Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 61 of 66
Found at i:23451867 original size:45 final size:44
Alignment explanation
Indices: 23451764--23451869 Score: 142
Period size: 45 Copynumber: 2.4 Consensus size: 44
23451754 TTTTTTTTCA
*
23451764 ACATGACGTGTAACAACCTAATCATGACGTATTACATGTTTTTGT
1 ACATGACGTGTAATAACCTAATCATGA-GTATTACATGTTTTTGT
* * *
23451809 ACATGACATGTAATAGCTTAATCATG-GTATGTAACATGTTTTTGT
1 ACATGACGTGTAATAACCTAATCATGAGTAT-T-ACATGTTTTTGT
23451854 ACATGACGTGTAATAA
1 ACATGACGTGTAATAA
23451870 TAATATTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
43 4 0.08
44 1 0.02
45 48 0.91
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (44 bp):
ACATGACGTGTAATAACCTAATCATGAGTATTACATGTTTTTGT
Found at i:23451972 original size:45 final size:45
Alignment explanation
Indices: 23451885--23451972 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 45
23451875 TTTTTTTTTA
* * * *
23451885 ACATGACGTGTAATAATTTAACCATGATATATTACATATTTTTGT
1 ACATGACGTGTAATAACTTAACCATAACATATCACATATTTTTGT
* * *
23451930 ACATGACGTGTAATAACTTAACTATAACGTATCACATGTTTTT
1 ACATGACGTGTAATAACTTAACCATAACATATCACATATTTTT
23451973 ATATATAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (45 bp):
ACATGACGTGTAATAACTTAACCATAACATATCACATATTTTTGT
Found at i:23452006 original size:25 final size:25
Alignment explanation
Indices: 23451968--23452018 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
23451958 GTATCACATG
*
23451968 TTTTTATATATAATTTTATTAAAAA
1 TTTTTATATATAATTTGATTAAAAA
* *
23451993 TTTTTTTATCTAATTTGATTAAAAA
1 TTTTTATATATAATTTGATTAAAAA
23452018 T
1 T
23452019 AATTAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
TTTTTATATATAATTTGATTAAAAA
Found at i:23457971 original size:25 final size:26
Alignment explanation
Indices: 23457941--23457989 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
23457931 TATGTCACGT
23457941 TATCATCAATTA-TAATATATCAATA
1 TATCATCAATTATTAATATATCAATA
** *
23457966 TATCATTTATTATTAATATGTCAA
1 TATCATCAATTATTAATATATCAA
23457990 ATGGTATTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (26 bp):
TATCATCAATTATTAATATATCAATA
Found at i:23458102 original size:29 final size:29
Alignment explanation
Indices: 23458069--23458124 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
23458059 ATTTCTTTCA
**
23458069 AAATAAAAATATAACGATTTGATTGAACG
1 AAATAAAAATATAAAAATTTGATTGAACG
23458098 AAATAAAAATATAAAAATTTGATTGAA
1 AAATAAAAATATAAAAATTTGATTGAA
23458125 TTTTTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.29
Consensus pattern (29 bp):
AAATAAAAATATAAAAATTTGATTGAACG
Found at i:23458906 original size:26 final size:27
Alignment explanation
Indices: 23458877--23458935 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
23458867 TTGCAAAACT
23458877 TTTTTAAATTAT-TTTAAAAATTTATA
1 TTTTTAAATTATATTTAAAAATTTATA
* * *
23458903 TTTTT-TATTATATTTAATAATTTTTA
1 TTTTTAAATTATATTTAAAAATTTATA
23458929 TATTTTA
1 T-TTTTA
23458936 TTTTAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 5 0.19
26 18 0.67
27 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTTAAATTATATTTAAAAATTTATA
Found at i:23458936 original size:26 final size:25
Alignment explanation
Indices: 23458884--23458937 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
23458874 ACTTTTTTAA
*
23458884 ATTATTTTAAAAATTTATATTTTTT
1 ATTATTTTAAAAATTTATATATTTT
* *
23458909 ATTATATTTAATAATTTTTATATTTT
1 ATTAT-TTTAAAAATTTATATATTTT
23458935 ATT
1 ATT
23458938 TTAAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
ATTATTTTAAAAATTTATATATTTT
Found at i:23458975 original size:29 final size:31
Alignment explanation
Indices: 23458942--23459015 Score: 73
Period size: 32 Copynumber: 2.4 Consensus size: 31
23458932 TTTATTTTAA
23458942 ATTAAATTAATATT-TA-TAAATAATAAT-T
1 ATTAAATTAATATTATATTAAATAATAATAT
* * *
23458970 AGTTAATTTTTATTTTATATTAAATAATAATAT
1 A-TTAA-ATTAATATTATATTAAATAATAATAT
23459003 ATTATAATTAATA
1 ATTA-AATTAATA
23459016 ATAATATGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
28 1 0.03
29 4 0.12
30 6 0.18
31 2 0.06
32 18 0.53
33 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (31 bp):
ATTAAATTAATATTATATTAAATAATAATAT
Found at i:23458979 original size:45 final size:48
Alignment explanation
Indices: 23458908--23459017 Score: 129
Period size: 46 Copynumber: 2.3 Consensus size: 48
23458898 TTATATTTTT
** *
23458908 TATTATATTTAATAATTTTTATA-TTTTATTTTAAATTAAAT-TAATA
1 TATTATAAATAATAATTGTTATATTTTTATTTTAAATTAAATATAATA
*
23458954 T-TTATAAATAATAATTAGTTA-ATTTTTATTTTATATTAAATAATAATA
1 TATTATAAATAATAATT-GTTATATTTTTATTTTAAATTAAAT-ATAATA
*
23459002 TATTATAATTAATAAT
1 TATTATAAATAATAAT
23459018 AATATGATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
45 14 0.26
46 21 0.39
48 6 0.11
49 13 0.24
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.55
Consensus pattern (48 bp):
TATTATAAATAATAATTGTTATATTTTTATTTTAAATTAAATATAATA
Found at i:23459016 original size:17 final size:15
Alignment explanation
Indices: 23458985--23459018 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
23458975 ATTTTTATTT
23458985 TATATTAAATAATAA
1 TATATTAAATAATAA
23459000 TATATTATAATTAATAA
1 TATATTA-AA-TAATAA
23459017 TA
1 TA
23459019 ATATGATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 2 0.12
17 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATATTAAATAATAA
Found at i:23462056 original size:17 final size:17
Alignment explanation
Indices: 23462031--23462064 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23462021 ATCAAACCGT
* *
23462031 TTGATTTAATTGGTTTA
1 TTGAATTAATTGATTTA
23462048 TTGAATTAATTGATTTA
1 TTGAATTAATTGATTTA
23462065 AAATATTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (17 bp):
TTGAATTAATTGATTTA
Found at i:23462730 original size:2 final size:2
Alignment explanation
Indices: 23462682--23462710 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23462672 CATTAATTTC
23462682 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23462711 ANTCATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23462776 original size:256 final size:254
Alignment explanation
Indices: 23462468--23462955 Score: 676
Period size: 256 Copynumber: 1.9 Consensus size: 254
23462458 TAAATATATA
*
23462468 TATATATATAATTAAATAAATATAGTATATATACATATATTCAATTTATACATAAACATTACTAT
1 TATATATATAATAAAATAAATATAGTATATATACATATATTCAATTTATACATAAACATTACTAT
* ** * * * * * *
23462533 AATTTATAATAAACTTTATTTATATAATTGTATTTAATAACTTTGTTGGTTATCACTTTTGATTT
66 AACTTATAATAAACTTTATTTATATAATTACACTTAATAACTTTATTAGCTATCACCTTAGATTT
* *
23462598 TT-TAACATATTGTTTATAATTAGTTGTTATTTATACAAACTTTGATATAAAATATTATAACATA
131 TTATAACATATTGTTTATAATTAATTATTATTTATACAAACTTTGATATAAAATATTATAACATA
* *
23462662 TAAGTTATGTCATTAATTTCATATATATATATATATATATATATATATAANTCATTAATTT
196 TAAGTTATATAATTAATTTCATATATATATATA-ATATATATATATATAA-TCATTAATTT
* * * *
23462723 TATATATATACATAAAATAAA-ATAATGT-TATATATATTTATTTAATTTATACATAAACATTAT
1 TATATATATA-ATAAAATAAATAT-A-GTATATATACATATATTCAATTTATACATAAACATTAC
* * * *
23462786 TATAACTTATAATAAGCTTTATTTATATGATTACACTTGATAAGTTTATTAGCTATCACCTTAGA
63 TATAACTTATAATAAACTTTATTTATATAATTACACTTAATAACTTTATTAGCTATCACCTTAGA
* * * *
23462851 TTTTTATAATATATTGTTTATAATTAATTATTATTTATATAAATTTTGATTTAAAATATTATAAC
128 TTTTTATAACATATTGTTTATAATTAATTATTATTTATACAAACTTTGATATAAAATATTATAAC
23462916 ATATAAGTTATATAATTAATTTCATATATATATATAATAT
193 ATATAAGTTATATAATTAATTTCATATATATATATAATAT
23462956 TATGAATGAA
Statistics
Matches: 203, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
255 12 0.06
256 102 0.50
257 89 0.44
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.48
Consensus pattern (254 bp):
