: 2187065--2187105 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2187055 CTCTAAAAAT
* *
2187065 AATTTAAAAATGAAATGAA
1 AATTTAAAAAAGAAAAGAA
2187084 AATTTAAAAAAAGAAAAGAA
1 AATTT-AAAAAAGAAAAGAA
2187104 AA
1 AA
2187106 AATGTTGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.20
Consensus pattern (19 bp):
AATTTAAAAAAGAAAAGAA
Found at i:2191388 original size:2 final size:2
Alignment explanation
Indices: 2191381--2191405 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2191371 TTTTAATTAT
2191381 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2191406 GAAATCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2191921 original size:29 final size:30
Alignment explanation
Indices: 2191889--2191983 Score: 97
Period size: 29 Copynumber: 3.2 Consensus size: 30
2191879 ATAGGCGTTT
2191889 GACT-ATTTTGTAACTTTTAATAGTCGAGG
1 GACTCATTTTGTAACTTTTAATAGTCGAGG
**** *
2191918 GACTCAACAAAGTAACTTTCT-ATAGTTGAGG
1 GACTC-ATTTTGTAACTTT-TAATAGTCGAGG
*
2191949 GA-TCATTTTGTAACTTTTAATAGTCAAGG
1 GACTCATTTTGTAACTTTTAATAGTCGAGG
2191978 GACTCA
1 GACTCA
2191984 ATAAAGCATT
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
28 1 0.02
29 23 0.46
30 5 0.10
31 20 0.40
32 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.36
Consensus pattern (30 bp):
GACTCATTTTGTAACTTTTAATAGTCGAGG
Found at i:2191936 original size:31 final size:31
Alignment explanation
Indices: 2191898--2191989 Score: 100
Period size: 31 Copynumber: 3.0 Consensus size: 31
2191888 TGACTATTTT
*
2191898 GTAACTTTTAATAGTCGAGGGACTCAACAAA
1 GTAACTTTTAATAGTCGAGGGACTCAATAAA
* ***
2191929 GTAACTTTCT-ATAGTTGAGGGA-TC-ATTTT
1 GTAACTTT-TAATAGTCGAGGGACTCAATAAA
*
2191958 GTAACTTTTAATAGTCAAGGGACTCAATAAA
1 GTAACTTTTAATAGTCGAGGGACTCAATAAA
2191989 G
1 G
2191990 CATTTCCTAT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
28 1 0.02
29 19 0.40
30 4 0.09
31 22 0.47
32 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (31 bp):
GTAACTTTTAATAGTCGAGGGACTCAATAAA
Found at i:2192090 original size:19 final size:20
Alignment explanation
Indices: 2192066--2192105 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2192056 ATAATCATTC
2192066 ATAAATAAA-TAAATTTAAA
1 ATAAATAAATTAAATTTAAA
*
2192085 ATAAATAAATTTAATTTAAA
1 ATAAATAAATTAAATTTAAA
2192105 A
1 A
2192106 ATATTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAATAAATTAAATTTAAA
Found at i:2192104 original size:15 final size:15
Alignment explanation
Indices: 2192068--2192098 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2192058 AATCATTCAT
2192068 AAATAAATAAATTTA
1 AAATAAATAAATTTA
2192083 AAATAAATAAATTTA
1 AAATAAATAAATTTA
2192098 A
1 A
2192099 TTTAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAAATAAATTTA
Found at i:2193570 original size:16 final size:16
Alignment explanation
Indices: 2193549--2193580 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2193539 AATAAATAAG
2193549 CGAACATAAACGAACA
1 CGAACATAAACGAACA
2193565 CGAACATAAACGAACA
1 CGAACATAAACGAACA
2193581 AAAATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.06
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:2193661 original size:10 final size:10
Alignment explanation
Indices: 2193646--2193720 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
2193636 CATTTAATAA
2193646 ATAAACGAAC
1 ATAAACGAAC
2193656 ATAAACGAAC
1 ATAAACGAAC
* *
2193666 ACAAAC-ATAA
1 ATAAACGA-AC
2193676 ATGAACACGAAC
1 AT-AA-ACGAAC
*
2193688 ATAAATGAAC
1 ATAAACGAAC
2193698 ----ACGAAC
1 ATAAACGAAC
2193704 ATAAACGAAC
1 ATAAACGAAC
2193714 ATAAACG
1 ATAAACG
2193721 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 5 0.10
9 1 0.02
10 35 0.69
11 4 0.08
