Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 86 of 344
Found at i:28571671 original size:8 final size:8
Alignment explanation
Indices: 28571658--28571683 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
28571648 AAGTCAAACC
28571658 ACTATGCT
1 ACTATGCT
28571666 ACTATGCT
1 ACTATGCT
28571674 ACTATGCT
1 ACTATGCT
28571682 AC
1 AC
28571684 CGCTGCGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (8 bp):
ACTATGCT
Found at i:28573443 original size:31 final size:31
Alignment explanation
Indices: 28573405--28573468 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
28573395 CCTTTTCATA
*
28573405 TTTCATATTTCATAACACTGGGTCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
28573436 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
28573467 TT
1 TT
28573469 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:28573737 original size:23 final size:23
Alignment explanation
Indices: 28573683--28573801 Score: 202
Period size: 23 Copynumber: 5.1 Consensus size: 23
28573673 CCTAGCCTCT
*
28573683 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
28573706 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
28573730 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
* *
28573753 TTCAATAACTGCGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
28573776 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
28573799 TTT
1 TTT
28573802 TGCACTTCCT
Statistics
Matches: 90, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
23 68 0.76
24 22 0.24
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:28573878 original size:20 final size:20
Alignment explanation
Indices: 28573852--28573916 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
28573842 ATGAATACAC
28573852 CATGTGCATATCATACATAT
1 CATGTGCATATCATACATAT
* *
28573872 TATGTGCATATCATACATGT
1 CATGTGCATATCATACATAT
*
28573892 CATGTGCATATCATACATAC
1 CATGTGCATATCATACATAT
28573912 CATGT
1 CATGT
28573917 TTATCAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
CATGTGCATATCATACATAT
Found at i:28578630 original size:20 final size:20
Alignment explanation
Indices: 28578603--28578649 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
28578593 TTATGATTAC
28578603 ACCATGTGCATATCATACAT
1 ACCATGTGCATATCATACAT
*
28578623 ATCATGTGCATATCATACAT
1 ACCATGTGCATATCATACAT
28578643 ACCATGT
1 ACCATGT
28578650 TTATCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (20 bp):
ACCATGTGCATATCATACAT
Found at i:28578728 original size:25 final size:25
Alignment explanation
Indices: 28578686--28578733 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28578676 ATATTTAAAC
* * *
28578686 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
28578711 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
28578734 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:28586772 original size:39 final size:39
Alignment explanation
Indices: 28586728--28586871 Score: 225
Period size: 39 Copynumber: 3.7 Consensus size: 39
28586718 TGTGTGAGAT
*
28586728 TTATATTCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
28586767 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
28586806 TTATATCCGGGCTAAATCCCAAAGGCATTCGTGCTAGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* **
28586845 TTATATCCGGGCAAAGTTTCGAAGGCA
1 TTATATCCGGGCTAAGTCCCGAAGGCA
28586872 ATTATGTTGG
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 96 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:28604356 original size:29 final size:29
Alignment explanation
Indices: 28604322--28604387 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
28604312 ATCAACCGCG
28604322 CACACTTAGTGCCATGCACTTT-AAACTCA
1 CACACTTAGTGCCATGCA-TTTCAAACTCA
**
28604351 CACACTTAGTGCCATGCATTTCAAGTTCA
1 CACACTTAGTGCCATGCATTTCAAACTCA
28604380 CACACTTA
1 CACACTTA
28604388 CCTTTTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.29
Consensus pattern (29 bp):
CACACTTAGTGCCATGCATTTCAAACTCA
Found at i:28604507 original size:175 final size:174
Alignment explanation
Indices: 28604209--28604537 Score: 568
Period size: 175 Copynumber: 1.9 Consensus size: 174
28604199 TACTCAAGGT
* * *
28604209 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCGTTCATATAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATATAAATAATTTATA
*
28604274 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
28604339 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCACAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCACAC
* *
28604383 ACTTACCTTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTAT
1 ACTTACC-TTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATATAAATAATTTAT
*
28604448 AGAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCATGCACACTTAGTGCCATG
65 AGAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATG
* *
28604513 TACTTTAAACTCGCACACTTAGTGC
130 CACTTTAAACTCACACACTTAGTGC
28604538 TGTACAATTT
Statistics
Matches: 145, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
174 7 0.05
175 138 0.95
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATATAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCACAC
Found at i:28604530 original size:29 final size:30
Alignment explanation
Indices: 28604496--28604568 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
28604486 AATCAACCAT
*
28604496 GCACACTTAGTGCCATGTAC-TTTAAACTC
1 GCACACTTAGTGCCATGTACATTTAAACCC
28604525 GCACACTTAGTG-C-TGTACAATTTAAACCC
1 GCACACTTAGTGCCATGTAC-ATTTAAACCC
28604554 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
28604569 ATCTCATGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
27 5 0.13
28 1 0.03
29 32 0.82
30 1 0.03
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (30 bp):
GCACACTTAGTGCCATGTACATTTAAACCC
Found at i:28612943 original size:28 final size:28
Alignment explanation
Indices: 28612903--28612981 Score: 113
Period size: 28 Copynumber: 2.8 Consensus size: 28
28612893 GCAATCCAAT
* * *
28612903 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
28612931 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
28612959 ATGGCACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
28612982 CGAATGATTC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:28621953 original size:17 final size:16
Alignment explanation
Indices: 28621931--28621964 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28621921 GGGGATGGTG
28621931 TTTGTTTGATGTTTATT
1 TTTGTTTG-TGTTTATT
*
28621948 TTTGTTTGTTTTTATT
1 TTTGTTTGTGTTTATT
28621964 T
1 T
28621965 CATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGTTTGTGTTTATT
Found at i:28623930 original size:79 final size:81
Alignment explanation
Indices: 28623786--28624003 Score: 238
Period size: 79 Copynumber: 2.7 Consensus size: 81
28623776 GAATCACGTA
* * * *
28623786 CCTTCGGAAT-TTAA-CCGGATATAGCAACTCATTCA-AATGCCTTCGGGACATT-GCCCGG-TT
1 CCTTCGG-ATCTTAACCCGGATATAGTAACTTA-GCACAATGCCTTCGGGAC-TTAGCCCGGAAT
28623846 ATAGTAACTCGCACAAATG
63 ATAGTAACTCGCACAAATG
* *
28623865 CCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCACCAATGCCTTCGGG-CTTAGCCCGGAAT-
1 CCTTC-GGATCTTAACCCGGATATAGTAACTTAGCA-CAATGCCTTCGGGACTTAGCCCGGAATA
28623926 TAGTAACTCGCACAAATG
64 TAGTAACTCGCACAAATG
** * *
28623944 CCTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAATGCCTTCGGGACTTAGCCCGGA
28624004 CATCATTCGA
Statistics
Matches: 117, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
78 7 0.06
79 68 0.58
80 42 0.36
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (81 bp):
CCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAATGCCTTCGGGACTTAGCCCGGAATATA
GTAACTCGCACAAATG
Found at i:28624003 original size:40 final size:40
Alignment explanation
Indices: 28623800--28624003 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
28623790 CGGAATTTAA
* ***
28623800 CCGGATATAGCAACTCATTCAAATGCCTTCGGGACATT-GC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGAC-TTAGC
* *
28623840 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28623880 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
28623919 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
28623959 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
28623999 CCGGA
1 CCGGA
28624004 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 34 0.24
40 93 0.66
41 12 0.09
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:28639929 original size:92 final size:89
Alignment explanation
Indices: 28639747--28640342 Score: 525
Period size: 92 Copynumber: 7.0 Consensus size: 89
28639737 CCTGTCACAT
* * *
28639747 ATACACTTTCACATTCAT--CATCGGCCATTTAGGCCTATCATA-TATACAC-TTCACATTCATC
1 ATACACTTTCACATTCATCACATCGGCTA-TTAGGCTTATCACACTATACACTTTCACATTCATC
* *
28639808 ACATCGGCCATTAGGCCTT-TAATAT
65 ACATCGG-CATTAGGCCTTATCATAC
28639833 ATACACTTTCACATTCATCACATCGGCTATTAGGACTTATCACACGTATTACACTTTCACATTCA
1 ATACACTTTCACATTCATCACATCGGCTATTAGG-CTTATCACAC-TA-TACACTTTCACATTCA
* *
28639898 TCACGTCGGCATTAGGCCTTATCACAC
63 TCACATCGGCATTAGGCCTTATCATAC
*
28639925 ATACACTTTCACATTCATCACGTCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCAT
1 ATACACTTTCACATTCATCACATCGGCTATTAGG-CTTATCACAC-TATACACTTTCACATTCAT
28639990 CACATCGGCTATTAGGCCTTATACATATATC
64 CACATCGGC-ATTAGGCCTTAT-C--ATA-C
28640021 ATACACTTTCACATTCATCACATCGGCTATTAGGCATTATCACAC-ATATCACCTTTCACATTC-
1 ATACACTTTCACATTCATCACATCGGCTATTAGGC-TTATCACACTATA-CA-CTTTCACATTCA
*
28640084 TCACGTC-GCTATTAGGCCTTATCA-AC
63 TCACATCGGC-ATTAGGCCTTATCATAC
28640110 ATTACA-TTT--CATTCAT-ACATCGGCTATTAGGC-TAT-A-AC-ATA-ACTTTCACATT-ATC
1 A-TACACTTTCACATTCATCACATCGGCTATTAGGCTTATCACACTATACACTTTCACATTCATC
28640165 ACATCGGC-TTA-GCC-TAT--TAC
65 ACATCGGCATTAGGCCTTATCATAC
* * *
28640185 A-ACACTTTCACATTCATCACATC-GC-ATTAGCACTTATCA-A-TAATATACATTCA-ATTCAT
1 ATACACTTTCACATTCATCACATCGGCTATTAG-GCTTATCACACT-ATACACTTTCACATTCAT
28640244 -ACATC-GCATTA-GCTCTTATC--A-
64 CACATCGGCATTAGGC-CTTATCATAC
* * *
28640265 ATATACTTTCAC-TTCA-CACATCGGCCA-T--CCTTAT----CTATACACTTTCACATTCA-CA
1 ATACACTTTCACATTCATCACATCGGCTATTAGGCTTATCACACTATACACTTTCACATTCATCA
*
28640320 -ATC-GCATTAGG-CTTATCACAC
66 CATCGGCATTAGGCCTTATCATAC
28640341 AT
1 AT
28640343 TACATCTCTT
Statistics
Matches: 444, Mismatches: 21, Indels: 100
0.79 0.04 0.18
Matches are distributed among these distances:
73 9 0.02
74 21 0.05
75 17 0.04
76 15 0.03
77 16 0.04
78 7 0.02
79 38 0.09
80 20 0.05
81 14 0.03
82 5 0.01
83 1 0.00
84 3 0.01
86 34 0.08
87 12 0.03
88 15 0.03
89 5 0.01
90 7 0.02
91 42 0.09
92 78 0.18
93 2 0.00
94 18 0.04
95 11 0.02
96 54 0.12
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (89 bp):