TATATATATAATAAAATAAATATAGTATATATACATATATTCAATTTATACATAAACATTACTAT
AACTTATAATAAACTTTATTTATATAATTACACTTAATAACTTTATTAGCTATCACCTTAGATTT
TTATAACATATTGTTTATAATTAATTATTATTTATACAAACTTTGATATAAAATATTATAACATA
TAAGTTATATAATTAATTTCATATATATATATAATATATATATATATAATCATTAATTT
Found at i:23462786 original size:22 final size:21
Alignment explanation
Indices: 23462760--23462810 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
23462750 TTATATATAT
*
23462760 TTATTTAATTTATACATAAACA
1 TTATTTAACTTATA-ATAAACA
* *
23462782 TTATTATAACTTATAATAAGCT
1 TTATT-TAACTTATAATAAACA
23462804 TTATTTA
1 TTATTTA
23462811 TATGATTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 15 0.60
23 8 0.32
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (21 bp):
TTATTTAACTTATAATAAACA
Found at i:23463107 original size:26 final size:26
Alignment explanation
Indices: 23463046--23463107 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
23463036 TGACCAACTA
**
23463046 AATTAATTTTATATTTGATTTGTTTG
1 AATTAATTTTATATTTGATCCGTTTG
* ** *
23463072 ATTTTTTTTTATATTTGATCCGTTTT
1 AATTAATTTTATATTTGATCCGTTTG
23463098 AATTAATTTT
1 AATTAATTTT
23463108 TTAAAAATAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.65
Consensus pattern (26 bp):
AATTAATTTTATATTTGATCCGTTTG
Found at i:23495616 original size:3 final size:3
Alignment explanation
Indices: 23495608--23495632 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
23495598 TCAAAGCCAT
23495608 GCA GCA GCA GCA GCA GCA GCA GCA G
1 GCA GCA GCA GCA GCA GCA GCA GCA G
23495633 GACATTACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.36, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:23501966 original size:2 final size:2
Alignment explanation
Indices: 23501955--23501990 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
23501945 TTTTAAGCTT
23501955 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
23501991 AGTCTAGTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:23502028 original size:2 final size:2
Alignment explanation
Indices: 23502021--23502047 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23502011 GTAAGTAAGN
23502021 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
23502048 ATGATTGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:23529082 original size:23 final size:23
Alignment explanation
Indices: 23529029--23529183 Score: 188
Period size: 23 Copynumber: 6.8 Consensus size: 23
23529019 TAGTTTCTAA
* *
23529029 TAAGGTATTGTGTGACTAGTT-G
1 TAAGGCATTGTGTGACTTGTTAG
*
23529051 -ATAGGCATTGCGTGACTTGTTAG
1 TA-AGGCATTGTGTGACTTGTTAG
*
23529074 TAAGGCATTGCGTGACTTGTTAG
1 TAAGGCATTGTGTGACTTGTTAG
* * *
23529097 TAAGGTATTGTGTGACTAGTTAA
1 TAAGGCATTGTGTGACTTGTTAG
*
23529120 TACGGCATTGTGTGACTTGTTAG
1 TAAGGCATTGTGTGACTTGTTAG
* *
23529143 TAAGGTATTGTGTGACTAGTTAG
1 TAAGGCATTGTGTGACTTGTTAG
*
23529166 TACGGCATTGTGTGACTT
1 TAAGGCATTGTGTGACTT
23529184 AGGCATTACT
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
21 1 0.01
22 16 0.14
23 95 0.84
24 1 0.01
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.38
Consensus pattern (23 bp):
TAAGGCATTGTGTGACTTGTTAG
Found at i:23529127 original size:46 final size:46
Alignment explanation
Indices: 23529035--23529183 Score: 212
Period size: 46 Copynumber: 3.3 Consensus size: 46
23529025 CTAATAAGGT
* * * * *
23529035 ATTGTGTGACTAGTT-G-ATAGGCATTGCGTGACTTGTTAGTAAGGC
1 ATTGTGTGACTTGTTAGTA-AGGTATTGTGTGACTAGTTAGTACGGC
* *
23529080 ATTGCGTGACTTGTTAGTAAGGTATTGTGTGACTAGTTAATACGGC
1 ATTGTGTGACTTGTTAGTAAGGTATTGTGTGACTAGTTAGTACGGC
23529126 ATTGTGTGACTTGTTAGTAAGGTATTGTGTGACTAGTTAGTACGGC
1 ATTGTGTGACTTGTTAGTAAGGTATTGTGTGACTAGTTAGTACGGC
23529172 ATTGTGTGACTT
1 ATTGTGTGACTT
23529184 AGGCATTACT
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
45 13 0.14
46 79 0.85
47 1 0.01
ACGTcount: A:0.22, C:0.10, G:0.30, T:0.38
Consensus pattern (46 bp):
ATTGTGTGACTTGTTAGTAAGGTATTGTGTGACTAGTTAGTACGGC
Found at i:23529144 original size:69 final size:68
Alignment explanation
Indices: 23529029--23529182 Score: 236
Period size: 69 Copynumber: 2.2 Consensus size: 68
23529019 TAGTTTCTAA
* *
23529029 TAAGGTATTGTGTGACTAGTTGATAGGCATTGCGTGACTTGTTAGTAAGGCATTGCGTGACTTGT
1 TAAGGTATTGTGTGACTAGTTAATAGGCATTGCGTGACTTGTTAGTAAGGCATTGCGTGACTAGT
23529094 TAG
66 TAG
* * *
23529097 TAAGGTATTGTGTGACTAGTTAATACGGCATTGTGTGACTTGTTAGTAAGGTATTGTGTGACTAG
1 TAAGGTATTGTGTGACTAGTTAATA-GGCATTGCGTGACTTGTTAGTAAGGCATTGCGTGACTAG
23529162 TTAG
65 TTAG
* *
23529166 TACGGCATTGTGTGACT
1 TAAGGTATTGTGTGACT
23529183 TAGGCATTAC
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
68 24 0.31
69 54 0.69
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.38
Consensus pattern (68 bp):
TAAGGTATTGTGTGACTAGTTAATAGGCATTGCGTGACTTGTTAGTAAGGCATTGCGTGACTAGT
TAG
Found at i:23529240 original size:22 final size:21
Alignment explanation
Indices: 23529215--23529276 Score: 79
Period size: 22 Copynumber: 2.9 Consensus size: 21
23529205 TCACACAATG
*
23529215 CCTAAAAACTAGTCACGTAATA
1 CCTAAAAAC-AATCACGTAATA
* *
23529237 CCTAAAATCAATCACGTAATG
1 CCTAAAAACAATCACGTAATA
23529258 CCTAAAAATCAATCACGTA
1 CCTAAAAA-CAATCACGTA
23529277 GTGATTAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.23
Consensus pattern (21 bp):
CCTAAAAACAATCACGTAATA
Found at i:23529251 original size:21 final size:22
Alignment explanation
Indices: 23529227--23529276 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
23529217 TAAAAACTAG
23529227 TCACGTAATACCT-AAAATCAA
1 TCACGTAATACCTAAAAATCAA
*
23529248 TCACGTAATGCCTAAAAATCAA
1 TCACGTAATACCTAAAAATCAA
23529270 TCACGTA
1 TCACGTA
23529277 GTGATTAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (22 bp):
TCACGTAATACCTAAAAATCAA
Found at i:23538368 original size:2 final size:2
Alignment explanation
Indices: 23538355--23538449 Score: 82
Period size: 2 Copynumber: 47.5 Consensus size: 2
23538345 TTTACTGGAG
* * * * *
23538355 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT GT GT GT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * *
23538397 GT AT AT AT AT GT GT AT AC AT AT GT GT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23538439 AT AT AT AT AT A
1 AT AT AT AT AT A
23538450 CACACATATG
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (2 bp):
AT
Found at i:23542616 original size:21 final size:22
Alignment explanation
Indices: 23542575--23542622 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
23542565 CTCTTTGGTA
* * *
23542575 TAGAAGAGATGAAGATGGAAAT
1 TAGAGGAGATAAAGATGGAAAG
23542597 TAGAGGAGATAAAG-TGGAAAG
1 TAGAGGAGATAAAGATGGAAAG
23542618 TAGAG
1 TAGAG
23542623 TTATATAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.48, C:0.00, G:0.35, T:0.17
Consensus pattern (22 bp):
TAGAGGAGATAAAGATGGAAAG
Found at i:23543494 original size:3 final size:3
Alignment explanation
Indices: 23543486--23543512 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
23543476 CAGTTCCCTC
23543486 CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA
23543513 AAGAAACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:23557167 original size:24 final size:24
Alignment explanation
Indices: 23557135--23557269 Score: 180
Period size: 24 Copynumber: 5.6 Consensus size: 24
23557125 GCGTCACTAG
* *
23557135 CGGTTGATGCACCATCATCCCCAC
1 CGGTCGATGCACCAGCATCCCCAC
*
23557159 CGGTCGATGCACCATCATCCCCAC
1 CGGTCGATGCACCAGCATCCCCAC
* *
23557183 CGGTCGATGCGCCAGCATTCCCAC
1 CGGTCGATGCACCAGCATCCCCAC
* * *
23557207 CTGTCTATGCACCAGCATTCCCAC
1 CGGTCGATGCACCAGCATCCCCAC
23557231 CGGTCGATGCACCAGCATCCCCAC
1 CGGTCGATGCACCAGCATCCCCAC
* *
23557255 CGGTTGACGCACCAG
1 CGGTCGATGCACCAG
23557270 TATTACCGCC