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.20, G:0.11, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:2193674 original size:16 final size:16
Alignment explanation
Indices: 2193653--2193719 Score: 89
Period size: 16 Copynumber: 4.2 Consensus size: 16
2193643 TAAATAAACG
2193653 AACATAAACGAACACA
1 AACATAAACGAACACA
* *
2193669 AACATAAATGAACACG
1 AACATAAACGAACACA
* *
2193685 AACATAAATGAACACG
1 AACATAAACGAACACA
*
2193701 AACATAAACGAACATA
1 AACATAAACGAACACA
2193717 AAC
1 AAC
2193720 GTTGGAGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.60, C:0.21, G:0.09, T:0.10
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:2193687 original size:32 final size:32
Alignment explanation
Indices: 2193642--2193714 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
2193632 CGTTCATTTA
2193642 ATAAAT-AA-ACGAACATAAACGAACACAAAC
1 ATAAATGAACACGAACATAAACGAACACAAAC
* *
2193672 ATAAATGAACACGAACATAAATGAACACGAAC
1 ATAAATGAACACGAACATAAACGAACACAAAC
*
2193704 ATAAACGAACA
1 ATAAATGAACA
2193715 TAAACGTTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 6 0.16
31 2 0.05
32 30 0.79
ACGTcount: A:0.60, C:0.19, G:0.10, T:0.11
Consensus pattern (32 bp):
ATAAATGAACACGAACATAAACGAACACAAAC
Found at i:2195244 original size:24 final size:24
Alignment explanation
Indices: 2195183--2195244 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
2195173 TATTAGGTTA
*
2195183 AACATAAATGAACGCACATAAACG
1 AACATAACTGAACGCACATAAACG
* *
2195207 AACATAACTAAACGCATATAAACG
1 AACATAACTGAACGCACATAAACG
*
2195231 AACATAACCGAACG
1 AACATAACTGAACG
2195245 TTCACGAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.53, C:0.23, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGCACATAAACG
Found at i:2196457 original size:13 final size:13
Alignment explanation
Indices: 2196439--2196468 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2196429 GACCCGACCC
2196439 GACCCGACCCGTT
1 GACCCGACCCGTT
2196452 GACCCGACCCGTT
1 GACCCGACCCGTT
2196465 GACC
1 GACC
2196469 GTTGACCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2198995 original size:24 final size:24
Alignment explanation
Indices: 2198963--2199054 Score: 132
Period size: 24 Copynumber: 3.8 Consensus size: 24
2198953 TTCGATTTGA
2198963 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
2198987 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
* * *
2199011 AATCTGATATGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
2199035 ATTCTGATCTGATACTTGAC
1 ATTCTGATCTGATACTTGAC
2199055 CTGATTTATG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
23 1 0.02
24 57 0.97
25 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:2201173 original size:5 final size:5
Alignment explanation
Indices: 2201163--2201187 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2201153 ACCGGTCATA
2201163 ACCCG ACCCG ACCCG ACCCG ACCCG
1 ACCCG ACCCG ACCCG ACCCG ACCCG
2201188 TTGACCCAAC
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:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:2201199 original size:13 final size:13
Alignment explanation
Indices: 2201177--2201237 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 13
2201167 GACCCGACCC
*
2201177 GACCCGACCCGTT
1 GACCCAACCCGTT
2201190 GACCCAACCCGACCTGTT
1 GACCCAA--C--CC-GTT
*
2201208 GACCCGACCCGTT
1 GACCCAACCCGTT
*
2201221 GACCCAGCCCGTT
1 GACCCAACCCGTT
2201234 GACC
1 GACC
2201238 GTTGACCCGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
13 24 0.62
14 2 0.05
15 1 0.03
16 1 0.03
17 2 0.05
18 9 0.23
ACGTcount: A:0.18, C:0.46, G:0.21, T:0.15
Consensus pattern (13 bp):
GACCCAACCCGTT
Found at i:2201199 original size:18 final size:18