ATACACTTTCACATTCATCACATCGGCTATTAGGCTTATCACACTATACACTTTCACATTCATCA
CATCGGCATTAGGCCTTATCATAC
Found at i:28639991 original size:47 final size:47
Alignment explanation
Indices: 28639742--28640173 Score: 508
Period size: 44 Copynumber: 9.7 Consensus size: 47
28639732 TCGGCCCTGT
*
28639742 CACATATACACTTTCACATTCAT--CATCGGCCATTTAGGCC-TAT--
1 CACATATACACTTTCACATTCATCACATCGGCTA-TTAGGCCTTATCA
* *
28639785 CATATATACAC-TTCACATTCATCACATCGGCCATTAGGCCTT-T-A
1 CACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCA
* *
28639829 -ATATATACACTTTCACATTCATCACATCGGCTATTAGGACTTATCA
1 CACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCA
* *
28639875 CACGTATTACACTTTCACATTCATCACGTCGGC-ATTAGGCCTTATCA
1 CACATA-TACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCA
*
28639922 CAC--ATACACTTTCACATTCATCACGTCGGCTATTAGGCCTTATCA
1 CACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCA
28639967 CACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATACA
1 CACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTAT-CA
* * *
28640015 TATATCATACACTTTCACATTCATCACATCGGCTATTAGGCATTATCA
1 CACAT-ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCA
*
28640063 CACATAT-CACCTTTCACATTC-TCACGTC-GCTATTAGGCCTTATCA
1 CACATATACA-CTTTCACATTCATCACATCGGCTATTAGGCCTTATCA
28640108 -ACAT-TACA-TTT--CATTCAT-ACATCGGCTATTAGG-C-TAT-A
1 CACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCA
28640146 -AC--ATA-ACTTTCACATT-ATCACATCGGCT
1 CACATATACACTTTCACATTCATCACATCGGCT
28640174 TAGCCTATTA
Statistics
Matches: 350, Mismatches: 16, Indels: 50
0.84 0.04 0.12
Matches are distributed among these distances:
36 1 0.00
37 5 0.01
38 5 0.01
39 16 0.05
40 10 0.03
41 10 0.03
42 14 0.04
43 29 0.08
44 71 0.20
45 35 0.10
46 9 0.03
47 71 0.20
48 35 0.10
49 39 0.11
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.33
Consensus pattern (47 bp):
CACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCA
Found at i:28640215 original size:38 final size:39
Alignment explanation
Indices: 28640015--28640289 Score: 148
Period size: 38 Copynumber: 6.8 Consensus size: 39
28640005 GCCTTATACA
* *
28640015 TATATCATACACTTTCACATTCATCACATCGGCTATTAGGCAT
1 TATAACATA-ACTTTCACATTCATCACATCGGC-ATTA-GC-C
*
28640058 TATCACACATATCACCTTTCACATTC-TCACGTC-GCTATTAGGCC
1 TAT-A-ACATA--A-CTTTCACATTCATCACATCGGC-ATTA-GCC
* *
28640102 TTATCAACATTACATTT--CATTCAT-ACATCGGCTATTAGGC
1 -TAT-AACATAAC-TTTCACATTCATCACATCGGC-ATTAGCC
28640142 TATAACATAACTTTCACATT-ATCACATCGGC-TTAGCC
1 TATAACATAACTTTCACATTCATCACATCGGCATTAGCC
*
28640179 TATTACA-ACACTTTCACATTCATCACATC-GCATTAGCAC
1 TATAACATA-ACTTTCACATTCATCACATCGGCATTAGC-C
* *
28640218 TTATCAATAATATACATTCA-ATTCAT-ACATC-GCATTAGCTC
1 -TAT-AA-CATA-ACTTTCACATTCATCACATCGGCATTAGC-C
*
28640259 T-TATCAATATACTTTCAC-TTCA-CACATCGGC
1 TATAAC-ATA-ACTTTCACATTCATCACATCGGC
28640290 CATCCTTATC
Statistics
Matches: 192, Mismatches: 17, Indels: 50
0.74 0.07 0.19
Matches are distributed among these distances:
36 1 0.01
37 27 0.14
38 42 0.22
39 19 0.10
40 15 0.08
41 24 0.12
42 11 0.06
43 10 0.05
44 5 0.03
45 19 0.10
46 8 0.04
47 11 0.06
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.34
Consensus pattern (39 bp):
TATAACATAACTTTCACATTCATCACATCGGCATTAGCC
Found at i:28643303 original size:25 final size:24
Alignment explanation
Indices: 28643266--28643315 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
28643256 AAAGAATTCG
28643266 CACACACACAGTGCCTCTAATCATT
1 CACACACACAGTG-CTCTAATCATT
* *
28643291 CACACACATAGTGCTCTATTCATT
1 CACACACACAGTGCTCTAATCATT
28643315 C
1 C
28643316 GTATTACACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.30, C:0.34, G:0.08, T:0.28
Consensus pattern (24 bp):
CACACACACAGTGCTCTAATCATT
Found at i:28643611 original size:40 final size:39
Alignment explanation
Indices: 28643477--28643670 Score: 237
Period size: 40 Copynumber: 4.9 Consensus size: 39
28643467 CGAATACACG
* * * * *
28643477 TCACCAGCATGATTGCTCTTCGGACCTAGCCCGGACATA
1 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACA
* * ** * *
28643516 ACACCAGCATGAATGCTCTTCGGGTTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACA
* *
28643555 TCA-TAGCACGAATGCTCTTCGGAACTTATCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGG-ACTTAGCCCGGATACA
28643594 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATACA
28643634 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
1 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGAT
28643671 TTAGTAACTC
Statistics
Matches: 135, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
38 17 0.13
39 48 0.36
40 68 0.50
41 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACA
Found at i:28643668 original size:80 final size:79
Alignment explanation
Indices: 28643477--28643749 Score: 259
Period size: 80 Copynumber: 3.5 Consensus size: 79
28643467 CGAATACACG
* * * * * * *
28643477 TCACCAGCATGATTGCTCTTC-GGACCTAGCCCGGACATAACACCAGCATGAATGCTCTTCGGGT
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCACTAGCATGAATGCTCTTCGGGC
* *
28643541 TTAGCACGGATATA
66 TTAGCCCGGATACA
* * * *
28643555 TCA-TAGCACGAATGCTCTTCGGAACTTATCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCACTAGCATGAATGCTCTTCGGG-
28643619 CTTAGCCCGGATACA
65 CTTAGCCCGGATACA
* * * **
28643634 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAATGC-CTTCGGG
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATA-TCACTAGCATGAATGCTCTTCGGG
* **
28643698 TCTTAGTCCGGATATGG
65 -CTTAGCCCGGATA-CA
* *
28643715 TCACTTAGCA-CAAAGC-CTTCGGGACTTAGCCCGGA
1 TCAC-TAGCATGAATGCTCTTCGGGACTTAGCCCGGA
28643750 CATCATTCAA
Statistics
Matches: 161, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
77 14 0.09
78 38 0.24
79 15 0.09
80 69 0.43
81 20 0.12
82 5 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCACTAGCATGAATGCTCTTCGGGC
TTAGCCCGGATACA
Found at i:28643695 original size:40 final size:40
Alignment explanation
Indices: 28643490--28643749 Score: 223
Period size: 40 Copynumber: 6.6 Consensus size: 40
28643480 CCAGCATGAT
* * * * *
28643490 TGCTCTTC-GGACCTAGCCCGGACATA-ACACCAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATAGTCACTAGCA-CAA
* *
28643529 TGCTCTTCGGG-TTTAGCACGGATATA-TCA-TAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC-AA
* * * *
28643567 TGCTCTTCGGAACTTATCCCGGATACA-TCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATAGTCACTAGCA-CAA
* *
28643607 TGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATAGTCACTAGCA-CAA
* * *
28643647 TGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATATAGTCACTAGCA-CAA
* * *
28643688 TGC-CTTCGGGTCTTAGTCCGGATATGGTCACTTAGCACAA
1 TGCTCTTCGGGACTTAGCCCGGATATAGTCAC-TAGCACAA
*
28643728 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
28643750 CATCATTCAA
Statistics
Matches: 184, Mismatches: 30, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
38 16 0.09
39 35 0.19
40 117 0.64
41 16 0.09
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAA
Found at i:28644097 original size:29 final size:29
Alignment explanation
Indices: 28644058--28644136 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
28644048 CTTAATAATC
*
28644058 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
* *
28644088 AACTCGCACACTTAGTGCTATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
28644117 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
28644137 ATCTCACAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 3 0.07
29 36 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:28644194 original size:42 final size:41
Alignment explanation
Indices: 28644118--28644218 Score: 184
Period size: 42 Copynumber: 2.4 Consensus size: 41
28644108 TGCATTTCAA
28644118 GCCCGCACACTTAGTGCCAATCTCACAACCTGAACACTTATT
1 GCCCGCACACTTAGTG-CAATCTCACAACCTGAACACTTATT
28644160 GCCCGCACACTTAGTGCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCAATCTCACAACC-TGAACACTTATT
28644202 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
28644219 TGAAAACCAA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
41 13 0.22
42 45 0.78
ACGTcount: A:0.27, C:0.36, G:0.15, T:0.23
Consensus pattern (41 bp):
GCCCGCACACTTAGTGCAATCTCACAACCTGAACACTTATT
Found at i:28646122 original size:37 final size:37
Alignment explanation
Indices: 28646061--28646139 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
28646051 TTATTACGAA
* * * *
28646061 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGAACAAAATCCCCACACGAAGTCATCGG
*
28646098 GTCTTACCCGAACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGAACAAAATCCCCACACGAAGTCATCGG
28646135 GTCTT
1 GTCTT
28646140 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGAACAAAATCCCCACACGAAGTCATCGG
Found at i:28646395 original size:47 final size:47
Alignment explanation
Indices: 28646256--28646495 Score: 272
Period size: 45 Copynumber: 5.4 Consensus size: 47
28646246 GCCTTTCGGA
* * * * * * *
28646256 CTTATCACATTTATGCACTTTCACATCCATTA-ATTGGCCACT-CGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28646301 CCTGTCACATATATACACTTT-ACATTCATCACATCGGCCA-TAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28646346 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28646393 CTTATCACATATATACACTTTCACATTCATCACA-CGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28646439 CTTA-CACACATATACAC-TTCACATTCATCAC-TC--CTA-TA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28646479 CTTAT-ACATATATACAC
1 CTTATCACATATATACAC
28646496 ATACATTCAC
Statistics
Matches: 174, Mismatches: 15, Indels: 17
0.84 0.07 0.08
Matches are distributed among these distances:
40 17 0.10
41 2 0.01
42 3 0.02
44 24 0.14
45 57 0.33
46 33 0.19
47 38 0.22
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28646622 original size:117 final size:106
Alignment explanation
Indices: 28646417--28646624 Score: 263
Period size: 117 Copynumber: 1.9 Consensus size: 106
28646407 ACACTTTCAC
*
28646417 ATTCATCACACGGCTATTAGGCCTTACACACATATACACTTCACATTCATCACTCCTATAGCCTT
1 ATTCATCACACGGCTATTAGGCCTTACACACATATACACTTCACATTCATCACTCCCATAGCCTT
*
28646482 ATACATATATACACATACATTCACATCCTATTACAATAACA
66 ATACATATATACACACACATTCACATCCTATTACAATAACA
* *
28646523 ATTCATCACATCGGCTATTAGGCCTTATTACATATATACATATACTTTCACATTCATCACATCGG
1 ATTCATCACA-CGGCTATTAGGCCTTA-CACACATATAC----AC-TTCACATTCATCAC-TC--
* *
28646588 CCATTAGCCTTATACATATATACATACACTTTCACAT
56 CCA-TAGCCTTATACATATATACACACACATTCACAT
28646625 TCATCACATC
Statistics
Matches: 85, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
106 10 0.12
107 16 0.19
108 9 0.11
112 2 0.02
113 14 0.16