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 99 1.00
ACGTcount: A:0.20, C:0.42, G:0.20, T:0.18
Consensus pattern (24 bp):
CGGTCGATGCACCAGCATCCCCAC
Found at i:23557285 original size:24 final size:24
Alignment explanation
Indices: 23557258--23557304 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
23557248 TCCCCACCGG
*
23557258 TTGACGCACCAGTATTACCGCCGT
1 TTGACGAACCAGTATTACCGCCGT
*
23557282 TTGATGAACCAGTATTACCGCCG
1 TTGACGAACCAGTATTACCGCCG
23557305 GAGGATTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (24 bp):
TTGACGAACCAGTATTACCGCCGT
Found at i:23557293 original size:72 final size:73
Alignment explanation
Indices: 23557138--23557293 Score: 199
Period size: 72 Copynumber: 2.2 Consensus size: 73
23557128 TCACTAGCGG
* * * * *
23557138 TTGATGCACCATCATCCCCACCGGTCGATGCACCATCATCCCCACCGGTCGATGCGCCAGCATTC
1 TTGATGCACCAGCATCCCCACCGGTCGATGCACCAGCATCCCCACCGGTCGACGCACCAGCATTA
23557203 CCACCTGT
66 CCACCTGT
* * * *
23557211 CT-ATGCACCAGCATTCCCACCGGTCGATGCACCAGCATCCCCACCGGTTGACGCACCAGTATTA
1 TTGATGCACCAGCATCCCCACCGGTCGATGCACCAGCATCCCCACCGGTCGACGCACCAGCATTA
*
23557275 CCGCC-GT
66 CCACCTGT
*
23557282 TTGATGAACCAG
1 TTGATGCACCAG
23557294 TATTACCGCC
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
71 3 0.04
72 66 0.94
73 1 0.01
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.20
Consensus pattern (73 bp):
TTGATGCACCAGCATCCCCACCGGTCGATGCACCAGCATCCCCACCGGTCGACGCACCAGCATTA
CCACCTGT
Found at i:23560364 original size:24 final size:24
Alignment explanation
Indices: 23560337--23560387 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
23560327 TGTTTTCTTT
*
23560337 TGTTCTTGTCCTTGCTGC-TGCTGC
1 TGTTCTTGTCCTTG-TCCTTGCTGC
*
23560361 TGTTCTTGTTCTTGTCCTTGCTGC
1 TGTTCTTGTCCTTGTCCTTGCTGC
23560385 TGT
1 TGT
23560388 CCTGTCGTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.00, C:0.25, G:0.24, T:0.51
Consensus pattern (24 bp):
TGTTCTTGTCCTTGTCCTTGCTGC
Found at i:23562118 original size:2 final size:2
Alignment explanation
Indices: 23562113--23562150 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
23562103 CTCTCTCTAC
23562113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23562151 AAAGATCGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23579556 original size:57 final size:58
Alignment explanation
Indices: 23579490--23579605 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
23579480 CCGAACAAAA
*
23579490 CAAAATAAAACAAACAAATGT-ACACCTGTTCCCATTTCCAGACATTACAGCATCCCG
1 CAAAATAAAACAAACAAATGTAACACCAGTTCCCATTTCCAGACATTACAGCATCCCG
*
23579547 CAAAATAAAACAGACAAATGTAACACCAGTTCCCATTTCCAGACATTACAGCATCCCG
1 CAAAATAAAACAAACAAATGTAACACCAGTTCCCATTTCCAGACATTACAGCATCCCG
23579605 C
1 C
23579606 GAATAAAGGA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 20 0.36
58 36 0.64
ACGTcount: A:0.41, C:0.30, G:0.09, T:0.20
Consensus pattern (58 bp):
CAAAATAAAACAAACAAATGTAACACCAGTTCCCATTTCCAGACATTACAGCATCCCG
Found at i:23595306 original size:23 final size:23
Alignment explanation
Indices: 23595276--23595326 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
23595266 AGATAAAAAC
*
23595276 GACGTCCCTCAAAGTAATGCAGA
1 GACGTCCCTCAAAGTAATACAGA
23595299 GACGTCCCTCAAAGTAATACAGA
1 GACGTCCCTCAAAGTAATACAGA
23595322 GACGT
1 GACGT
23595327 TATCCATCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (23 bp):
GACGTCCCTCAAAGTAATACAGA
Found at i:23606002 original size:2 final size:2
Alignment explanation
Indices: 23605995--23606056 Score: 67
Period size: 2 Copynumber: 32.0 Consensus size: 2
23605985 TAACAAGGAG
23605995 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
** *
23606035 -A CTN GA GA GA GA GA GG GA GA GA
1 GA -GA GA GA GA GA GA GA GA GA GA
23606057 ACTCTGGTCT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
1 3 0.06
2 48 0.94
ACGTcount: A:0.45, C:0.02, G:0.50, T:0.02
Consensus pattern (2 bp):
GA
Found at i:23616956 original size:18 final size:18
Alignment explanation
Indices: 23616933--23616980 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
23616923 GTCGATGCCG
23616933 GCGACTCCTGG-GACACCA
1 GCGACTCC-GGTGACACCA
23616951 GCGACTCCGGTGACACC-
1 GCGACTCCGGTGACACCA
*
23616968 GACGACGCCGGTG
1 G-CGACTCCGGTG
23616981 TCAGCGCGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 3 0.11
18 24 0.89
ACGTcount: A:0.19, C:0.38, G:0.33, T:0.10
Consensus pattern (18 bp):
GCGACTCCGGTGACACCA
Found at i:23624191 original size:5 final size:5
Alignment explanation
Indices: 23624181--23624206 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
23624171 CTTGACTTTT
23624181 CTTCC CTTCC CTTCC CTTCC CTTCC C
1 CTTCC CTTCC CTTCC CTTCC CTTCC C
23624207 AGTCCTTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (5 bp):
CTTCC
Found at i:23625616 original size:23 final size:22
Alignment explanation
Indices: 23625576--23625618 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
23625566 TAATTTCTTG
*
23625576 AAAAATAAATATATTAAAATTA
1 AAAAATAAATATAATAAAATTA
*
23625598 AAAAATAAATTTTAATAAAAT
1 AAAAATAAA-TATAATAAAAT
23625619 AGACACCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAAATAAATATAATAAAATTA
Found at i:23639656 original size:2 final size:2
Alignment explanation
Indices: 23639649--23639689 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
23639639 TCCAACACAA
23639649 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23639690 TAATTTAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23642687 original size:2 final size:2
Alignment explanation
Indices: 23642680--23642711 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
23642670 ACTGAAATGA
23642680 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23642712 TTAGAACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23643800 original size:23 final size:24
Alignment explanation
Indices: 23643774--23643818 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
23643764 AATCGGCCGA
23643774 AAAAGAATA-TACTTAACTAAAGT
1 AAAAGAATACTACTTAACTAAAGT
** *
23643797 AAAATCATACTATTTAACTAAA
1 AAAAGAATACTACTTAACTAAA
23643819 AAAATGAGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (24 bp):
AAAAGAATACTACTTAACTAAAGT
Found at i:23649614 original size:12 final size:11
Alignment explanation
Indices: 23649575--23649612 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
23649565 GGAACTAATT
23649575 ATTTTTTTTCC
1 ATTTTTTTTCC
23649586 ATTTTTTTTCC
1 ATTTTTTTTCC
23649597 ATTTGTTTTT-C
1 ATTT-TTTTTCC
23649608 ATTTT
1 ATTTT
23649613 GTGGCTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 1 0.04
11 20 0.77
12 5 0.19
ACGTcount: A:0.11, C:0.13, G:0.03, T:0.74
Consensus pattern (11 bp):
ATTTTTTTTCC
Found at i:23665566 original size:69 final size:69
Alignment explanation
Indices: 23665483--23665692 Score: 194
Period size: 69 Copynumber: 3.0 Consensus size: 69
23665473 TTAACTTGTT
* * * * *
23665483 ACACGCCATGTACAAAAACCTGTGACAAGTCGTGGTTAGCGTATTACATGTTATATATAAAAATA
1 ACACGCCATATACAAAAACCTGTGACAAGTCATGGTTAGCGTATTACACGCTATATACAAAAATA
23665548 TGTG
66 TGTG
* * * * *
23665552 ACACGTCATATACAAAAATCTGTGATAAGTCATGGTTAGCGTGTTACACGCTATGTACAAAAATA
1 ACACGCCATATACAAAAACCTGTGACAAGTCATGGTTAGCGTATTACACGCTATATACAAAAATA
23665617 TGTG
66 TGTG
* * * * * * * *
23665621 -CAAAGCCA-AGTACAAAATCCTGTGACAAATTATGATTAG-GTTGTTACACGCCATGTACAAAA
1 AC-ACGCCATA-TACAAAAACCTGTGACAAGTCATGGTTAGCG-TATTACACGCTATATACAAAA
23665683 ACT-TGTG
63 A-TATGTG
23665690 ACA
1 ACA
23665693 AGTCATGATT
Statistics
Matches: 117, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
68 3 0.03
69 112 0.96
70 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (69 bp):