Alignment explanation
Indices: 2201172--2201218 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
2201162 AACCCGACCC
2201172 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
* *
2201190 GACCCAACCCGACCTGTT
1 GACCCGACCCGACCCGTT
2201208 GACCCGACCCG
1 GACCCGACCCG
2201219 TTGACCCAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.19, C:0.49, G:0.21, T:0.11
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:2201241 original size:7 final size:7
Alignment explanation
Indices: 2201229--2201260 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
2201219 TTGACCCAGC
2201229 CCGTTGA
1 CCGTTGA
2201236 CCGTTGA
1 CCGTTGA
2201243 CCCGTTGA
1 -CCGTTGA
2201251 CCGTTGA
1 CCGTTGA
2201258 CCG
1 CCG
2201261 GCGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:2201248 original size:15 final size:15
Alignment explanation
Indices: 2201228--2201269 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
2201218 GTTGACCCAG
2201228 CCCGTTGACCGTTGA
1 CCCGTTGACCGTTGA
2201243 CCCGTTGACCGTTGA
1 CCCGTTGACCGTTGA
2201258 CCGGCGTTGACC
1 CC--CGTTGACC
2201270 ACTGTTGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 17 0.68
17 8 0.32
ACGTcount: A:0.12, C:0.36, G:0.29, T:0.24
Consensus pattern (15 bp):
CCCGTTGACCGTTGA
Found at i:2203772 original size:24 final size:24
Alignment explanation
Indices: 2203740--2203831 Score: 132
Period size: 24 Copynumber: 3.8 Consensus size: 24
2203730 TTCGATTTGA
2203740 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
2203764 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
* *
2203788 AATCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
2203812 ATTCTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
2203832 CTGATTTATG
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
23 1 0.02
24 58 0.97
25 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:2210318 original size:43 final size:43
Alignment explanation
Indices: 2210257--2210346 Score: 171
Period size: 43 Copynumber: 2.1 Consensus size: 43
2210247 ATATGATCCT
2210257 TGGCGATAGTAGGAGGATTGACCAGAACTATGGCGCAATTGTA
1 TGGCGATAGTAGGAGGATTGACCAGAACTATGGCGCAATTGTA
*
2210300 TGGCGATAGTAGGAGGATTGACCATAACTATGGCGCAATTGTA
1 TGGCGATAGTAGGAGGATTGACCAGAACTATGGCGCAATTGTA
2210343 TGGC
1 TGGC
2210347 AACAGTTGGG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.24
Consensus pattern (43 bp):
TGGCGATAGTAGGAGGATTGACCAGAACTATGGCGCAATTGTA
Found at i:2213233 original size:45 final size:45
Alignment explanation
Indices: 2213204--2213512 Score: 413
Period size: 45 Copynumber: 6.9 Consensus size: 45
2213194 ACTATAACAT
* * * *
2213204 CTTTTTTGTTGATAATGCACCCATATGCATTTTAACTATAGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATA
* *
2213249 CTTTTCTATTGATAATGTACCCATATACATTTCAACCATAGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATA
* *
2213294 CTTTTCTGTTGATAATGGACCCATATACATTTCAACCATAGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATA
* *
2213339 TTTTTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATA
* * * ** * *
2213384 ATTTTCTGTTGATAATGCACACATATGTATTTCAACTCTAGCATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATA
* * *
2213429 CTTTTATGTTGATAATGTACCCATATACATTTCAACTAAAATATGA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTAT-A
*
2213475 -TTTTCTATTGATAATGTACCCATATACATTTCAACTAT
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTAT
2213513 GGCATCATTT
Statistics
Matches: 232, Mismatches: 31, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
45 231 1.00
46 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATA
Found at i:2213534 original size:135 final size:135