114 2 0.02
116 2 0.02
117 30 0.35
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (106 bp):
ATTCATCACACGGCTATTAGGCCTTACACACATATACACTTCACATTCATCACTCCCATAGCCTT
ATACATATATACACACACATTCACATCCTATTACAATAACA
Found at i:28646623 original size:49 final size:50
Alignment explanation
Indices: 28646306--28646758 Score: 352
Period size: 49 Copynumber: 9.2 Consensus size: 50
28646296 CTCGCCCTGT
28646306 CACATAT--ATACACTTT-ACATTCATCACATCGGCCA-TAGGCCTTAT-
1 CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATA
*
28646351 CACATAT--ATACACTTTCACATTCATCGCATCGGCCATTAGGCCTTAT-
1 CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATA
*
28646398 CACATAT--ATACACTTTCACATTCATCACA-CGGCTATTAGGCC-T-TA
1 CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATA
* *
28646443 CACACAT--ATACAC-TTCACATTCATCAC-TC--CTA-TA-GCCTTATA
1 CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATA
* * * ** * * **
28646485 CATATATACACATACA-TTCACATCCTATTACAATAACAATTCATCACA-TCGGCTATTAGG
1 CACATAT--ACATACACTT-TCA--C-ATT-C-ATCAC-A-TCGGC-CATTAGGC-CTTATA
*
28646545 C-CTTATTACATATATACATATACTTTCACATTCATCACATCGGCCATTA-GCCTTATA
1 CACATA-TAC----ATAC----ACTTTCACATTCATCACATCGGCCATTAGGCCTTATA
*
28646602 CATATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-
1 CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATA
28646651 CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-
1 CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATA
* *
28646700 TACATAT--ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCA
1 CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-A
28646749 CACATATACA
1 CACATATACA
28646759 CTCTCTTGGC
Statistics
Matches: 337, Mismatches: 29, Indels: 78
0.76 0.07 0.18
Matches are distributed among these distances:
40 3 0.01
41 3 0.01
42 10 0.03
44 16 0.05
45 29 0.09
46 36 0.11
47 79 0.23
49 89 0.26
50 10 0.03
51 2 0.01
52 4 0.01
53 4 0.01
55 2 0.01
57 8 0.02
58 10 0.03
59 8 0.02
60 6 0.02
61 4 0.01
62 5 0.01
63 3 0.01
64 1 0.00
66 3 0.01
67 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.32
Consensus pattern (50 bp):
CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATA
Found at i:28646750 original size:96 final size:96
Alignment explanation
Indices: 28646523--28646750 Score: 361
Period size: 96 Copynumber: 2.3 Consensus size: 96
28646513 TACAATAACA
* *
28646523 ATTCATCACATCGGCTATTAGGCCTTATTACATATATACATATACTTTCACATTCATCACATCGG
1 ATTCATCACATCGGCTATTAGGCCTTA-T-CACATATACATACACTTTCACATTCATCACATCGG
28646588 CCATTAGCCTTATACATATATACATACACTTTCAC
64 CCATTAGCCTTATACA-ATATA-ATACACTTTCAC
*
28646623 ATTCATCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCGGCC
1 ATTCATCACATCGGCTATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCGGCC
28646688 ATTAGGCCTTATTAC-ATAT-ATACACTTTCAC
66 ATTA-GCCTTA-TACAATATAATACACTTTCAC
28646719 ATTCATCACATCGGCTATTAGGCCTTATCACA
1 ATTCATCACATCGGCTATTAGGCCTTATCACA
28646751 CATATACACT
Statistics
Matches: 122, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
96 43 0.35
98 43 0.35
99 7 0.06
100 29 0.24
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (96 bp):
ATTCATCACATCGGCTATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCGGCC
ATTAGCCTTATACAATATAATACACTTTCAC
Found at i:28650739 original size:27 final size:27
Alignment explanation
Indices: 28650709--28650885 Score: 167
Period size: 27 Copynumber: 6.5 Consensus size: 27
28650699 AAATTGTACA
* *
28650709 GCACTAAGGGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTG
** *
28650736 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGATTTGACTATG-TG
* * *
28650763 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTG
* * *
28650790 GCACTAAGAGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGA-TTTGACTATGTG
* *
28650818 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGATTTGACTATGTG
* * * *
28650845 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGATTTGACTATGTG
*
28650872 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
28650886 GGCTCAATAT
Statistics
Matches: 123, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 101 0.82
28 22 0.18
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTG
Found at i:28650822 original size:82 final size:81
Alignment explanation
Indices: 28650709--28650864 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
28650699 AAATTGTACA
* * * *
28650709 GCACTAAGGGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGAGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
28650773 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28650790 GCACTAAGAGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGAGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
28650855 TGCGAGTTGA
65 TGCGAATTGA
28650865 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.77
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGAGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28658415 original size:27 final size:25
Alignment explanation
Indices: 28658380--28658492 Score: 100
Period size: 27 Copynumber: 4.2 Consensus size: 25
28658370 AGCATGGCTG
*
28658380 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAG-CA
*
28658406 CCAGATACAGATAATCGTGGCAAAGCTA
1 CCAGA-ACAGATAAT-GTGGCAGAGC-A
*
28658434 CCAGAACAGATCTATGTGGCAGAGCCA
1 CCAGAACAGAT-AATGTGGCAGAG-CA
* *
28658461 CCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATAA--TGTGGCAGAG-CA
28658489 CCAG
1 CCAG
28658493 GACGCTTCCT
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
26 6 0.08
27 35 0.48
28 32 0.44
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (25 bp):
CCAGAACAGATAATGTGGCAGAGCA
Found at i:28658463 original size:55 final size:54
Alignment explanation
Indices: 28658380--28658492 Score: 147
Period size: 55 Copynumber: 2.1 Consensus size: 54
28658370 AGCATGGCTG
* *
28658380 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAA-TCGTGGCAAAGCTA
1 CCAGAACAGATAATGTGACAGAGCCACCAGAT-CAGATAATTCGTGGCAAAGCCA
* * * *
28658434 CCAGAACAGATCTATGTGGCAGAGCCACCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGAT-AATGTGACAGAGCCACCAGATCAGATAATTCGTGGCAAAGCCA
28658489 CCAG
1 CCAG
28658493 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
54 18 0.35
55 33 0.65
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATCAGATAATTCGTGGCAAAGCCA
Found at i:28660919 original size:15 final size:16
Alignment explanation
Indices: 28660899--28660931 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28660889 AATTTATTCT
*
28660899 AAAG-AAAATAAAAGA
1 AAAGAAAAAAAAAAGA
28660914 AAAGAAAAAAAAAAGA
1 AAAGAAAAAAAAAAGA
28660930 AA
1 AA
28660932 TCTAATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAGAAAAAAAAAAGA
Found at i:28666289 original size:39 final size:39
Alignment explanation
Indices: 28666263--28666381 Score: 211
Period size: 39 Copynumber: 3.1 Consensus size: 39
28666253 GTCCAGCACG
*
28666263 TAGCCTGCGGACCTAAAGTCCGGATATAATTCTCGCATA
1 TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCATA
*
28666302 TAGCCTGCGGACATGAAGTCCGGATATAATTCTCGCATA
1 TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCATA
*
28666341 TAGCCTGTGGACCTGAAGTCCGGATATAATTCTCGCATA
1 TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCATA
28666380 TA
1 TA
28666382 TATATTCACA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 76 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.27
Consensus pattern (39 bp):
TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCATA
Found at i:28668110 original size:12 final size:12
Alignment explanation
Indices: 28668093--28668117 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28668083 GTATATAGGG
28668093 TGGCAAAATGGC
1 TGGCAAAATGGC
28668105 TGGCAAAATGGC
1 TGGCAAAATGGC
28668117 T
1 T
28668118 TTACAAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.20
Consensus pattern (12 bp):
TGGCAAAATGGC
Found at i:28672519 original size:39 final size:40
Alignment explanation
Indices: 28672418--28672602 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 40
28672408 TCGAATGATG
* * *
28672418 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
28672457 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
28672498 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
28672537 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * * *
28672576 AACCGGGCTATGTCCCAAAAGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
28672603 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 35 0.29
40 77 0.63
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:28672624 original size:79 final size:79
Alignment explanation
Indices: 28672471--28672635 Score: 183
Period size: 79 Copynumber: 2.1 Consensus size: 79
28672461 GGACTAAGAT
* * * **
28672471 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCAAAAGCATTGGAACGAGTTACTAA
* *
28672536 ATCTGGGTTAAGTC
66 ATCTCGGTTAAATC
* *
28672550 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCAAAAGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCAAAAGCATTGGAACGAGTTA-C
* *
28672613 TATATC-CGGTTAAATT
63 TAAATCTCGGTTAAATC
28672629 CCGAAGG
1 CCGAAGG
28672636 TACGTGATTC
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.68
80 21 0.29
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCAAAAGCATTGGAACGAGTTACTAA
ATCTCGGTTAAATC
Found at i:28680611 original size:39 final size:40
Alignment explanation
Indices: 28680511--28680695 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
28680501 TCGAATGATG
* * * *
28680511 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
28680551 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
** * *
28680591 TTTGGGCTAAG-CCCGAAGGCATTGGCGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28680630 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
28680671 -CCGGGCTATGTCCCGAAAGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28680696 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
39 32 0.27
40 78 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28680717 original size:79 final size:79
Alignment explanation
Indices: 28680564--28680728 Score: 183
Period size: 79 Copynumber: 2.1 Consensus size: 79
28680554 GGACTAAGAT
*** * **
28680564 CCGAAGGCATTTGTGCGAGTTACTAATTTTGGGCTAAGCCCGAAGGCATTGGCGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAAGCATTGGAACGAGTTACTAA
*
28680629 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
28680643 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAAGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAAGCATTGGAACGAGTTA-C
* *