ACACGCCATATACAAAAACCTGTGACAAGTCATGGTTAGCGTATTACACGCTATATACAAAAATA
TGTG
Found at i:23665567 original size:114 final size:114
Alignment explanation
Indices: 23665386--23665614 Score: 302
Period size: 114 Copynumber: 2.0 Consensus size: 114
23665376 CACGCCATGT
* * * *
23665386 ACCTGTGACAAGCTATGGTTAGTGTGTTATATGCTATATACAAAAATATGTGACACGTCATGCAC
1 ACCTGTGACAAGCTATGGTTAGCGTATTACATGCTATATACAAAAATATGTGACACGTCATACAC
*
23665451 AAAAA-CTTATGATAAG-CTATGGTTAACTTGTTACACGCCATGTACAAAA
66 AAAAATC-TATGATAAGTC-ATGGTTAACGTGTTACACGCCATGTACAAAA
* * * *
23665500 ACCTGTGACAAG-TCGTGGTTAGCGTATTACATGTTATATATAAAAATATGTGACACGTCATATA
1 ACCTGTGACAAGCT-ATGGTTAGCGTATTACATGCTATATACAAAAATATGTGACACGTCATACA
* * *
23665564 CAAAAATCTGTGATAAGTCATGGTTAGCGTGTTACACGCTATGTACAAAA
65 CAAAAATCTATGATAAGTCATGGTTAACGTGTTACACGCCATGTACAAAA
23665614 A
1 A
23665615 TATGTGCAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
113 1 0.01
114 97 0.97
115 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (114 bp):
ACCTGTGACAAGCTATGGTTAGCGTATTACATGCTATATACAAAAATATGTGACACGTCATACAC
AAAAATCTATGATAAGTCATGGTTAACGTGTTACACGCCATGTACAAAA
Found at i:23665583 original size:24 final size:24
Alignment explanation
Indices: 23665535--23665584 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
23665525 ATTACATGTT
* *
23665535 ATATATAAAAATATGTGACACGTC
1 ATATACAAAAATATGTGACAAGTC
* *
23665559 ATATACAAAAATCTGTGATAAGTC
1 ATATACAAAAATATGTGACAAGTC
23665583 AT
1 AT
23665585 GGTTAGCGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (24 bp):
ATATACAAAAATATGTGACAAGTC
Found at i:23665728 original size:45 final size:45
Alignment explanation
Indices: 23665625--23665721 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 45
23665615 TATGTGCAAA
* * * *
23665625 GCCAAGTACAAAATCCTGTGACAAATTATGATTAGGTTGTTACAC
1 GCCATGTACAAAAACTTGTGACAAATCATGATTAGGTTGTTACAC
*
23665670 GCCATGTACAAAAACTTGTGACAAGTCATGATTAGGTTGTTACAC
1 GCCATGTACAAAAACTTGTGACAAATCATGATTAGGTTGTTACAC
*
23665715 GTCATGT
1 GCCATGT
23665722 TGAAAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (45 bp):
GCCATGTACAAAAACTTGTGACAAATCATGATTAGGTTGTTACAC
Found at i:23665775 original size:24 final size:25
Alignment explanation
Indices: 23665738--23665784 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
23665728 AAAATACTGT
23665738 TGTTACACGCCAT-GTAAAAAAACA
1 TGTTACACGCCATGGTAAAAAAACA
* * *
23665762 TGTTATACGTCATGGTTAAAAAA
1 TGTTACACGCCATGGTAAAAAAA
23665785 GGTTGTTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (25 bp):
TGTTACACGCCATGGTAAAAAAACA
Found at i:23665824 original size:32 final size:32
Alignment explanation
Indices: 23665787--23665870 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 32
23665777 TTAAAAAAGG
*
23665787 TTGTTACACGTCATATTGAAAAAAAAATATTA
1 TTGTTACACGACATATTGAAAAAAAAATATTA
* * *
23665819 TTGTTACACGCCATGTTG---AAACAATATTA
1 TTGTTACACGACATATTGAAAAAAAAATATTA
* *
23665848 TTGTTATACGACATATTTAAAAA
1 TTGTTACACGACATATTGAAAAA
23665871 CATTTTGTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
29 24 0.57
32 18 0.43
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.36
Consensus pattern (32 bp):
TTGTTACACGACATATTGAAAAAAAAATATTA
Found at i:23679201 original size:18 final size:18
Alignment explanation
Indices: 23679178--23679215 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
23679168 AGAGTAACCG
23679178 GCAGTTTTGACATCATTT
1 GCAGTTTTGACATCATTT
23679196 GCAGTTTTGACATCATTT
1 GCAGTTTTGACATCATTT
23679214 GC
1 GC
23679216 CATGCGTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (18 bp):
GCAGTTTTGACATCATTT
Found at i:23702515 original size:19 final size:19
Alignment explanation
Indices: 23702493--23702530 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
23702483 AATTTTAATT
*
23702493 TTTTTTTAAATTTTTATAA
1 TTTTTTTAAAATTTTATAA
23702512 TTTTTTTAAAATTTTATAA
1 TTTTTTTAAAATTTTATAA
23702531 ACTTTTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTTTAAAATTTTATAA
Found at i:23702536 original size:19 final size:19
Alignment explanation
Indices: 23702495--23702536 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
23702485 TTTTAATTTT
* **
23702495 TTTTTAAATTTTTATAATT
1 TTTTTAAAATTTTATAAAC
23702514 TTTTTAAAATTTTATAAAC
1 TTTTTAAAATTTTATAAAC
23702533 TTTT
1 TTTT
23702537 AATGATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTAAAATTTTATAAAC
Found at i:23703511 original size:2 final size:2
Alignment explanation
Indices: 23703504--23703544 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
23703494 ACATTTAATC
*
23703504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23703545 AATGACACCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23704840 original size:7 final size:7
Alignment explanation
Indices: 23704828--23704853 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
23704818 ATAAATAATT
23704828 TTATTAA
1 TTATTAA
23704835 TTATTAA
1 TTATTAA
23704842 TTATTAA
1 TTATTAA
23704849 TTATT
1 TTATT
23704854 TTTATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTATTAA
Found at i:23704872 original size:19 final size:20
Alignment explanation
Indices: 23704845--23704883 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
23704835 TTATTAATTA
*
23704845 TTAATTATTTT-TATATTTT
1 TTAAATATTTTATATATTTT
23704864 TTAAATATTTTATATATTTT
1 TTAAATATTTTATATATTTT
23704884 AACTTATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTAAATATTTTATATATTTT
Found at i:23704923 original size:17 final size:14
Alignment explanation
Indices: 23704887--23704914 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
23704877 ATATTTTAAC
23704887 TTATAATTATTATA
1 TTATAATTATTATA
23704901 TTATAATTATTATA
1 TTATAATTATTATA
23704915 AAATTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATAATTATTATA
Found at i:23710366 original size:2 final size:2
Alignment explanation
Indices: 23710323--23710354 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
23710313 GCTCCTCTTC
23710323 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
23710355 AATTGCCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:23713389 original size:11 final size:11
Alignment explanation
Indices: 23713360--23713393 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
23713350 TTAATGACAT
23713360 TTAA-CATTAA
1 TTAATCATTAA
23713370 TTGAATCATTAA
1 TT-AATCATTAA
23713382 TTAATCATTAA
1 TTAATCATTAA
23713393 T
1 T
23713394 GTGTTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.09
11 12 0.55
12 8 0.36
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (11 bp):
TTAATCATTAA
Found at i:23718066 original size:12 final size:12
Alignment explanation
Indices: 23718049--23718086 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
23718039 AGGGTAAACC
23718049 GGGGGCTTAGTT
1 GGGGGCTTAGTT
*
23718061 GGGGGCTGAGTT
1 GGGGGCTTAGTT
*
23718073 GGTGGCTTAGTT
1 GGGGGCTTAGTT
23718085 GG
1 GG
23718087 AGGGTGAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.08, C:0.08, G:0.53, T:0.32
Consensus pattern (12 bp):
GGGGGCTTAGTT
Found at i:23718071 original size:60 final size:60
Alignment explanation
Indices: 23717976--23718089 Score: 183
Period size: 60 Copynumber: 1.9 Consensus size: 60
23717966 GTGGGTATGT
* * *
23717976 TGGAGGGTGAACTGGTGGCTTAGTCGGGGGATGAGTTGGTGGCTTAGTTGGAGGCTTCAC
1 TGGAGGGTAAACCGGGGGCTTAGTCGGGGGATGAGTTGGTGGCTTAGTTGGAGGCTTCAC
* *
23718036 TGGAGGGTAAACCGGGGGCTTAGTTGGGGGCTGAGTTGGTGGCTTAGTTGGAGG
1 TGGAGGGTAAACCGGGGGCTTAGTCGGGGGATGAGTTGGTGGCTTAGTTGGAGG
23718090 GTGAACTGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.15, C:0.11, G:0.47, T:0.27
Consensus pattern (60 bp):
TGGAGGGTAAACCGGGGGCTTAGTCGGGGGATGAGTTGGTGGCTTAGTTGGAGGCTTCAC
