Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 152 of 199
Found at i:45508037 original size:49 final size:47
Alignment explanation
Indices: 45507978--45508132 Score: 117
Period size: 46 Copynumber: 3.3 Consensus size: 47
45507968 GAATTCAATC
45507978 AATATCAAGTTACGATATACTATCAGAAATCAAGAAAATATTTATACA
1 AATATCAAGTTAC-ATATACTATCAGAAATCAAGAAAATATTTATACA
* * * ** ** *
45508026 AATATACAAGTTGCATA-A-TTTAATCAATCAA-ATGA-ATTCA-ATC-
1 AATAT-CAAGTTACATATACTATCAGAAATCAAGAAAATATTTATA-CA
* *
45508069 AATAT-AAGTTACTATATACTATCGGAAATCAAGCAAATATTTATACA
1 AATATCAAGTTAC-ATATACTATCAGAAATCAAGAAAATATTTATACA
*
45508116 AATATACAAGTTGCATA
1 AATAT-CAAGTTACATA
45508133 ATTTGGTCAA
Statistics
Matches: 77, Mismatches: 19, Indels: 22
0.65 0.16 0.19
Matches are distributed among these distances:
41 6 0.08
42 3 0.04
43 7 0.09
44 13 0.17
45 3 0.04
46 14 0.18
47 7 0.09
48 11 0.14
49 13 0.17
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.31
Consensus pattern (47 bp):
AATATCAAGTTACATATACTATCAGAAATCAAGAAAATATTTATACA
Found at i:45508124 original size:90 final size:90
Alignment explanation
Indices: 45507928--45508206 Score: 423
Period size: 90 Copynumber: 3.1 Consensus size: 90
45507918 CAATGGTGAG
* * * * *
45507928 TTATACAAATATACAACTTGCATAATTCACTAAATCATATGAATTCAATCAATATCAAGTTACGA
1 TTATACAAATATACAAGTTGCATAATTTAATCAATCAAATGAATTCAATCAATAT-AAGTTACGA
*
45507993 TATACTATCAGAAATCAAGAAAATAT
65 TATACTATCGGAAATCAAGAAAATAT
*
45508019 TTATACAAATATACAAGTTGCATAATTTAATCAATCAAATGAATTCAATCAATATAAGTTACTAT
1 TTATACAAATATACAAGTTGCATAATTTAATCAATCAAATGAATTCAATCAATATAAGTTACGAT
*
45508084 ATACTATCGGAAATCAAGCAAATAT
66 ATACTATCGGAAATCAAGAAAATAT
** * * *
45508109 TTATACAAATATACAAGTTGCATAATTTGGTCAATCAAACGAATTCAATTAGTATAAGTTACGAT
1 TTATACAAATATACAAGTTGCATAATTTAATCAATCAAATGAATTCAATCAATATAAGTTACGAT
*
45508174 ATACTATCGAAAATCAAGAAAATAT
66 ATACTATCGGAAATCAAGAAAATAT
45508199 TTATACAA
1 TTATACAA
45508207 TTCAATATGC
Statistics
Matches: 172, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 122 0.71
91 50 0.29
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.32
Consensus pattern (90 bp):
TTATACAAATATACAAGTTGCATAATTTAATCAATCAAATGAATTCAATCAATATAAGTTACGAT
ATACTATCGGAAATCAAGAAAATAT
Found at i:45515822 original size:87 final size:86
Alignment explanation
Indices: 45515716--45515878 Score: 238
Period size: 87 Copynumber: 1.9 Consensus size: 86
45515706 TACATGCATA
* * *
45515716 AGGTTGATTTCTTACTCTTAATGAATTCATACCCCAAG-GTTTGGGTGGTCCTATTGAGATGGAC
1 AGGTTGATTTCTTAATCTTAATGAATTCATA-CCCAAGAGTTTGGGTGGTCCTATTGAAACGGAC
45515780 TTGATGAATTCACCGACATGTG
65 TTGATGAATTCACCGACATGTG
* * * *
45515802 AGGTTGAGTTTCTTAATCTTAATGAGTTTATATCCTAGAGTTTGGGTGGTCCTATTGAAACGGAC
1 AGGTTGA-TTTCTTAATCTTAATGAATTCATACCCAAGAGTTTGGGTGGTCCTATTGAAACGGAC
45515867 TTGATGAATTCA
65 TTGATGAATTCA
45515879 ACGAATTTAA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
86 11 0.16
87 57 0.84
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (86 bp):
AGGTTGATTTCTTAATCTTAATGAATTCATACCCAAGAGTTTGGGTGGTCCTATTGAAACGGACT
TGATGAATTCACCGACATGTG
Found at i:45517676 original size:27 final size:27
Alignment explanation
Indices: 45517616--45517677 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
45517606 CGTTTCGTTA
* *
45517616 GACTATCCTGTATTTAACATCCTGTTG
1 GACTATCTTGTATTTAACATCCTGTAG
* *
45517643 GATTATCTTGTGTTTAACATCAC-GTAG
1 GACTATCTTGTATTTAACATC-CTGTAG
45517670 GACTATCT
1 GACTATCT
45517678 ACGATGCCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 28 0.97
28 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.40
Consensus pattern (27 bp):
GACTATCTTGTATTTAACATCCTGTAG
Found at i:45518995 original size:18 final size:18
Alignment explanation
Indices: 45518958--45518995 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
45518948 AAAAAATCAC
*
45518958 ATTTTTTATATTTAATAT
1 ATTTTTTATATTTAAAAT
45518976 ATTTTTTA-ATTTCAAAAT