28680706 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
28680722 CCGAAGG
1 CCGAAGG
28680729 TACGTGATTC
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.65
80 23 0.32
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAAGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:28684738 original size:15 final size:15
Alignment explanation
Indices: 28684720--28684753 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28684710 CACCACTAGG
28684720 TTTTGCACTCTGAAA
1 TTTTGCACTCTGAAA
* *
28684735 TTTTTCTCTCTGAAA
1 TTTTGCACTCTGAAA
28684750 TTTT
1 TTTT
28684754 TCTTTCTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.53
Consensus pattern (15 bp):
TTTTGCACTCTGAAA
Found at i:28684765 original size:14 final size:15
Alignment explanation
Indices: 28684727--28684756 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28684717 AGGTTTTGCA
28684727 CTCTGAAATTTTTCT
1 CTCTGAAATTTTTCT
28684742 CTCTGAAATTTTTCT
1 CTCTGAAATTTTTCT
28684757 TTCTCAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (15 bp):
CTCTGAAATTTTTCT
Found at i:28700751 original size:28 final size:26
Alignment explanation
Indices: 28700720--28700785 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 26
28700710 TTGAAATCAT
*
28700720 CTTTTCCAAAACCAAATTTTAGGAAAAA
1 CTTTTCAAAAACCAAATTTTA--AAAAA
* * *
28700748 CTTTTTAAAACCCTAATTTTAAAAAA
1 CTTTTCAAAAACCAAATTTTAAAAAA
*
28700774 ATTTTCAAAAAC
1 CTTTTCAAAAAC
28700786 TCATTCAACA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
26 14 0.45
28 17 0.55
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (26 bp):
CTTTTCAAAAACCAAATTTTAAAAAA
Found at i:28701647 original size:27 final size:27
Alignment explanation
Indices: 28701617--28701692 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
28701607 AACAGTATCA
28701617 TGGCAAAGCCACCAGTATCAGAATATG
1 TGGCAAAGCCACCAGTATCAGAATATG
* **
28701644 TGGCTAAGCCACCAG-GGCAGCAAATATG
1 TGGCAAAGCCACCAGTATCAG--AATATG
*
28701672 TGG-AAAGCCACTAGTAT-AGAA
1 TGGCAAAGCCACCAGTATCAGAA
28701693 CTTCTTCCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
25 2 0.05
26 3 0.08
27 25 0.64
28 9 0.23
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (27 bp):
TGGCAAAGCCACCAGTATCAGAATATG
Found at i:28704346 original size:43 final size:43
Alignment explanation
Indices: 28704298--28704384 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
28704288 ATCACATGTA
* *
28704298 TCGCATCCATTATGAACTCGGACCACTCAACGAGCTCGGATGC
1 TCGCATCCATAATGAACTCGGACCACTCAACGAGCTCAGATGC
*
28704341 TCGCATCCATAATGAACTCGGACCACTCAATGAGCTCAGATGC
1 TCGCATCCATAATGAACTCGGACCACTCAACGAGCTCAGATGC
28704384 T
1 T
28704385 ACATATATCA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.22
Consensus pattern (43 bp):
TCGCATCCATAATGAACTCGGACCACTCAACGAGCTCAGATGC
Found at i:28712924 original size:79 final size:81
Alignment explanation
Indices: 28712788--28712970 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
28712778 TCGAATGATG
* *
28712788 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
28712852 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
28712867 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
28712929 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
28712947 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28712971 TGAACGAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.65
80 30 0.34
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:28712986 original size:40 final size:40
Alignment explanation
Indices: 28712789--28712972 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
28712779 CGAATGATGT
* * * *
28712789 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
28712829 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
28712869 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28712907 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28712948 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
28712973 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 34 0.27
40 80 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:28712994 original size:79 final size:79
Alignment explanation
Indices: 28712841--28713005 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
28712831 GGACTAAGAT
* **
28712841 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
28712906 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
28712920 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
28712983 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
28712999 CCGAAGG
1 CCGAAGG
28713006 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:28715486 original size:68 final size:70
Alignment explanation
Indices: 28715333--28715490 Score: 171
Period size: 68 Copynumber: 2.3 Consensus size: 70
28715323 CTAGCCAATT
* * *
28715333 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCATCACTTGGGATGACACATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGGATCACACATGCGACCTAGCTACA
**
28715398 TTTATC
65 CATATC
* * * *
28715404 TCTCTCGTAACTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTACT
1 TATCTCGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGGATCACACATGCGACCTAGCTAC-
*
28715466 ACATA-G
64 ACATATC
28715472 TATCTCGTAGCTCTCTTGT
1 TATCTCGTAGCTCTCTTGT
28715491 ACACATGATG
Statistics
Matches: 73, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
68 38 0.52
69 3 0.04
70 2 0.03
71 30 0.41
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (70 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGGATCACACATGCGACCTAGCTACAC
ATATC
Found at i:28720868 original size:27 final size:27
Alignment explanation
Indices: 28720838--28721015 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28720828 ATATTGAGTC
* * * *
28720838 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28720865 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28720892 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28720920 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28720947 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28720974 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28721001 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28721016 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28720977 original size:82 final size:81
Alignment explanation
Indices: 28720859--28721014 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28720849 TGCTATATAA
* *
28720859 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28720924 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28720941 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28721005 CACTTAGTGC
65 CACTTAGTGC
28721015 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28724705 original size:22 final size:20
Alignment explanation
Indices: 28724660--28724713 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
28724650 TTACAACAAT
*
28724660 AATAGTACATATAATTTAAA
1 AATAGTACATATAATTAAAA
*
28724680 AATAGTACCATTATTATTAAAA
1 AATAGTA-CA-TATAATTAAAA
28724702 AATAGTTACATA
1 AATAG-TACATA
28724714 AATCTCTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 7 0.24
21 4 0.14
22 16 0.55
23 2 0.07
ACGTcount: A:0.52, C:0.07, G:0.06, T:0.35
Consensus pattern (20 bp):
AATAGTACATATAATTAAAA
Found at i:28725154 original size:21 final size:21
Alignment explanation
Indices: 28725130--28725171 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28725120 TTAAGGTGTA
28725130 TGCCTAGCAATTGCACCTTAG
1 TGCCTAGCAATTGCACCTTAG
*
28725151 TGCCTAGCAATTGTACCTTAG
1 TGCCTAGCAATTGCACCTTAG
28725172 CGCCAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (21 bp):
TGCCTAGCAATTGCACCTTAG
Found at i:28727342 original size:26 final size:26
Alignment explanation
Indices: 28727306--28727359 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
28727296 GTTGTGGTTG
*
28727306 ATAGATTAACTAAATCAGCGCATTTT
1 ATAGATTAACTAAATCAGCCCATTTT
28727332 ATAGATTAACTAAATCAGCCCATTTT
1 ATAGATTAACTAAATCAGCCCATTTT
28727358 AT
1 AT
28727360 TCTAGTACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (26 bp):
ATAGATTAACTAAATCAGCCCATTTT
Found at i:28730754 original size:93 final size:93
Alignment explanation
Indices: 28730621--28730792 Score: 256
Period size: 93 Copynumber: 1.8 Consensus size: 93
28730611 ACCCATAAGT
* * * * *
28730621 GAACTCGGACTCAACTCAATGAGCTTGGGCGTTCGAATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTTCGACATTCGAATCCATAAGTGAACTCAGACTCAACTCAA
28730686 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
28730714 GAACTCGAACTCAACTCAACGAG-TTCCGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGAACTCAACTCAACGAGCTT-CGACATTCGAATCCATAAGTGAACTCAGACTCAACTCA
*
28730778 ACGAGTTCGGATGCC
65 ACGAGCTCGGATGCC
28730793 CAAATACCCT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
92 2 0.03
93 68 0.97
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTTCGACATTCGAATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:28730775 original size:46 final size:44
Alignment explanation
Indices: 28730613--28730786 Score: 152
Period size: 46 Copynumber: 3.8 Consensus size: 44
28730603 TGTAACCCAC
* * * *
28730613 CCATAAGTGAACTCGGACTCAACTCAATGAGCTTGGGCGTTCGAAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TT-CGCATTCGCAT
* * * *
28730659 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGCATTCGC-A--T
* *** *
28730705 ACATCTCTCGAACTCGAACTCAACTCAACGAGTTCCGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTT-CG-CATTCGCAT
28730752 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
28730787 GATGCCCAAA
Statistics
Matches: 99, Mismatches: 22, Indels: 15
0.73 0.16 0.11
Matches are distributed among these distances:
44 4 0.04
45 3 0.03
46 58 0.59
47 27 0.27
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (44 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGCATTCGCAT
Found at i:28730807 original size:46 final size:45
Alignment explanation
Indices: 28730664--28730807 Score: 105
Period size: 46 Copynumber: 3.1 Consensus size: 45
28730654 CGAATCCATA
* * * * *
28730664 AGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA-ATAC-CCT
* * * * * *
28730711 -CTCGAACTCGAACTCAACTCAACGAGTTCCGACATTCGC-AT-CCAT
1 AGT-GAACTCGGACTCAACTCAACGAGTT-CG-GATGCCCAATACCCT
28730756 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATACCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AATACCCT
28730803 AGTGA
1 AGTGA
28730808 TATGTCACTT
Statistics
Matches: 72, Mismatches: 17, Indels: 17
0.68 0.16 0.16
Matches are distributed among these distances:
44 4 0.06
45 3 0.04
46 33 0.46
47 27 0.38
48 2 0.03
49 3 0.04