Found at i:23718079 original size:24 final size:24
Alignment explanation
Indices: 23718036--23718104 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
23718026 GAGGCTTCAC
* * *
23718036 TGGAGGGTAAACCGGGGGCTTAGT
1 TGGAGGGTGAACTGGTGGCTTAGT
**
23718060 TGG-GGGCTGAGTTGGTGGCTTAGT
1 TGGAGGG-TGAACTGGTGGCTTAGT
23718084 TGGAGGGTGAACTGGTGGCTT
1 TGGAGGGTGAACTGGTGGCTT
23718105 GGGTGGGTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
23 3 0.08
24 30 0.83
25 3 0.08
ACGTcount: A:0.14, C:0.10, G:0.48, T:0.28
Consensus pattern (24 bp):
TGGAGGGTGAACTGGTGGCTTAGT
Found at i:23718104 original size:48 final size:48
Alignment explanation
Indices: 23718000--23718091 Score: 112
Period size: 48 Copynumber: 1.9 Consensus size: 48
23717990 GTGGCTTAGT
* * * * *
23718000 CGGGGGATGAGTTGGTGGCTTAGTTGGAGGCTTCACTGGAGGGTAAAC
1 CGGGGGCTTAGTTGGGGGCTGAGTTGGAGGCTTAACTGGAGGGTAAAC
* **
23718048 CGGGGGCTTAGTTGGGGGCTGAGTTGGTGGCTTAGTTGGAGGGT
1 CGGGGGCTTAGTTGGGGGCTGAGTTGGAGGCTTAACTGGAGGGT
23718092 GAACTGGTGG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 36 1.00
ACGTcount: A:0.14, C:0.11, G:0.48, T:0.27
Consensus pattern (48 bp):
CGGGGGCTTAGTTGGGGGCTGAGTTGGAGGCTTAACTGGAGGGTAAAC
Found at i:23718118 original size:33 final size:33
Alignment explanation
Indices: 23718081--23718143 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
23718071 TTGGTGGCTT
23718081 AGTTGGAGGGTGAACTGGTGGCTTGGGTGGGTA
1 AGTTGGAGGGTGAACTGGTGGCTTGGGTGGGTA
* *
23718114 AGTTGGTGGTTGAACTGGTGGCTTGGGTGG
1 AGTTGGAGGGTGAACTGGTGGCTTGGGTGG
23718144 AGCGTAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.13, C:0.06, G:0.51, T:0.30
Consensus pattern (33 bp):
AGTTGGAGGGTGAACTGGTGGCTTGGGTGGGTA
Found at i:23718184 original size:24 final size:24
Alignment explanation
Indices: 23718115--23718187 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
23718105 GGGTGGGTAA
23718115 GTTGGTGGTTGAACTGGTGGCTTG
1 GTTGGTGGTTGAACTGGTGGCTTG
* * * *
23718139 GGTGGAGCG-T-AAGTTGGCGGCTTG
1 GTTGGTG-GTTGAA-CTGGTGGCTTG
23718163 GTTGGTGGTTGAACTGGTGGCTTG
1 GTTGGTGGTTGAACTGGTGGCTTG
23718187 G
1 G
23718188 GCGGAGCGTA
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
23 3 0.08
24 31 0.84
25 3 0.08
ACGTcount: A:0.10, C:0.10, G:0.48, T:0.33
Consensus pattern (24 bp):
GTTGGTGGTTGAACTGGTGGCTTG
Found at i:23718208 original size:24 final size:24
Alignment explanation
Indices: 23718133--23718211 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
23718123 TTGAACTGGT
23718133 GGCTTGGGTGGAGCGTAAGTTGGC
1 GGCTTGGGTGGAGCGTAAGTTGGC
* * * *
23718157 GGCTTGGTTGGTG-GTTGAA-CTGGT
1 GGCTTGGGTGGAGCG-T-AAGTTGGC
*
23718181 GGCTTGGGCGGAGCGTAAGTTGGC
1 GGCTTGGGTGGAGCGTAAGTTGGC
23718205 GGCTTGG
1 GGCTTGG
23718212 TTGGTGGCTT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
23 3 0.07
24 36 0.86
25 3 0.07
ACGTcount: A:0.10, C:0.13, G:0.49, T:0.28
Consensus pattern (24 bp):
GGCTTGGGTGGAGCGTAAGTTGGC
Found at i:23718230 original size:48 final size:48
Alignment explanation
Indices: 23718115--23718218 Score: 199
Period size: 48 Copynumber: 2.2 Consensus size: 48
23718105 GGGTGGGTAA
*
23718115 GTTGGTGGTTGAACTGGTGGCTTGGGTGGAGCGTAAGTTGGCGGCTTG
1 GTTGGTGGTTGAACTGGTGGCTTGGGCGGAGCGTAAGTTGGCGGCTTG
23718163 GTTGGTGGTTGAACTGGTGGCTTGGGCGGAGCGTAAGTTGGCGGCTTG
1 GTTGGTGGTTGAACTGGTGGCTTGGGCGGAGCGTAAGTTGGCGGCTTG
23718211 GTTGGTGG
1 GTTGGTGG
23718219 CTTGGGTGGT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.10, C:0.11, G:0.49, T:0.31
Consensus pattern (48 bp):
GTTGGTGGTTGAACTGGTGGCTTGGGCGGAGCGTAAGTTGGCGGCTTG
Found at i:23718332 original size:18 final size:18
Alignment explanation
Indices: 23718289--23718338 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
23718279 AGTGGGTGGA
23718289 GGGGTGGGTGGATGAGGATG
1 GGGGTGGG-GG-TGAGGATG
*
23718309 GGGGTGGGGGTGAGGGTG
1 GGGGTGGGGGTGAGGATG
* *
23718327 GTGGTGGTGGTG
1 GGGGTGGGGGTG
23718339 GTGATGACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 17 0.63
19 2 0.07
20 8 0.30
ACGTcount: A:0.08, C:0.00, G:0.70, T:0.22
Consensus pattern (18 bp):
GGGGTGGGGGTGAGGATG
Found at i:23740247 original size:10 final size:11
Alignment explanation
Indices: 23740232--23740260 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
23740222 CTTCCCAAAC
23740232 AAAAGAAAAG-
1 AAAAGAAAAGA
23740242 AAAAGAAAAGA
1 AAAAGAAAAGA
23740253 AAAAGAAA
1 AAAAGAAA
23740261 TTGAAGGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:23741987 original size:16 final size:17
Alignment explanation
Indices: 23741956--23741991 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
23741946 CTTTTTGCTA
*
23741956 ATTATCATTATAATTTT
1 ATTATAATTATAATTTT
23741973 ATTATAATT-TAATTTT
1 ATTATAATTATAATTTT
23741989 ATT
1 ATT
23741992 TAGTAACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATAATTATAATTTT
Found at i:23745282 original size:19 final size:19
Alignment explanation
Indices: 23745258--23745294 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
23745248 AATTTTTATG
23745258 ATCTTTATC-CAAAGAATTT
1 ATCTTTA-CACAAAGAATTT
23745277 ATCTTTACACAAAGAATT
1 ATCTTTACACAAAGAATT
23745295 AACATATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (19 bp):
ATCTTTACACAAAGAATTT
Found at i:23761196 original size:17 final size:17
Alignment explanation
Indices: 23761174--23761207 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23761164 TTTTTTTTTG
*
23761174 GTTTAAAATAGATTTAT
1 GTTTAAAATAAATTTAT
*
23761191 GTTTAAAGTAAATTTAT
1 GTTTAAAATAAATTTAT
23761208 AACAAGGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
GTTTAAAATAAATTTAT
Found at i:23770218 original size:23 final size:25
Alignment explanation
Indices: 23770183--23770240 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 25
23770173 ATCAGTTTAT
* *
23770183 TTTTTAT-TTTTTTTAA-AAAATTA
1 TTTTTATAATTTTATAATAAAATTA
23770206 TTTTTATAATTTTATAATAAAATTA
1 TTTTTATAATTTTATAATAAAATTA
23770231 --TTTATAATTT
1 TTTTTATAATTT
23770241 AATTTATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 17 0.55
24 7 0.23
25 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTTTATAATTTTATAATAAAATTA
Found at i:23774132 original size:45 final size:45
Alignment explanation
Indices: 23773976--23774135 Score: 205
Period size: 45 Copynumber: 3.6 Consensus size: 45
23773966 ACAATCTAAT
*
23773976 CATGACGTGTAACAACCTAATCATAACTTGTCACATGTTTTTGTA
1 CATGACGTGTAACAACCTAATCATGACTTGTCACATGTTTTTGTA
* * * * * *
23774021 CATGGCGTGCAACAACCTAA-CTACGACTTGTCAGATATTTTTATA
1 CATGACGTGTAACAACCTAATC-ATGACTTGTCACATGTTTTTGTA
* * *
23774066 TATGACGTGTAACAACTTAATCATGACTTGTCATATGTTTTTGTA
1 CATGACGTGTAACAACCTAATCATGACTTGTCACATGTTTTTGTA
*
23774111 CGTGACGTGTAACAACCTAATCATG
1 CATGACGTGTAACAACCTAATCATG
23774136 GCGTGTAACA
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
44 1 0.01
45 93 0.98
46 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (45 bp):
CATGACGTGTAACAACCTAATCATGACTTGTCACATGTTTTTGTA
Found at i:23778519 original size:36 final size:36
Alignment explanation
Indices: 23778467--23778547 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
23778457 AATCACGTCA
* * *
23778467 TTCAATTGTAACAGTGTAGGTGCCTCCCTACCTAGG
1 TTCAGTTGTAACAGTGTAGATGCCTCCCTACCCAGG
* * *
23778503 TTTAGTTGTAGCAGTGTCGATGCCTCCCTACCCAGG
1 TTCAGTTGTAACAGTGTAGATGCCTCCCTACCCAGG
23778539 TTCAGTTGT
1 TTCAGTTGT
23778548 GTTCCACTAC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (36 bp):
TTCAGTTGTAACAGTGTAGATGCCTCCCTACCCAGG
Found at i:23788252 original size:2 final size:2
Alignment explanation
Indices: 23788245--23788289 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
23788235 CTTTTATAAT