Alignment explanation
Indices: 2213212--2213550 Score: 378
Period size: 135 Copynumber: 2.5 Consensus size: 135
2213202 ATCTTTTTTG
* * * * * * **** * * *
2213212 TTGATAATGCACCCATATGCATTTTAACTATAGTATACTTTTCTATTGATAATGTACCCATATAC
1 TTGATAATGTACCCATATACATTTCAACCATAGCATAATTTTCTGCCAATAATGCACACATATGC
* * * *
2213277 ATTTCAACCATAGTATACTTTTCTGTTGATAATGGACCCATATACATTTCAACCATAGTATATTT
66 ATTTCAACCATAGCATACTTTTATGTTGATAATGGACCCATATACATTTCAACCAAAATATATTT
*
2213342 TTCTG
131 TTCTA
* *** *
2213347 TTGATAATGTACCCATATACATTTCAACCATAGTATAATTTTCTGTTGATAATGCACACATATGT
1 TTGATAATGTACCCATATACATTTCAACCATAGCATAATTTTCTGCCAATAATGCACACATATGC
* *
2213412 ATTTCAACTC-TAGCATACTTTTATGTTGATAATGTACCCATATACATTTCAACTAAAATATGA-
66 ATTTCAAC-CATAGCATACTTTTATGTTGATAATGGACCCATATACATTTCAACCAAAATAT-AT
2213475 TTTTCTA
129 TTTTCTA
* * *
2213482 TTGATAATGTACCCATATACATTTCAACTATGGCATCA-TTTCATGCCAATAATGCACACATATG
1 TTGATAATGTACCCATATACATTTCAACCATAGCATAATTTTC-TGCCAATAATGCACACATATG
2213546 CATTT
65 CATTT
2213551 TTCTTTTATA
Statistics
Matches: 176, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
134 4 0.02
135 170 0.97
136 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (135 bp):
TTGATAATGTACCCATATACATTTCAACCATAGCATAATTTTCTGCCAATAATGCACACATATGC
ATTTCAACCATAGCATACTTTTATGTTGATAATGGACCCATATACATTTCAACCAAAATATATTT
TTCTA
Found at i:2218568 original size:26 final size:26
Alignment explanation
Indices: 2218539--2218608 Score: 63
Period size: 25 Copynumber: 2.7 Consensus size: 26
2218529 GGGTTTTTCG
2218539 TTGACCATTGACTTTGAATTTG-TCTT
1 TTGACCATTGACTTTGAATTTGAT-TT
*** *
2218565 TTGATTGTTG-CTTTGACTTTGATTT
1 TTGACCATTGACTTTGAATTTGATTT
* *
2218590 TTTACCATTAACTTTGAAT
1 TTGACCATTGACTTTGAAT
2218609 CATTGACTTT
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
25 17 0.53
26 15 0.47
ACGTcount: A:0.20, C:0.13, G:0.14, T:0.53
Consensus pattern (26 bp):
TTGACCATTGACTTTGAATTTGATTT
Found at i:2219184 original size:29 final size:29
Alignment explanation
Indices: 2219142--2219246 Score: 120
Period size: 29 Copynumber: 3.6 Consensus size: 29
2219132 GGCATAACCC
* **
2219142 CATCCTGGTTCTGCATGGGATTAAATTTA
1 CATCCTGATTCTGCATGGGATTAAATCCA
*
2219171 CATCCTGATTCTGCATGGGATTAAATCCC
1 CATCCTGATTCTGCATGGGATTAAATCCA
* *
2219200 CGTCCTAATTCTGCATGGGATTAAATCCA
1 CATCCTGATTCTGCATGGGATTAAATCCA
** * *
2219229 TGTCTTGATTCTACATGG
1 CATCCTGATTCTGCATGG
2219247 ATCCTCTACG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (29 bp):
CATCCTGATTCTGCATGGGATTAAATCCA
Found at i:2220957 original size:19 final size:19
Alignment explanation
Indices: 2220933--2220969 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2220923 ATCTACCACA
*
2220933 TTAATAGCACCTATTTGAT
1 TTAATAACACCTATTTGAT
2220952 TTAATAACACCTATTTGA
1 TTAATAACACCTATTTGA
2220970 GCTTCAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (19 bp):
TTAATAACACCTATTTGAT
Found at i:2222870 original size:24 final size:24
Alignment explanation
Indices: 2222829--2222885 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
2222819 TTTATGTTTA
2222829 TTTACATTCATTCATTTGT-TTTCG
1 TTTACATTCATTCATTTGTCTTT-G
* **
2222853 TTTACATTCGTTTGTTTGTCTTTG
1 TTTACATTCATTCATTTGTCTTTG
2222877 TTTATCATT
1 TTTA-CATT
2222886 TTAACGAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.14, C:0.14, G:0.11, T:0.61
Consensus pattern (24 bp):
TTTACATTCATTCATTTGTCTTTG
Found at i:2222946 original size:31 final size:31
Alignment explanation
Indices: 2222906--2222972 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
2222896 AATTTAAACA
*
2222906 AACAAGAACAAGCTACAGTCCTTAACGAAAG
1 AACACGAACAAGCTACAGTCCTTAACGAAAG
* * *
2222937 AACACGAACAAGCTACATTCCTTAACGTACG