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAATACCCT
Found at i:28733276 original size:27 final size:27
Alignment explanation
Indices: 28733243--28733306 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
28733233 CCCCAAGGTA
*
28733243 GGTAAAATGACCAAAATACCCCTATAG
1 GGTAAAATGACCAAAATACCCCTAGAG
* ***
28733270 GGTAAAATGACTATTTTACCCCTAGAG
1 GGTAAAATGACCAAAATACCCCTAGAG
28733297 GGT-AAATGAC
1 GGTAAAATGAC
28733307 TGATTTGTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 7 0.22
27 25 0.78
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (27 bp):
GGTAAAATGACCAAAATACCCCTAGAG
Found at i:28733312 original size:27 final size:27
Alignment explanation
Indices: 28733259--28733312 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
28733249 ATGACCAAAA
*
28733259 TACCCCTATAGGGTAAAATGACTATTT
1 TACCCCTAGAGGGTAAAATGACTATTT
28733286 TACCCCTAGAGGGT-AAATGACTGATTT
1 TACCCCTAGAGGGTAAAATGACT-ATTT
28733313 GTGCTATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (27 bp):
TACCCCTAGAGGGTAAAATGACTATTT
Found at i:28733506 original size:20 final size:20
Alignment explanation
Indices: 28733483--28733611 Score: 186
Period size: 20 Copynumber: 6.5 Consensus size: 20
28733473 GTGGACCTAC
28733483 TGATGGCTTTGTGCCACTAT
1 TGATGGCTTTGTGCCACTAT
*
28733503 TGATGGCTTTGTGCCGCTAT
1 TGATGGCTTTGTGCCACTAT
* *
28733523 TGATGTCTTTGTGCCACTAG
1 TGATGGCTTTGTGCCACTAT
*
28733543 TGATGGCTTTGTGCCACTAG
1 TGATGGCTTTGTGCCACTAT
*
28733563 TGATGGCTTTGTGACACTAT
1 TGATGGCTTTGTGCCACTAT
* *
28733583 TGATGGCTTTGTGCCCCTAC
1 TGATGGCTTTGTGCCACTAT
*
28733603 CGATGGCTT
1 TGATGGCTT
28733612 CGAGCCGCTA
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 98 1.00
ACGTcount: A:0.14, C:0.21, G:0.27, T:0.38
Consensus pattern (20 bp):
TGATGGCTTTGTGCCACTAT
Found at i:28733622 original size:20 final size:20
Alignment explanation
Indices: 28733584--28733623 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28733574 TGACACTATT
* *
28733584 GATGGCTTTGTGCCCCTACC
1 GATGGCTTCGAGCCCCTACC
*
28733604 GATGGCTTCGAGCCGCTACC
1 GATGGCTTCGAGCCCCTACC
28733624 CATAGCTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.28, T:0.25
Consensus pattern (20 bp):
GATGGCTTCGAGCCCCTACC
Found at i:28733632 original size:60 final size:60
Alignment explanation
Indices: 28733508--28733635 Score: 139
Period size: 60 Copynumber: 2.1 Consensus size: 60
28733498 ACTATTGATG
* * * ** * * *** *
28733508 GCTTTGTGCCGCTATTGATGTCTTTGTGCCACTAGTGATGGCTTTGTGCCACTAGTGATG
1 GCTTTGTGACACTATTGATGGCTTTGTGCCACTACCGATGGCTTCGAGCCACTACCCATA
* *
28733568 GCTTTGTGACACTATTGATGGCTTTGTGCCCCTACCGATGGCTTCGAGCCGCTACCCATA
1 GCTTTGTGACACTATTGATGGCTTTGTGCCACTACCGATGGCTTCGAGCCACTACCCATA
28733628 GCTTTGTG
1 GCTTTGTG
28733636 CCATATACTG
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.14, C:0.24, G:0.27, T:0.35
Consensus pattern (60 bp):
GCTTTGTGACACTATTGATGGCTTTGTGCCACTACCGATGGCTTCGAGCCACTACCCATA
Found at i:28733676 original size:26 final size:26
Alignment explanation
Indices: 28733647--28733722 Score: 91
Period size: 26 Copynumber: 2.9 Consensus size: 26
28733637 CATATACTGA
* *
28733647 TACTGGCAGCTTTGCTGTGTTACTAT
1 TACTGGCAGCTTTGCTGCGATACTAT
*
28733673 TACTGGCAGCTTTGCTGCGATATTAT
1 TACTGGCAGCTTTGCTGCGATACTAT
* *
28733699 TACTAGG-AGCTATGCTGCAATACT
1 TACT-GGCAGCTTTGCTGCGATACT
28733723 GGTGTGTTGG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 41 0.95
27 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (26 bp):
TACTGGCAGCTTTGCTGCGATACTAT
Found at i:28735498 original size:42 final size:43
Alignment explanation
Indices: 28735438--28735568 Score: 124
Period size: 43 Copynumber: 3.1 Consensus size: 43
28735428 GTCATAGGAT
*
28735438 TCGATATGTG-TTATCGTGTAAGACCATGTCTGGGACGTTAGCA
1 TCGATATTTGATT-TCGTGTAAGACCATGTCTGGGACGTTAGCA
* * * *
28735481 TTG-TATTTGATTTCGTGTAAGACCCTTTCTGGGACAGTGA-CA
1 TCGATATTTGATTTCGTGTAAGACCATGTCTGGGAC-GTTAGCA
* * * * * *
28735523 TCGATATTTGATTACATGTAAGACCACGTTTAGGACGTTGGCA
1 TCGATATTTGATTTCGTGTAAGACCATGTCTGGGACGTTAGCA
28735566 TCG
1 TCG
28735569 TACGAGCTTT
Statistics
Matches: 69, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
42 32 0.46
43 37 0.54
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (43 bp):
TCGATATTTGATTTCGTGTAAGACCATGTCTGGGACGTTAGCA
Found at i:28745397 original size:17 final size:17
Alignment explanation
Indices: 28745377--28745410 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28745367 GGGTTACCTT
28745377 TGACACCCACCAAGAAA
1 TGACACCCACCAAGAAA
28745394 TGACACCCACCAAGAAA
1 TGACACCCACCAAGAAA
28745411 GATTTGGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.35, G:0.12, T:0.06
Consensus pattern (17 bp):
TGACACCCACCAAGAAA
Found at i:28763953 original size:47 final size:47
Alignment explanation
Indices: 28763899--28764090 Score: 262
Period size: 47 Copynumber: 4.1 Consensus size: 47
28763889 TTAGGATTTT
** * *
28763899 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
28763946 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
28763993 ATGTGATGAATGTGAGCATGCAGATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
28764040 ATGTGATGAAT-AGAACATGCATATAT-TGGTAAAGCCAAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
28764085 ATGTGA
1 ATGTGA
28764091 AATATGTATG
Statistics
Matches: 130, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
45 21 0.16
46 11 0.08
47 98 0.75
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:28763999 original size:22 final size:22
Alignment explanation
Indices: 28763928--28764046 Score: 59
Period size: 22 Copynumber: 5.1 Consensus size: 22
28763918 GTATATATGA
28763928 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* * *
28763950 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCCG-A-ATGGC-CA-ATGT
28763975 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* *
28763997 GATGAATGTG-AGCAT-G-CAGATGTGT
1 GAT-AA-G-GCCGAATGGCCA-A--TGT
28764022 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
28764044 GAT
1 GAT
28764047 GAATAGAACA
Statistics
Matches: 71, Mismatches: 10, Indels: 32
0.63 0.09 0.28
Matches are distributed among these distances:
22 20 0.28
23 17 0.24
24 17 0.24
25 17 0.24
ACGTcount: A:0.32, C:0.13, G:0.31, T:0.24
Consensus pattern (22 bp):
GATAAGGCCGAATGGCCAATGT
Found at i:28764379 original size:36 final size:36
Alignment explanation
Indices: 28764297--28764404 Score: 189
Period size: 36 Copynumber: 3.0 Consensus size: 36
28764287 GGAAATATAT
28764297 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT-TG
28764334 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTG
* *
28764370 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
28764405 CGTCTGAGCT
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
36 35 0.51
37 34 0.49
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.26
Consensus pattern (36 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTG
Found at i:28765833 original size:79 final size:80
Alignment explanation
Indices: 28765673--28766098 Score: 648
Period size: 79 Copynumber: 5.4 Consensus size: 80
28765663 TGAAATTGAG
28765673 AGTGATAT-TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGT-CCG
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
* *
28765736 AAGAGCATTTGTGTT
66 AAGAGCATTCGTGCT
* *
28765751 AGTGATATATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTAGTGATGTATCCGAGCTAAGTCCCG
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
28765815 AAGAGCATTCGTGCT
66 AAGAGCATTCGTGCT
* *
28765830 AGTGATGTATCCGGGCTAAGT-CCGAAGAGCATTTGTGCTAGTGATATATCCGGGCTAAGTCCCG
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
28765894 AAGAGCATTCGTGCT
66 AAGAGCATTCGTGCT
* * *
28765909 AGTGATATATTC-GGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTCCCG
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
28765973 AAGAGCATTCGTGCT
66 AAGAGCATTCGTGCT
* * * * * *
28765988 AGTGATGTATCCAGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATTCGTGCTAA-CCCCG
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
28766052 AAGAGCATTCGTGCT
66 AAGAGCATTCGTGCT
* * *
28766067 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
28766099 ATCATGCTGG
Statistics
Matches: 317, Mismatches: 27, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
78 53 0.17
79 223 0.70
80 41 0.13
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
AAGAGCATTCGTGCT
Found at i:28766110 original size:40 final size:40
Alignment explanation
Indices: 28765673--28766098 Score: 648
Period size: 39 Copynumber: 10.8 Consensus size: 40
28765663 TGAAATTGAG
28765673 AGTGATAT-TCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
28765712 AGTGATATATCCGGGCTAAGT-CCGAAGAGCATTTGTGTT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
28765751 AGTGATATATCCGGGCTAAGT-CCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
28765790 AGTGATGTATCCGAGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
28765830 AGTGATGTATCCGGGCTAAGT-CCGAAGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
28765869 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
28765909 AGTGATATATTC-GGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
28765948 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
28765988 AGTGATGTATCCAGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
28766028 AGTGATATATTCGTGCTAA-CCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
28766067 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
28766099 ATCATGCTGG
Statistics
Matches: 353, Mismatches: 29, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
39 186 0.53
40 167 0.47
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:28770173 original size:47 final size:47
Alignment explanation
Indices: 28770119--28770311 Score: 287
Period size: 47 Copynumber: 4.1 Consensus size: 47
28770109 TAGGATTTTC
** * *
28770119 TGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCAA
1 TGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAA
*
28770166 TGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCCA
1 TGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAA
* *
28770213 TGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAA
1 TGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAA
* * * *
28770260 TGTGATGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTAA
1 TGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAA
28770307 TGTGA
1 TGTGA
28770312 AATATGTATG
Statistics
Matches: 132, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 132 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
TGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAA
Found at i:28770626 original size:37 final size:37
Alignment explanation
Indices: 28770522--28770626 Score: 174
Period size: 37 Copynumber: 2.8 Consensus size: 37
28770512 ATATATTCCT
*
28770522 GGTAAGACCCGATGACTACGTGTGGAGATTATGTCCG
1 GGTAAGACCCGATGACTACGTGTGGAGATTTTGTCCG
*
28770559 GGTAAGACTCGATGACTACGTGTGGAGATTTTGTCCG
1 GGTAAGACCCGATGACTACGTGTGGAGATTTTGTCCG
* *
28770596 GGTAAGACCCGATAACTTCGTGTGGAGATTT
1 GGTAAGACCCGATGACTACGTGTGGAGATTT
28770627 CGTCTGAGCT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (37 bp):
GGTAAGACCCGATGACTACGTGTGGAGATTTTGTCCG
Found at i:28771809 original size:39 final size:39
Alignment explanation
Indices: 28771766--28771971 Score: 297
Period size: 39 Copynumber: 5.3 Consensus size: 39
28771756 GTGTGAGATA
* *
28771766 TATATCCGGGCTAATTCCCGAAGGCATTTGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* *
28771805 TATATCTGAGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* *
28771844 TATATCCGAGCTAAGTCCCAAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
*
28771883 TATACCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* * * *
28771922 TATATCCAGGCTAAGTCCCGACGGC-TTTGTGCTGGTAT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
*
28771960 TATATTCGGGCT
1 TATATCCGGGCT
28771972 TAAAGTCCTG
Statistics
Matches: 151, Mismatches: 16, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
38 21 0.14
39 130 0.86
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (39 bp):
TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
Found at i:28778552 original size:39 final size:39
Alignment explanation
Indices: 28778509--28778724 Score: 299
Period size: 39 Copynumber: 5.5 Consensus size: 39
28778499 GTGTGAGATA
* *
28778509 TATATCCGGGCTAAATCCCGAAGGCATTTGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* *
28778548 TATATCCGAGCTAAGTCCCGAAGGCATTCGTGCTTGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* *
28778587 TATATCCGAGCTAAGTCTCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* *
28778626 TATACCCAGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* * *
28778665 TATATCCGGTCTAAGTCCCGAAGGC-TTTGTGCTGGTAT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
*
28778703 TATATCTGGGCTTAAAGTCCCG
1 TATATCCGGGC-T-AAGTCCCG
28778725 CATGCTTCAT
Statistics
Matches: 158, Mismatches: 17, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
38 20 0.13
39 130 0.82
40 8 0.05
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (39 bp):
TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
Found at i:28781943 original size:39 final size:39
Alignment explanation
Indices: 28781820--28781941 Score: 190
Period size: 39 Copynumber: 3.1 Consensus size: 39
28781810 GCCCGAATAC
*
28781820 ATTTCCAGCACGTAGCCTGCGGACCTCAAGTCCAGATAT
1 ATTTCCAGCACGTAGCCTGCGGACCTCAAGTCCGGATAT
* *
28781859 ATTTCCAGCACGTAGCTTGTGGACCTCAAGTCCGGATAT
1 ATTTCCAGCACGTAGCCTGCGGACCTCAAGTCCGGATAT
* *
28781898 ATTTCTAGCACGTAGCCTGCGAACCTCAAGTCCGGATAT
1 ATTTCCAGCACGTAGCCTGCGGACCTCAAGTCCGGATAT
*
28781937 GTTTC
1 ATTTC
28781942 TAAATATCAT
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (39 bp):
ATTTCCAGCACGTAGCCTGCGGACCTCAAGTCCGGATAT
Found at i:28786690 original size:39 final size:39
Alignment explanation
Indices: 28786636--28786726 Score: 182
Period size: 39 Copynumber: 2.3 Consensus size: 39
28786626 TGTTACACTG
28786636 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
28786675 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
28786714 AGCCCGGATATAA
1 AGCCCGGATATAA
28786727 TTCTCCATTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.18
Consensus pattern (39 bp):
AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
Found at i:28793625 original size:20 final size:20
Alignment explanation
Indices: 28793600--28793646 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
28793590 AACAGGGGTC
28793600 ACACGCCTGTGTGGCTTGGG
1 ACACGCCTGTGTGGCTTGGG
*
28793620 ACACGCTTGTGTGGCTTGGG
1 ACACGCCTGTGTGGCTTGGG
28793640 ACACGCC
1 ACACGCC
28793647 CGTGCGGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.28, G:0.36, T:0.23
Consensus pattern (20 bp):
ACACGCCTGTGTGGCTTGGG
Found at i:28799828 original size:21 final size:21
Alignment explanation
Indices: 28799804--28799874 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
28799794 TATCACGAAC
28799804 TCAGACCATAACTCAATGAGT
1 TCAGACCATAACTCAATGAGT
*
28799825 TCAGATATCACATATA-TC-ATGAGC
1 TCAG--A-C-CATA-ACTCAATGAGT
* *
28799849 TCAAACCACAACTCAATGAGT
1 TCAGACCATAACTCAATGAGT
28799870 TCAGA
1 TCAGA
28799875 TTACATAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
19 1 0.03
20 5 0.13
21 14 0.37
22 1 0.03
23 1 0.03
24 9 0.24
25 6 0.16
26 1 0.03
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (21 bp):
TCAGACCATAACTCAATGAGT
Found at i:28799837 original size:45 final size:45
Alignment explanation
Indices: 28799787--28799875 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
28799777 AAAACATGTG
* *
28799787 TCACATATATCACGAACTCAGACCATAACTCAATGAGTTCAGATA
1 TCACATATATCACGAACTCAAACCACAACTCAATGAGTTCAGATA
* *
28799832 TCACATATATCATGAGCTCAAACCACAACTCAATGAGTTCAGAT
1 TCACATATATCACGAACTCAAACCACAACTCAATGAGTTCAGAT
28799876 TACATAAGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (45 bp):
TCACATATATCACGAACTCAAACCACAACTCAATGAGTTCAGATA
Found at i:28830036 original size:40 final size:40
Alignment explanation
Indices: 28829938--28830161 Score: 224
Period size: 40 Copynumber: 5.7 Consensus size: 40
28829928 TTGAATGCTG
* * *
28829938 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
** * *
28829977 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * **
28830017 TTCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* **
28830057 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28830097 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
28830136 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
28830162 AACGAGGAGC
Statistics
Matches: 159, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
39 51 0.32
40 100 0.63
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28830179 original size:79 final size:80
Alignment explanation
Indices: 28830012--28830194 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
28830002 GTGCGAGATA
* ** * *
28830012 CTAAATTCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
28830077 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * *
28830092 TTAAATCCGGGTTAAGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
28830156 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
28830171 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
28830195 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 15 0.17
79 45 0.52
80 27 0.31
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:28838027 original size:39 final size:40
Alignment explanation
Indices: 28837876--28838045 Score: 216
Period size: 40 Copynumber: 4.3 Consensus size: 40
28837866 GGACTAAGAT
* * *
28837876 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* *
28837916 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGATAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* ** *
28837956 CCGAAGGCATTCGTGTGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * * *
28837996 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
28838035 CCGAAGGCATT
1 CCGAAGGCATT
28838046 TGAACGAGGA
Statistics
Matches: 117, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 35 0.30
40 82 0.70
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:28838065 original size:79 final size:80
Alignment explanation
Indices: 28837898--28838080 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
28837888 GTGCGAGATA
* *
28837898 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGATAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGATAAGTCCCGAAGG
*** **
28837963 CATTCGTGTGAGTTG
66 CATTCGAACGAGGAG
* * * * *
28837978 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGATAAGTCCCGAAGG
*
28838042 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
28838057 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
28838081 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGATAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:28864632 original size:40 final size:40
Alignment explanation
Indices: 28864574--28864805 Score: 374
Period size: 40 Copynumber: 5.8 Consensus size: 40
28864564 AACATTGGAT
28864574 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
28864614 TATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
28864654 CATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
28864694 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
28864734 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTCA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
28864774 TATGTCCGGGTTAAGACCCGAAGGCAAATATG
1 TATATCCGGGCTAAGACCCGAAGGCAATTATG
28864806 TTTGCGGCTG
Statistics
Matches: 176, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 176 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
Found at i:28871305 original size:13 final size:13
Alignment explanation
Indices: 28871287--28871311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28871277 GGGATTTAAT
28871287 GAATAAAAGAAAA
1 GAATAAAAGAAAA
28871300 GAATAAAAGAAA
1 GAATAAAAGAAA
28871312 GCAAATGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (13 bp):
GAATAAAAGAAAA
Found at i:28872684 original size:40 final size:40
Alignment explanation
Indices: 28872625--28872812 Score: 313
Period size: 40 Copynumber: 4.7 Consensus size: 40
28872615 GAGCACTGGA
* *
28872625 ATATATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
28872665 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
28872705 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
*
28872745 ATATATCCGGGTTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
28872785 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
28872813 ATGTGTTTGT
Statistics
Matches: 142, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
Found at i:28883159 original size:87 final size:86
Alignment explanation
Indices: 28883044--28883332 Score: 363
Period size: 87 Copynumber: 3.4 Consensus size: 86
28883034 TATTCTGATA
* * *
28883044 TTTTT-ATTTCTGTTTC-AAAAATCGACTCATATAGCGAGAGATGAGTTGAGCCTCAGGGCACAC
1 TTTTTAATTTATGTTTCAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGGCACAC
28883107 TGAGGTATGCTT-AGTTTGTGT
66 TGAGGTATG-TTCAGTTTGTGT
* *