23788245 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
23788288 TA
1 TA
23788290 AAATAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:23790451 original size:12 final size:12
Alignment explanation
Indices: 23790436--23790469 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
23790426 GTGGCGGCAA
23790436 GAGAGAGAAAGT
1 GAGAGAGAAAGT
23790448 GAGAGAGGAAAGT
1 GAGAGA-GAAAGT
23790461 GAAGAGAGA
1 G-AGAGAGA
23790470 GAAAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 9 0.45
14 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.44, T:0.06
Consensus pattern (12 bp):
GAGAGAGAAAGT
Found at i:23790475 original size:16 final size:15
Alignment explanation
Indices: 23790434--23790473 Score: 66
Period size: 14 Copynumber: 2.8 Consensus size: 15
23790424 GAGTGGCGGC
23790434 AAGAGAGAGAAAGTG
1 AAGAGAGAGAAAGTG
23790449 -AGAGAG-GAAAGTG
1 AAGAGAGAGAAAGTG
23790462 AAGAGAGAGAAA
1 AAGAGAGAGAAA
23790474 AGAAAAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.30
14 12 0.52
15 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.40, T:0.05
Consensus pattern (15 bp):
AAGAGAGAGAAAGTG
Found at i:23791637 original size:9 final size:8
Alignment explanation
Indices: 23791618--23791657 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
23791608 ATCTAAATAG
23791618 AAAATAAA
1 AAAATAAA
23791626 AAAATAAAA
1 AAAAT-AAA
*
23791635 AAAATAAT
1 AAAATAAA
23791643 AAAATAAA
1 AAAATAAA
*
23791651 TAAATAA
1 AAAATAA
23791658 TCCATGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAATAAA
Found at i:23791640 original size:17 final size:17
Alignment explanation
Indices: 23791618--23791650 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
23791608 ATCTAAATAG
23791618 AAAATAAAAAAATAAAA
1 AAAATAAAAAAATAAAA
*
23791635 AAAATAATAAAATAAA
1 AAAATAAAAAAATAAA
23791651 TAAATAATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAATAAAAAAATAAAA
Found at i:23793115 original size:35 final size:35
Alignment explanation
Indices: 23793069--23793141 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
23793059 GTCTAAATGA
23793069 CTGTCAGTACAAGTATTTACACCTCACATCCATGC
1 CTGTCAGTACAAGTATTTACACCTCACATCCATGC
23793104 CTGTCAGTACAAGTATTTACACCTCACATCCATGC
1 CTGTCAGTACAAGTATTTACACCTCACATCCATGC
23793139 CTG
1 CTG
23793142 CAAGCTTTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.27, C:0.32, G:0.12, T:0.29
Consensus pattern (35 bp):
CTGTCAGTACAAGTATTTACACCTCACATCCATGC
Found at i:23800646 original size:2 final size:2
Alignment explanation
Indices: 23800641--23800691 Score: 65
Period size: 2 Copynumber: 27.5 Consensus size: 2
23800631 CTAAACTAAT
23800641 TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA TA TA -A TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
23800679 TT TA TA TA TA TA T
1 TA TA TA TA TA TA T
23800692 TAGAAAGATT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
1 4 0.09
2 40 0.91
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:23804596 original size:13 final size:13
Alignment explanation
Indices: 23804578--23804606 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
23804568 TAACTTGTCG
23804578 TATAAGGTACATA
1 TATAAGGTACATA
23804591 TATAAGGTACATA
1 TATAAGGTACATA
23804604 TAT
1 TAT
23804607 TAACTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (13 bp):
TATAAGGTACATA
Found at i:23805508 original size:26 final size:26
Alignment explanation
Indices: 23805478--23805547 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
23805468 TTACTTTTTG
23805478 TGAAAAATATGTTGTTGAC-ACCATGT
1 TGAAAAATATGTTGTT-ACAACCATGT
**
23805504 TGAAAAATATAATGTTACATACCATGT
1 TGAAAAATATGTTGTTACA-ACCATGT
23805531 T-AAAAATATAGTTGTTA
1 TGAAAAATAT-GTTGTTA
23805548 AATGTCATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 2 0.05
26 22 0.59
27 13 0.35
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (26 bp):
TGAAAAATATGTTGTTACAACCATGT
Found at i:23805546 original size:27 final size:27
Alignment explanation
Indices: 23805480--23805574 Score: 81
Period size: 27 Copynumber: 3.6 Consensus size: 27
23805470 ACTTTTTGTG
23805480 AAAAATAT-GTTGTTGAC--ACCATGTT
1 AAAAATATAGTTGTT-ACATACCATGTT
*
23805505 GAAAAATATA-ATGTTACATACCATGTT
1 -AAAAATATAGTTGTTACATACCATGTT
* **
23805532 AAAAATATAGTTGTTAAATGTCATGTT
1 AAAAATATAGTTGTTACATACCATGTT
* * *
23805559 CAAAATTTATTTGTTA
1 AAAAATATAGTTGTTA
23805575 TATGTTATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
25 2 0.04
26 21 0.37
27 34 0.60
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (27 bp):
AAAAATATAGTTGTTACATACCATGTT
Found at i:23805590 original size:27 final size:27
Alignment explanation
Indices: 23805533--23805590 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
23805523 TACCATGTTA
*
23805533 AAAATATAGTTGTTAAATGTCATGTTC
1 AAAATATAGTTGTTAAATGTCATATTC
* * * * *
23805560 AAAATTTATTTGTTATATGTTATATTG
1 AAAATATAGTTGTTAAATGTCATATTC
23805587 AAAA
1 AAAA
23805591 ATGTAATTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (27 bp):
AAAATATAGTTGTTAAATGTCATATTC
Found at i:23805615 original size:28 final size:28
Alignment explanation
Indices: 23805584--23805658 Score: 91
Period size: 26 Copynumber: 2.8 Consensus size: 28
23805574 ATATGTTATA
*
23805584 TTGAAAAATGTAATTATTACACGTCACG
1 TTGAAAAATGTAATTATTACACATCACG
* * *
23805612 TTG--AAATTTAATTATTACACATTATG
1 TTGAAAAATGTAATTATTACACATCACG
*
23805638 TTGAAAAATGTAATTGTTACA
1 TTGAAAAATGTAATTATTACA
23805659 TGCTATGTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 22 0.56
28 17 0.44
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (28 bp):
TTGAAAAATGTAATTATTACACATCACG
Found at i:23805619 original size:54 final size:54
Alignment explanation
Indices: 23805561--23805712 Score: 155
Period size: 54 Copynumber: 2.8 Consensus size: 54
23805551 GTCATGTTCA
* **
23805561 AAATTTATTTGTTATATGTTATATTGAAAAATGTAATTATTACACG-TCACGTTG
1 AAATTTAATTGTTATACATTATATTGAAAAATGTAATTATTACACGCT-ACGTTG
* * * * * *
23805615 AAATTTAATTATTACACATTATGTTGAAAAATGTAATTGTTACATGCTATGTTG
1 AAATTTAATTGTTATACATTATATTGAAAAATGTAATTATTACACGCTACGTTG
* * * *
23805669 AAGATTTAGTTGTTATACCTCATATTG-AAAATTTAATTATTACA
1 AA-ATTTAATTGTTATACATTATATTGAAAAATGTAATTATTACA
23805713 AATTATATTG
Statistics
Matches: 79, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
54 60 0.76
55 19 0.24
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (54 bp):
AAATTTAATTGTTATACATTATATTGAAAAATGTAATTATTACACGCTACGTTG
Found at i:23805655 original size:82 final size:82
Alignment explanation
Indices: 23805560--23805780 Score: 239
Period size: 82 Copynumber: 2.7 Consensus size: 82
23805550 TGTCATGTTC
* * * * * * * *
23805560 AAAATTTATTTGTTATATGTTATATTGAAAAATGTAATTATTACACGTCACGTTGAAATTTAATT
1 AAAATATAATTGTTACATGCTATATTGAAAAATTTAATTGTTACACATCATGTTGAAATTTAATT
* *
23805625 ATTACACATTATGTTGA
66 ATTACAAATTATATTGA
* * * * * * *
23805642 AAAATGTAATTGTTACATGCTATGTTG-AAGATTTAGTTGTTATACCTCATATTGAAAATTTAAT
1 AAAATATAATTGTTACATGCTATATTGAAAAATTTAATTGTTACACATCATGTTG-AAATTTAAT
23805706 TATTACAAATTATATTGA
65 TATTACAAATTATATTGA
* * *
23805724 AAAATATAGTTATTACATGCCATATT-AAAAATTTAATTGTTACACATCATGTTGAAA
1 AAAATATAATTGTTACATGCTATATTGAAAAATTTAATTGTTACACATCATGTTGAAA
23805781 AATGTAGTTG
Statistics
Matches: 112, Mismatches: 25, Indels: 5
0.79 0.18 0.04
Matches are distributed among these distances:
81 22 0.20
82 90 0.80
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (82 bp):
AAAATATAATTGTTACATGCTATATTGAAAAATTTAATTGTTACACATCATGTTGAAATTTAATT
ATTACAAATTATATTGA
Found at i:23805748 original size:55 final size:55
Alignment explanation
Indices: 23805689--23805795 Score: 151
Period size: 55 Copynumber: 1.9 Consensus size: 55