1 AACACGAACAAGCTACAGTCCTTAACGAAAG
2222968 AACAC
1 AACAC
2222973 AAATTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.27, G:0.13, T:0.15
Consensus pattern (31 bp):
AACACGAACAAGCTACAGTCCTTAACGAAAG
Found at i:2236414 original size:21 final size:19
Alignment explanation
Indices: 2236381--2236421 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
2236371 TACATCAAGG
2236381 TCTTTGTGGAGGCCATGAAA
1 TCTTTGTGGAGGCCAT-AAA
*
2236401 TCTTTCGTTGAGGCCATAAA
1 TCTTT-GTGGAGGCCATAAA
2236421 T
1 T
2236422 TCCTGTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (19 bp):
TCTTTGTGGAGGCCATAAA
Found at i:2249383 original size:22 final size:22
Alignment explanation
Indices: 2249358--2249402 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2249348 ATCTAGAAGA
2249358 TTAGCTCGTTGGCAGATCTTGT
1 TTAGCTCGTTGGCAGATCTTGT
*
2249380 TTAGCTGGTTGGCAGATCTTGT
1 TTAGCTCGTTGGCAGATCTTGT
2249402 T
1 T
2249403 ATCAGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.13, C:0.16, G:0.29, T:0.42
Consensus pattern (22 bp):
TTAGCTCGTTGGCAGATCTTGT
Found at i:2252506 original size:136 final size:136
Alignment explanation
Indices: 2252262--2252987 Score: 1137
Period size: 136 Copynumber: 5.3 Consensus size: 136
2252252 GGAAACAAAA
* *
2252262 ATCCTTAGATAATCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATTTTAAAGATGG
1 ATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCATGTTATCTCAAATATTTTAAAGATGG
* * *
2252327 CTAGATGTCCTCATCACGAAGGAACAATGTCATATACCAATCAGAACTCCTCATCACGAAGGAGT
66 CCAGATGTCCTCATCAAGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCACGAAGGAGT
*
2252392 CGCATC
131 CGCGTC
* *
2252398 ATCCTTAGATAACTAGACGTCCTCATCATGAAGGAACCATGTTATCTCAAATATTTTAAAGATGG
1 ATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCATGTTATCTCAAATATTTTAAAGATGG
* * * * *
2252463 CCAGGTCTCCTCATCACGAAAGAACAATGTCATATACCAATCAGAACTCCTCATCACGAAGGAGT
66 CCAGATGTCCTCATCAAGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCACGAAGGAGT
2252528 CGCGTC
131 CGCGTC
*
2252534 ATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACTATGTTATCTCAAATATTTTAAAGATGG
1 ATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCATGTTATCTCAAATATTTTAAAGATGG
* * **
2252599 CCAGATGTCCTCATCAAAAAGGAACAATGTCATCTACCAATCAGAACTCCTTATCACGAAAAAGT
66 CCAGATGTCCTCATCAAGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCACGAAGGAGT
2252664 CGCGTC
131 CGCGTC
*** *
2252670 AAAGTTAGATAACCAGACGTCCTCATCATGAAGGAACCATGTTATCTCAAATATTTTAAAGATGG
1 ATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCATGTTATCTCAAATATTTTAAAGATGG
* *
2252735 CCAGTTGTCCTCATCAAGAAGGAACAATGTCATCTACCAATCAGAACTCCTCGTCACGAAGGAGT
66 CCAGATGTCCTCATCAAGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCACGAAGGAGT
*
2252800 CGTGTC
131 CGCGTC
* *
2252806 ATCCTTAAATAACCAGACGTCCTCATCATGAAGGAACCATGTTATCTCAAATATTTTAAAGATGG
1 ATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCATGTTATCTCAAATATTTTAAAGATGG
* * * *
2252871 TCAGATGTCCTCATCAAGAAGGAACAATGTCATCTACCAATAAGAACTTCTCATCACGAAGAAGT
66 CCAGATGTCCTCATCAAGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCACGAAGGAGT
2252936 CGCGTC
131 CGCGTC
* * * *
2252942 ATCCTTAGATAACCAGACGTTCTCATCCCGAATGAACCGTGTTATC
1 ATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCATGTTATC
2252988 ACTATTTATC
Statistics
Matches: 540, Mismatches: 50, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
136 540 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (136 bp):
ATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCATGTTATCTCAAATATTTTAAAGATGG
CCAGATGTCCTCATCAAGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCACGAAGGAGT
CGCGTC
Done.