28883128 TTTTTAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGATTTGAGCCTCAGGGCACA
1 TTTTTAATTTATGTTTC-AAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGGCACA
28883193 CTGAGGTATGTTCAGTTTGTGT
65 CTGAGGTATGTTCAGTTTGTGT
* ** *
28883215 TTTTTAATTTATGTTTCAAAAAATCAACTCATATTGCGAGA-AGCGAGTTGAGCCTCAGGATACG
1 TTTTTAATTTATGTTTCAAAAAATCAACTCATATTGCGAGAGA-TGAGTTGAGCCTCAGGGCACA
* * * *
28883279 CTGAGGTATTTTCAATTTCTAT
65 CTGAGGTATGTTCAGTTTGTGT
* *
28883301 TTTTCAATTTATATTTTTC-AAAAATCAACTCA
1 TTTTTAA-TT-TATGTTTCAAAAAATCAACTCA
28883333 NNNNNNNNNN
Statistics
Matches: 181, Mismatches: 17, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
84 5 0.03
85 10 0.06
86 66 0.36
87 93 0.51
88 7 0.04
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.38
Consensus pattern (86 bp):
TTTTTAATTTATGTTTCAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGGCACAC
TGAGGTATGTTCAGTTTGTGT
Found at i:28883306 original size:14 final size:14
Alignment explanation
Indices: 28883287--28883321 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
28883277 CGCTGAGGTA
*
28883287 TTTTCAATTTCTAT
1 TTTTCAATTTATAT
28883301 TTTTCAATTTATAT
1 TTTTCAATTTATAT
28883315 TTTTCAA
1 TTTTCAA
28883322 AAATCAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTATAT
Found at i:28898537 original size:40 final size:40
Alignment explanation
Indices: 28898479--28898710 Score: 374
Period size: 40 Copynumber: 5.8 Consensus size: 40
28898469 AACATTGGAT
28898479 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
28898519 TATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
28898559 CATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
28898599 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
28898639 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTCA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
28898679 TATGTCCGGGTTAAGACCCGAAGGCAAATATG
1 TATATCCGGGCTAAGACCCGAAGGCAATTATG
28898711 TTTGCGGCTG
Statistics
Matches: 176, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 176 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
Found at i:28905760 original size:40 final size:40
Alignment explanation
Indices: 28905702--28905933 Score: 374
Period size: 40 Copynumber: 5.8 Consensus size: 40
28905692 AACATTGGAT
28905702 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
28905742 TATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
28905782 CATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
28905822 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
28905862 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTCA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
28905902 TATGTCCGGGTTAAGACCCGAAGGCAAATATG
1 TATATCCGGGCTAAGACCCGAAGGCAATTATG
28905934 TTTGCGGCTG
Statistics
Matches: 176, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 176 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
Found at i:28909708 original size:35 final size:35
Alignment explanation
Indices: 28909642--28909709 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
28909632 ACATATTCAT
* *
28909642 GATCAATTCCATATTAATATAGGTCTTATAGGTAA
1 GATCAATTCCATATTAATACAGGTCTCATAGGTAA
* *
28909677 GATCAATTTCATATTAATGCA-GTCATCATAGGT
1 GATCAATTCCATATTAATACAGGTC-TCATAGGT
28909710 GCTTTACATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 3 0.11
35 25 0.89
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (35 bp):
GATCAATTCCATATTAATACAGGTCTCATAGGTAA
Found at i:28912284 original size:47 final size:47
Alignment explanation
Indices: 28912215--28912370 Score: 285
Period size: 47 Copynumber: 3.3 Consensus size: 47
28912205 CCCTTCGGGA
* *
28912215 CTTATCACATTTATACACTTTCACATTCATCACGTCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28912262 CTTATCACATATATACACTTTCACATTCATCACACCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28912309 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28912356 CTTATCACATATATA
1 CTTATCACATATATA
28912371 TATACACTTT
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 105 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28922273 original size:7 final size:6
Alignment explanation
Indices: 28922247--28922271 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28922237 TAAATATGTA
28922247 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
28922272 TAAGAACAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:28939483 original size:20 final size:21
Alignment explanation
Indices: 28939444--28939483 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28939434 GTTATAATGA
*
28939444 CCACACGGGCGTGTTGCCCTT
1 CCACACCGGCGTGTTGCCCTT
28939465 CCACACCGGCGTG-TGCCCT
1 CCACACCGGCGTGTTGCCCT
28939484 GATTCAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.10, C:0.42, G:0.28, T:0.20
Consensus pattern (21 bp):
CCACACCGGCGTGTTGCCCTT
Found at i:28959112 original size:46 final size:46
Alignment explanation
Indices: 28959062--28959237 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
28959052 TGATTGAGCA
28959062 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28959108 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
28959153 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-C
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28959200 CCCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28959238 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 61 0.55
47 29 0.26
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28959218 original size:93 final size:93
Alignment explanation
Indices: 28959059--28959230 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
28959049 GGATGATTGA
**
28959059 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATCCCCGAACTCGTTGAGT
28959124 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
28959152 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-CCCCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATCCCC-GAACTCGTTGAG
28959216 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
28959231 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATCCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28962794 original size:46 final size:45
Alignment explanation
Indices: 28962691--28962907 Score: 197
Period size: 46 Copynumber: 4.7 Consensus size: 45
28962681 AGGTGCAGGC
* * * *
28962691 GCCGATGCCATGTCTCAGACAAGGTCTTACACTGAC-ACATCTCGTA-
1 GCCGATG-CATGTCCCAGAC-ATGTCTTACACTGGCTTCATCTCG-AG
* *
28962737 GCTGATACATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTT-CATCTCGAG
* * * * * *
28962783 GCCGATGCATGTCCCAAACATGTCTTACACTAGCACTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC-TTCATCTCGAG
* * *
28962829 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TCAT-CTCGAG
28962877 GCCGATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
28962908 AGCACACAAA
Statistics
Matches: 139, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
44 13 0.09
45 12 0.09
46 64 0.46
47 28 0.20
48 21 0.15
49 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTCATCTCGAG
Found at i:28964919 original size:39 final size:39
Alignment explanation
Indices: 28964802--28965024 Score: 233
Period size: 39 Copynumber: 5.6 Consensus size: 39
28964792 GCTCCTCGTT
* * *
28964802 CAAATGCCTTCGGGACATAGCCTGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
28964842 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
*
28964882 CAAATACCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
28964921 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* * *
28964960 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TCGCA
28965001 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
28965025 CATCATTCAA
Statistics
Matches: 162, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
39 92 0.57
40 59 0.36
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:28969511 original size:21 final size:21
Alignment explanation
Indices: 28969485--28969528 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
28969475 TAGACACAGC
**
28969485 GGGTGTTGAGTTTTTGAGATT
1 GGGTGTTGAGTTTCGGAGATT
28969506 GGGTGTTGAGTTTCGGAGATT
1 GGGTGTTGAGTTTCGGAGATT
28969527 GG
1 GG
28969529 TTGTAATTAA
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:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (21 bp):
GGGTGTTGAGTTTCGGAGATT
Found at i:28973524 original size:8 final size:8
Alignment explanation
Indices: 28973500--28973543 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
28973490 TTCTCTCACA
28973500 TTTTC-TT
1 TTTTCATT
**
28973507 TTTTTTTT
1 TTTTCATT
28973515 TTTTCATT
1 TTTTCATT
28973523 TTTTCATT
1 TTTTCATT
28973531 TTTTCATT
1 TTTTCATT
28973539 CTTTT
1 -TTTT
28973544 TTTGTATTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
7 4 0.12
8 24 0.75
9 4 0.12
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTCATT
Found at i:28973526 original size:16 final size:16
Alignment explanation
Indices: 28973500--28973546 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
28973490 TTCTCTCACA
28973500 TTTTC-TTTTTTTTTT
1 TTTTCATTTTTTTTTT
**
28973515 TTTTCATTTTTTCATT
1 TTTTCATTTTTTTTTT
28973531 TTTTCATTCTTTTTTT
1 TTTTCATT-TTTTTTT
28973547 GTATTCTTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 5 0.19
16 16 0.62
17 5 0.19
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTCATTTTTTTTTT
Found at i:28974150 original size:22 final size:22
Alignment explanation
Indices: 28974109--28974149 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
28974099 AATATAAAAC
28974109 AAAAAAAATATGAAGTTTTTAG
1 AAAAAAAATATGAAGTTTTTAG
*
28974131 AAAAAAAAT-TTAAGTTTTT
1 AAAAAAAATATGAAGTTTTT
28974150 TTGTCTCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (22 bp):
AAAAAAAATATGAAGTTTTTAG
Found at i:28974866 original size:20 final size:19
Alignment explanation
Indices: 28974827--28974870 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
28974817 TGATTAGATA
*
28974827 GTGTAAGTGAATTTTGAAT
1 GTGTAAGTGAATTCTGAAT
28974846 GGTGTAAGTGAATTCCT-AAT
1 -GTGTAAGTGAATT-CTGAAT
28974866 GTGTA
1 GTGTA
28974871 TCTATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 5 0.23
20 16 0.73
21 1 0.05
ACGTcount: A:0.30, C:0.05, G:0.27, T:0.39
Consensus pattern (19 bp):
GTGTAAGTGAATTCTGAAT
Found at i:28978522 original size:39 final size:39
Alignment explanation
Indices: 28978474--28978552 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
28978464 AAAAGAAAGT
* *
28978474 AAGAATAACTAGTTATGGGCTCCAACTTATGGTAAGAAA
1 AAGAATAACTAGTTATGGGCTCCAACTAATAGTAAGAAA
28978513 AAGAATAACTAGTTATGGGCTCCAACTAATAGTAAGAAA