23805679 TGTTATACCT
* *
23805689 CATATTGAAAATTTAATTATTACAAATTATATTGAAAAATATAGTTATTACATGC
1 CATATTAAAAATTTAATTATTACAAATCATATTGAAAAATATAGTTATTACATGC
* * * * *
23805744 CATATTAAAAATTTAATTGTTACACATCATGTTGAAAAATGTAGTTGTTACA
1 CATATTAAAAATTTAATTATTACAAATCATATTGAAAAATATAGTTATTACA
23805796 CATAATGATA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.39
Consensus pattern (55 bp):
CATATTAAAAATTTAATTATTACAAATCATATTGAAAAATATAGTTATTACATGC
Found at i:23816643 original size:24 final size:24
Alignment explanation
Indices: 23816599--23816645 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
23816589 TATTGAGATT
23816599 ATTTTTTCACATTTTATATAAAAA
1 ATTTTTTCACATTTTATATAAAAA
23816623 ATTTGTTTCA-ATTATTA-ATAAAA
1 ATTT-TTTCACATT-TTATATAAAA
23816646 TAATATAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (24 bp):
ATTTTTTCACATTTTATATAAAAA
Found at i:23822053 original size:2 final size:2
Alignment explanation
Indices: 23822046--23822072 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23822036 CTACAAATTG
23822046 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
23822073 AAGACTTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23826498 original size:2 final size:2
Alignment explanation
Indices: 23826491--23826520 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23826481 AAACACGCGT
23826491 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
23826521 CGGAAAGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:23826551 original size:2 final size:2
Alignment explanation
Indices: 23826544--23826572 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23826534 TCTTCTTTNT
23826544 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
23826573 CGAAAGGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:23852473 original size:12 final size:13
Alignment explanation
Indices: 23852448--23852481 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
23852438 TTATTAAGAA
23852448 AAAAAATTTATAT
1 AAAAAATTTATAT
23852461 AAAAAATTT-TAT
1 AAAAAATTTATAT
23852473 -AAAAATTTA
1 AAAAAATTTA
23852482 ATATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 8 0.40
12 3 0.15
13 9 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAAAATTTATAT
Found at i:23852919 original size:23 final size:23
Alignment explanation
Indices: 23852876--23852920 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
23852866 TGAAATATTT
* *
23852876 TTTATTATAATTATTAGTAAAAA
1 TTTATTATAATTATAAATAAAAA
23852899 TTTATT-TAATTTATAAATAAAA
1 TTTATTATAA-TTATAAATAAAA
23852921 TTTTGAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTATTATAATTATAAATAAAAA
Found at i:23852991 original size:15 final size:16
Alignment explanation
Indices: 23852964--23852996 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
23852954 TTATTTTAAT
23852964 AATATTGAATAATTTA
1 AATATTGAATAATTTA
23852980 AATATT-AATAATTTA
1 AATATTGAATAATTTA
23852995 AA
1 AA
23852997 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
AATATTGAATAATTTA
Found at i:23852998 original size:16 final size:17
Alignment explanation
Indices: 23852958--23852998 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
23852948 AAGTTTTTAT
23852958 TTTAATAATATTGAATAA
1 TTTAA-AATATTGAATAA
23852976 TTT-AAATATT-AATAA
1 TTTAAAATATTGAATAA
23852991 TTTAAAAT
1 TTTAAAAT
23852999 TTTTAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.36
16 10 0.45
17 1 0.05
18 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
TTTAAAATATTGAATAA
Found at i:23853174 original size:20 final size:20
Alignment explanation
Indices: 23853151--23853196 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
23853141 TTGATTCGTA
23853151 AAATATTTTAT-ATTTAAAAT
1 AAATATTTTATCATTT-AAAT
* *
23853171 AAATTTTTTATCCTTTAAAT
1 AAATATTTTATCATTTAAAT
23853191 AAATAT
1 AAATAT
23853197 AAATCTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATATTTTATCATTTAAAT
Found at i:23861767 original size:20 final size:20
Alignment explanation
Indices: 23861740--23861786 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
23861730 AAGGTGTATT
23861740 TAAA-TTTTTAAAATAATTTA
1 TAAATTTTTTAAAAT-ATTTA
* *
23861760 -AAATTTTTTTAACTATTTA
1 TAAATTTTTTAAAATATTTA
23861779 TAAATTTT
1 TAAATTTT
23861787 AAAATCTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TAAATTTTTTAAAATATTTA
Found at i:23868777 original size:22 final size:22
Alignment explanation
Indices: 23868752--23868806 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
23868742 GTGATTAGTG
*
23868752 TTTAAGTATTGCATGACTAATT
1 TTTAGGTATTGCATGACTAATT
*
23868774 TTTAGGTATTGCTTGACTAATT
1 TTTAGGTATTGCATGACTAATT
23868796 TTTAGGTATTG
1 TTTAGGTATTG
23868807 TGTAACTGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.49
Consensus pattern (22 bp):
TTTAGGTATTGCATGACTAATT
Found at i:23868883 original size:45 final size:45
Alignment explanation
Indices: 23868833--23868927 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
23868823 TGATATTGTA
* *
23868833 TGACTAGTTGAT-AGGCATTACGTAATTAGTTAGTAAGACATTGCG
1 TGACTAGTTAATAAGGCATTACGTAACTAGTTAGTAAG-CATTGCG
** *
23868878 TGACTAGTTAATAAGGCATTACGTAACTAGTTTTTAAGCATTGTG
1 TGACTAGTTAATAAGGCATTACGTAACTAGTTAGTAAGCATTGCG
23868923 TGACT
1 TGACT
23868928 TAGGTATTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 22 0.50
46 22 0.50
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.36
Consensus pattern (45 bp):
TGACTAGTTAATAAGGCATTACGTAACTAGTTAGTAAGCATTGCG
Found at i:23868885 original size:23 final size:22
Alignment explanation
Indices: 23868833--23868927 Score: 73
Period size: 23 Copynumber: 4.2 Consensus size: 22
23868823 TGATATTGTA
* * *
23868833 TGACTAGTTGATAGGCATTACG
1 TGACTAGTTAATAAGCATTGCG
* * *
23868855 TAATTAGTTAGTAAGACATTGCG
1 TGACTAGTTAATAAG-CATTGCG
*
23868878 TGACTAGTTAATAAGGCATTACG
1 TGACTAGTTAATAA-GCATTGCG
* ** *
23868901 TAACTAGTTTTTAAGCATTGTG
1 TGACTAGTTAATAAGCATTGCG
23868923 TGACT
1 TGACT
23868928 TAGGTATTGT
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
22 20 0.36
23 34 0.62
24 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.36
Consensus pattern (22 bp):
TGACTAGTTAATAAGCATTGCG
Found at i:23869010 original size:23 final size:23
Alignment explanation
Indices: 23868938--23869011 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 23
23868928 TAGGTATTGT
* * *
23868938 CTAAAAATC-AATCACGCAATAT
1 CTAAAAATCTAGTCACACAATAC
* *
23868960 CT-ACAATCTAGTCACATAATAC
1 CTAAAAATCTAGTCACACAATAC
*
23868982 CTAAAAATC-AGTCACACAATGC
1 CTAAAAATCTAGTCACACAATAC
23869004 CTAAAAAT
1 CTAAAAAT
23869012 AAAAAACATA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 5 0.12
22 32 0.76
23 5 0.12
ACGTcount: A:0.47, C:0.24, G:0.05, T:0.23
Consensus pattern (23 bp):
CTAAAAATCTAGTCACACAATAC
Found at i:23869081 original size:22 final size:22
Alignment explanation
Indices: 23869056--23869107 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
23869046 AAACCAGTCT
23869056 CACAATACCTAAAAACTAATAA
1 CACAATACCTAAAAACTAATAA
**
23869078 CACAATGTCTAAAAACTAATAA
1 CACAATACCTAAAAACTAATAA
*
23869100 TACAATAC
1 CACAATAC
23869108 ATAATATCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.56, C:0.21, G:0.02, T:0.21
Consensus pattern (22 bp):
CACAATACCTAAAAACTAATAA
Found at i:23870450 original size:18 final size:19
Alignment explanation
Indices: 23870427--23870466 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
23870417 AATGTTCAAA
23870427 ATTTTTTTAAA-AATAAAT
1 ATTTTTTTAAATAATAAAT
*
23870445 A-TTTTTTAAATTATAAAT
1 ATTTTTTTAAATAATAAAT
23870463 ATTT
1 ATTT
23870467 GATTTTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 9 0.47
18 8 0.42
19 2 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTTTTAAATAATAAAT
Found at i:23873324 original size:16 final size:18
Alignment explanation
Indices: 23873288--23873326 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
23873278 AATCTAAGTT
23873288 TATTATTTTATTATTAAAA
1 TATTATTTTATTATT-AAA
23873307 TATTATTTTA-TATT-AA
1 TATTATTTTATTATTAAA
23873323 TATT
1 TATT
23873327 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
18 4 0.20
19 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTATTTTATTATTAAA
Found at i:23874487 original size:17 final size:18
Alignment explanation
Indices: 23874455--23874491 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
23874445 CATTATCAGA
23874455 TCTCTTTCTCTTTTTTTTC
1 TCTCTTTCTC-TTTTTTTC
23874474 TCTCTTTCTCTTTTTTTC
1 TCTCTTTCTCTTTTTTTC
23874492 ATGAAACAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (18 bp):
TCTCTTTCTCTTTTTTTC
Found at i:23878785 original size:2 final size:2
Alignment explanation
Indices: 23878778--23878804 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23878768 CATCATCATC
23878778 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
23878805 GAATGTCCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23884365 original size:15 final size:15
Alignment explanation
Indices: 23884345--23884377 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
23884335 ATTTCTATAA
23884345 TATTGTTATTATTAT
1 TATTGTTATTATTAT
*
23884360 TATTGTTATTGTTAT
1 TATTGTTATTATTAT
23884375 TAT
1 TAT
23884378 CCTCCCCTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (15 bp):
TATTGTTATTATTAT
Found at i:23894227 original size:2 final size:2
Alignment explanation
Indices: 23894220--23894254 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
23894210 CAGGAAAAAT
*
23894220 GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
23894255 AAAATGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:23897342 original size:23 final size:23
Alignment explanation
Indices: 23897316--23897366 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
23897306 GTGAAGCTGT
*
23897316 AATAACTATCTTCAGATAAAAGC
1 AATAACTATCTTCAGATAAAAGA
23897339 AATAACTATCTTCAGATAAAAGA
1 AATAACTATCTTCAGATAAAAGA
23897362 AATAA
1 AATAA
23897367 AATAAGACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.53, C:0.14, G:0.08, T:0.25
Consensus pattern (23 bp):
AATAACTATCTTCAGATAAAAGA
Found at i:23897986 original size:135 final size:135
Alignment explanation
Indices: 23897803--23898086 Score: 358
Period size: 135 Copynumber: 2.1 Consensus size: 135
23897793 CTCTGCAAAC
* * * * * ** *
23897803 TATTACTACAGAAAGATTCTGAAGGTCCATCATTTTTGGCCTCACCATTAGATGAATC-GCTAGC
1 TATTACCACAGGATGATTCTGAAGATCCATCACTTTTCACCTCACCATTAGATGAATCACCT-GC
* * * * *
23897867 AGCTGAAACTGGTTG-GCATTCTTGCTTAGGGGCTGTAAAACCCCCATTTGCTTGACAATAATTC
65 AGCTGAAACTGGTTGCCCATT-TTCCTTAGGGACTATAAAACCCCCATTTGCTTGACAATAAGTC
23897931 TGGGAGTT
129 TGGGA-TT
* **
23897939 T-TTACCACAGGATGATTCTGAAGATTCATCACTTTTCACCTCACCATTAGATGCGTCACCTGCA
1 TATTACCACAGGATGATTCTGAAGATCCATCACTTTTCACCTCACCATTAGATGAATCACCTGCA
* *
23898003 GCTGAAAGTGGTTGCCCATTTTCCTTAGGGACTATAAAACCCCCATTTGCTTGATAATAAGTCTG
66 GCTGAAACTGGTTGCCCATTTTCCTTAGGGACTATAAAACCCCCATTTGCTTGACAATAAGTCTG
23898068 GGATT
131 GGATT
23898073 TATTACCACAGGAT
1 TATTACCACAGGAT
23898087 TTTGAAGTTT
Statistics
Matches: 127, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
134 3 0.02
135 117 0.92
136 7 0.06
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (135 bp):
TATTACCACAGGATGATTCTGAAGATCCATCACTTTTCACCTCACCATTAGATGAATCACCTGCA
GCTGAAACTGGTTGCCCATTTTCCTTAGGGACTATAAAACCCCCATTTGCTTGACAATAAGTCTG
GGATT
Found at i:23898498 original size:11 final size:12
Alignment explanation
Indices: 23898469--23898499 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
23898459 GGATGACCGC
23898469 CATTTAAACAGT
1 CATTTAAACAGT
23898481 CATTTAAACAGT
1 CATTTAAACAGT
23898493 -ATTTAAA
1 CATTTAAA
23898500 GGACGAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (12 bp):
CATTTAAACAGT
Found at i:23912346 original size:21 final size:21
Alignment explanation
Indices: 23912322--23912367 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
23912312 AAACTAGAAC
*
23912322 TAAAATTACTAGTAACACCCT
1 TAAAATTACTAGTAACACCAT
*
23912343 TAAAATTATTAGTAACACCAT
1 TAAAATTACTAGTAACACCAT
23912364 TAAA
1 TAAA
23912368 GCATTCCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.30
Consensus pattern (21 bp):
TAAAATTACTAGTAACACCAT
Found at i:23916214 original size:22 final size:21
Alignment explanation
Indices: 23916175--23916218 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
23916165 TCTTCATGAC
*
23916175 TAATAATTAATTAATTATTAT
1 TAATAATAAATTAATTATTAT
*
23916196 TAATAATAATATTACTTATTAT
1 TAATAATAA-ATTAATTATTAT
23916218 T
1 T
23916219 TTATATCTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TAATAATAAATTAATTATTAT
Found at i:23916349 original size:33 final size:33
Alignment explanation
Indices: 23916306--23916375 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 33
23916296 AACATATTAT
*
23916306 ATCATCATCAATTATAATATGTTAA-TATATCAC
1 ATCATAATCAATTATAATA-GTTAAGTATATCAC
*
23916339 ATCATAATCAATTATGATAGTTAAGTATATCAC
1 ATCATAATCAATTATAATAGTTAAGTATATCAC
23916372 ATCA
1 ATCA
23916376 ACGTTATATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 5 0.15
33 29 0.85
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (33 bp):
ATCATAATCAATTATAATAGTTAAGTATATCAC
Found at i:23917690 original size:6 final size:6
Alignment explanation
Indices: 23917679--23917707 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
23917669 CAGACCCCAT
23917679 TCCCCC TCCCCC TCCCCC TCCCCC TCCCC
1 TCCCCC TCCCCC TCCCCC TCCCCC TCCCC
23917708 GTAGAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.83, G:0.00, T:0.17
Consensus pattern (6 bp):
TCCCCC
Found at i:23927644 original size:2 final size:2
Alignment explanation
Indices: 23927637--23927670 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
23927627 TCTGTTAGAT
23927637 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
23927671 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:23927717 original size:2 final size:2
Alignment explanation
Indices: 23927712--23927745 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
23927702 ANGTTAGTAT
23927712 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
23927746 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:23936729 original size:2 final size:2
Alignment explanation
Indices: 23936722--23936768 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
23936712 TGTTTTACCT
23936722 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23936764 TA TA T
1 TA TA T
23936769 GTAGAAAGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23946020 original size:9 final size:9
Alignment explanation
Indices: 23945994--23946029 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
23945984 AATTTTTATA
23945994 ATTATAATT
1 ATTATAATT
*
23946003 AAT-TAATT
1 ATTATAATT
23946011 ATTATAATT
1 ATTATAATT
23946020 ATTATAATT
1 ATTATAATT
23946029 A
1 A
23946030 ATTAAACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
ATTATAATT
Found at i:23947706 original size:25 final size:25
Alignment explanation
Indices: 23947655--23947707 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
23947645 TTACTATTTA
*
23947655 ATTATTGTTAAAAATTTATAAAGAT
1 ATTATTGTTAAAAATATATAAAGAT
*
23947680 ATTATTGTTAAAAGTAT-TAAAGTAT
1 ATTATTGTTAAAAATATATAAAG-AT
23947705 ATT
1 ATT
23947708 TAAAAGTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (25 bp):
ATTATTGTTAAAAATATATAAAGAT
Done.