1 AAGAATAACTAGTTATGGGCTCCAACTAATAGTAAGAAA
28978552 A
1 A
28978553 TAGATGGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (39 bp):
AAGAATAACTAGTTATGGGCTCCAACTAATAGTAAGAAA
Found at i:28979738 original size:8 final size:8
Alignment explanation
Indices: 28979725--28979749 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28979715 AATAAAAAAA
28979725 ATTAAATT
1 ATTAAATT
28979733 ATTAAATT
1 ATTAAATT
28979741 ATTAAATT
1 ATTAAATT
28979749 A
1 A
28979750 AAATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTAAATT
Found at i:28982243 original size:18 final size:17
Alignment explanation
Indices: 28982217--28982265 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
28982207 GTAAGGGTAA
*
28982217 ATTTTATTTTTTAATATT
1 ATTTAATTTTTTAAT-TT
28982235 ATTTAATTTTTATAATTT
1 ATTTAATTTTT-TAATTT
*
28982253 AATTAATATTTTT
1 ATTTAAT-TTTTT
28982266 TATAATAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 19 0.70
19 8 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTAATTTTTTAATTT
Found at i:28984482 original size:28 final size:27
Alignment explanation
Indices: 28984438--28984502 Score: 94
Period size: 28 Copynumber: 2.4 Consensus size: 27
28984428 GCATCTGATA
*
28984438 CTGATTCTGTATTGGGCTTAGGCCCAC
1 CTGATTCTGTATTGGGCTAAGGCCCAC
*
28984465 CTGATTCTATTATTGGGCTAAGGCCCAC
1 CTGATTCT-GTATTGGGCTAAGGCCCAC
*
28984493 CTGATACTGT
1 CTGATTCTGT
28984503 TTCTACAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 9 0.27
28 24 0.73
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (27 bp):
CTGATTCTGTATTGGGCTAAGGCCCAC
Found at i:28987963 original size:7 final size:7
Alignment explanation
Indices: 28987948--28987978 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
28987938 AACATAGTCA
*
28987948 ATTTCGT
1 ATTTAGT
28987955 ATTTAGT
1 ATTTAGT
28987962 ATTTAGT
1 ATTTAGT
28987969 ATTTAGT
1 ATTTAGT
28987976 ATT
1 ATT
28987979 ATGTATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.58
Consensus pattern (7 bp):
ATTTAGT
Found at i:28989156 original size:58 final size:58
Alignment explanation
Indices: 28988980--28989158 Score: 214
Period size: 59 Copynumber: 3.1 Consensus size: 58
28988970 ATTGATTTAT
* * * *
28988980 TTTTGAATATTTTTGTTCAAATTATTTGTATATTGTTTCATTTAATAAAGTATAAGTTA
1 TTTTGAATATTTTTGTACAAATTATTT-TATATTGTTTCATTTAATAAAATAGAAGTTC
* * * **
28989039 TTTTGAAAATTTTTGTAAAAATTATTTTTATATTATTTCATTTAATAAAATAGCTGTTC
1 TTTTGAATATTTTTGTACAAATTA-TTTTATATTGTTTCATTTAATAAAATAGAAGTTC
* ** * *
28989098 TTTTGAATATTTTTGTACAAATCAAATAATATTGTTTCATTTAATAAATTAGAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTATATTGTTTCATTTAATAAAATAGAAGTTC
28989156 TTT
1 TTT
28989159 CAATGTGGAC
Statistics
Matches: 100, Mismatches: 19, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
58 30 0.30
59 67 0.67
60 3 0.03
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.52
Consensus pattern (58 bp):
TTTTGAATATTTTTGTACAAATTATTTTATATTGTTTCATTTAATAAAATAGAAGTTC
Found at i:28990486 original size:13 final size:13
Alignment explanation
Indices: 28990464--28990496 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
28990454 AAGGGTTTGT
28990464 TTAT-TAAACTAA
1 TTATCTAAACTAA
28990476 TTATCTAAACTAA
1 TTATCTAAACTAA
*
28990489 TTAACTAA
1 TTATCTAA
28990497 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:29003896 original size:29 final size:29
Alignment explanation
Indices: 29003846--29003934 Score: 108
Period size: 29 Copynumber: 3.0 Consensus size: 29
29003836 AAAAAAAATC
*
29003846 CATCTCGTCAAAATAATATTTTTCAGAACA
1 CATCTCGTCAAAATTAT-TTTTTCAGAACA
* *
29003876 CAT-TACGTCAAATTTATTTTTTCAGAACC
1 CATCT-CGTCAAAATTATTTTTTCAGAACA
*
29003905 CATCTTGTCAAAATTATTTTTTCCAGAACA
1 CATCTCGTCAAAATTATTTTTT-CAGAACA
29003935 ATACTTAGTA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
29 30 0.60
30 20 0.40
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (29 bp):
CATCTCGTCAAAATTATTTTTTCAGAACA
Found at i:29005540 original size:43 final size:43
Alignment explanation
Indices: 29005486--29005593 Score: 126
Period size: 43 Copynumber: 2.5 Consensus size: 43
29005476 GCCCATGTTT
*
29005486 CCAGACTGTGTACAATTTGAAATAGGGTCACACGGCCATGTCG
1 CCAGACCGTGTACAATTTGAAATAGGGTCACACGGCCATGTCG
** ** * *
29005529 CCAGACCGTGTACAATTCAAAATAGGGTCATGCGGCTATGTGG
1 CCAGACCGTGTACAATTTGAAATAGGGTCACACGGCCATGTCG
* * *
29005572 CTAGACCGTCTACGATTTGAAA
1 CCAGACCGTGTACAATTTGAAA
29005594 CAGTGTAACA
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (43 bp):
CCAGACCGTGTACAATTTGAAATAGGGTCACACGGCCATGTCG
Found at i:29009775 original size:45 final size:45
Alignment explanation
Indices: 29009697--29009819 Score: 156
Period size: 45 Copynumber: 2.7 Consensus size: 45
29009687 TGCCATTGTG
* ** *** *
29009697 TCTTTCAGTTATGGTCTTACTCACTTCCGTCATAATGCCATAGCT
1 TCTTTCAGCTATGGTCTTACTCGTTTTAATCATAATGCCATAGCA
*
29009742 TCTTTCAGCTATGGTCTTACTCGTTTTAATCATATTGCCATAGCA
1 TCTTTCAGCTATGGTCTTACTCGTTTTAATCATAATGCCATAGCA
* *
29009787 TCTTTCATCTATGGTCTTACTTGTTTTAATCAT
1 TCTTTCAGCTATGGTCTTACTCGTTTTAATCAT
29009820 GTTTATGATA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (45 bp):
TCTTTCAGCTATGGTCTTACTCGTTTTAATCATAATGCCATAGCA
Found at i:29011737 original size:21 final size:22
Alignment explanation
Indices: 29011691--29011739 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
29011681 TGATTTAATT
*
29011691 TAATATATTCTTAATTATTTAA
1 TAATATATTCTTAATTATATAA
29011713 -AATATATT-TATAATT-TATAA
1 TAATATATTCT-TAATTATATAA
29011733 TAATATA
1 TAATATA
29011740 AAATAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATATATTCTTAATTATATAA
Found at i:29013801 original size:48 final size:48
Alignment explanation
Indices: 29013742--29013968 Score: 332
Period size: 48 Copynumber: 4.7 Consensus size: 48
29013732 CCGTGGTAAA
* *
29013742 TGTGCCTGTGTAAGACCATGTCTAGGACATGGCATCGGTGATGATATG
1 TGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGTGATGATATG
*
29013790 TGTGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGTGATGATATG
1 TGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGTGATGATATG
* * * *
29013838 CGTGTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCGATGATATG
1 TGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGTGATGATATG
*
29013886 TGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGTGATGATATG
1 TGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGTGATGATATG
* *
29013934 TGAAT-TCA-TGTAAGACCATGTCGGGGACATGGCAT
1 TG--TGCCAGTGTAAGACCATGTCTGGGACATGGCAT
29013969 TGGTACTTTA
Statistics
Matches: 161, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
48 159 0.99
49 1 0.01
50 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.28
Consensus pattern (48 bp):
TGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGTGATGATATG
Found at i:29017081 original size:24 final size:24
Alignment explanation
Indices: 29017054--29017151 Score: 153
Period size: 24 Copynumber: 4.0 Consensus size: 24
29017044 AAAGGCTGTC
29017054 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
29017078 GGAG-AGAATTTAGGAGCTGATAAG
1 GGAGAAG-ATTTAGGAGCTGATAAG
* *
29017102 GGAGAGGATTTAGGAGCTGATAAA
1 GGAGAAGATTTAGGAGCTGATAAG
29017126 GGAGAAGATTTAGGAGCTGATCAAG
1 GGAGAAGATTTAGGAGCTGAT-AAG
29017151 G
1 G
29017152 AGCAGGAGTT
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
23 2 0.03
24 61 0.91
25 4 0.06
ACGTcount: A:0.37, C:0.05, G:0.38, T:0.20
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:29018302 original size:31 final size:31
Alignment explanation
Indices: 29018267--29018327 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
29018257 AAATTGGAAT
29018267 AAAGGGCCAACGCGCCCAATTCGGTAAGAAA
1 AAAGGGCCAACGCGCCCAATTCGGTAAGAAA
29018298 AAAGGGCCAACGCGCCCAATTCGGTAAGAA
1 AAAGGGCCAACGCGCCCAATTCGGTAAGAA
29018328 CCCTCGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.26, G:0.26, T:0.10
Consensus pattern (31 bp):
AAAGGGCCAACGCGCCCAATTCGGTAAGAAA
Found at i:29027472 original size:40 final size:40
Alignment explanation
Indices: 29027417--29027618 Score: 199
Period size: 40 Copynumber: 5.0 Consensus size: 40
29027407 TAAATGCTTT
* * *
29027417 CAGGGATACCAAAGTACAAACAGGGGCACGTATGTGTAAA
1 CAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAAA
* * * * *
29027457 TAGAGGTGCCGAAGTACAAGCAGGGGCACGTATGTGTAAA
1 CAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAAA
* ** *
29027497 TAGGGGTACCGAAGTACAAGTAGGAGCACGTATGTGCAAA
1 CAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAAA
* ** * * * *
29027537 CAGGTGTATTGAAGTACGAATAGGGGCACATATGTCCAAA
1 CAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAAA
* *
29027577 CAGGGGTACCGAAGTATGAAA-AGGGGCACGTATGTACAAA
1 CAGGGGTACCGAAGTA-CAAACAGGGGCACGTATGTGCAAA
29027617 CA
1 CA
29027619 TTCAATAATT
Statistics
Matches: 134, Mismatches: 27, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
40 132 0.99
41 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.31, T:0.17
Consensus pattern (40 bp):
CAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAAA
Found at i:29036845 original size:19 final size:19
Alignment explanation
Indices: 29036823--29036887 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 19
29036813 AATTATAAAA
29036823 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTTT
*
29036842 AAAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTT-TT
29036861 AAAATTTCAAAATTTATATTTTT
1 AAAA-TTCAAAA--TA-ATTTTT
29036884 AAAA
1 AAAA
29036888 AATATATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 4 0.11
19 17 0.45
20 7 0.18
22 1 0.03
23 5 0.13
24 4 0.11
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:29036852 original size:39 final size:41
Alignment explanation
Indices: 29036809--29036887 Score: 101
Period size: 39 Copynumber: 2.0 Consensus size: 41
29036799 TCTCTCACAA
29036809 CAAAA-ATTATAAAAAAAATTCAAAA-TA-ATTTTTAAAATT
1 CAAAATATT-TAAAAAAAATTCAAAATTATATTTTTAAAATT
* *
29036848 CAAAATATTTATAAAAATTTCAAAATTTATATTTTTAAAA
1 CAAAATATTTAAAAAAAATTCAAAA-TTATATTTTTAAAA
29036888 AATATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 19 0.56
40 3 0.09
41 2 0.06
42 10 0.29
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (41 bp):
CAAAATATTTAAAAAAAATTCAAAATTATATTTTTAAAATT
Found at i:29036911 original size:11 final size:11
Alignment explanation
Indices: 29036897--29036930 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
29036887 AAATATATAT
29036897 AAAAATTCT-A
1 AAAAATTCTAA
29036907 AAAAATTCTAA
1 AAAAATTCTAA
29036918 AAAAATTCTAA
1 AAAAATTCTAA
29036929 AA
1 AA
29036931 TATATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAAATTCTAA
Done.