1 ATTTTTTATATTT-AAAAT
45518994 AT
1 AT
45518996 ATAGTGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTTTATATTTAAAAT
Found at i:45526127 original size:21 final size:21
Alignment explanation
Indices: 45526101--45526145 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
45526091 TAATCTCACC
*
45526101 GTATCCAATCTCACCGCTACA
1 GTATCCAATCTCACCACTACA
*
45526122 GTATCCAATCTCACCATTACA
1 GTATCCAATCTCACCACTACA
45526143 GTA
1 GTA
45526146 ACTAATTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.33, G:0.09, T:0.27
Consensus pattern (21 bp):
GTATCCAATCTCACCACTACA
Found at i:45539865 original size:2 final size:2
Alignment explanation
Indices: 45539858--45539908 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
45539848 ATTAAACCAT
45539858 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
45539900 TA TA TA TA T
1 TA TA TA TA T
45539909 GTTTTTGTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45540525 original size:22 final size:22
Alignment explanation
Indices: 45540497--45540554 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
45540487 TTTATTGTTC
45540497 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
45540519 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
45540541 AGCCATGAGAGCTT
1 AAACATGAGAGCTT
45540555 GGTCTTGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:45542102 original size:52 final size:52
Alignment explanation
Indices: 45541984--45542084 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
45541974 AAAACAAAGC
*
45541984 TTACATATATTGATTGAAAAATAAATTATGTTTAACATATGACAATATTAGA
1 TTACATATATTAATTGAAAAATAAATTATGTTTAACATATGACAATATTAGA
*
45542036 TTACATATATTAATTGAAAAATAAATTATGTTTAACTTATGACAATATT
1 TTACATATATTAATTGAAAAATAAATTATGTTTAACATATGACAATATT
45542085 GTAATTTATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.41
Consensus pattern (52 bp):
TTACATATATTAATTGAAAAATAAATTATGTTTAACATATGACAATATTAGA
Found at i:45544101 original size:3 final size:3
Alignment explanation
Indices: 45544059--45544089 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
45544049 TTTTTAAATT
*
45544059 TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
45544090 AGATGTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:45544152 original size:17 final size:19
Alignment explanation
Indices: 45544130--45544169 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
45544120 TATTTACTTT
45544130 TATTTTA-T-TTTATTATG
1 TATTTTATTCTTTATTATG
45544147 TATTTTATTCCTTTATTATG
1 TATTTTATT-CTTTATTATG
45544167 TAT
1 TAT
45544170 ATATTTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 1 0.05
20 12 0.60
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (19 bp):
TATTTTATTCTTTATTATG
Found at i:45544415 original size:2 final size:2
Alignment explanation
Indices: 45544410--45544444 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
45544400 TTTTACCTAT
45544410 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45544445 TTCATTTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45553194 original size:2 final size:2
Alignment explanation
Indices: 45553175--45553222 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
45553165 TGTAACTTGT
* *
45553175 TA TA T- TA TA T- TT TA TA TA TA TA TA TA AA 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
45553215 TA TA TA TA
1 TA TA TA TA
45553223 ATTTTATTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45556601 original size:39 final size:39
Alignment explanation
Indices: 45556527--45556601 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
45556517 AGTATCAAAA
*
45556527 TTTATATATTTCATATATCATAATATTAACCAATTTGAG
1 TTTATATATTTCATATATCATAATATTAACAAATTTGAG
*
45556566 TTTATATATTTCATATATCATAATATTAATAAATTT
1 TTTATATATTTCATATATCATAATATTAACAAATTT
45556602 AAATATCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (39 bp):
TTTATATATTTCATATATCATAATATTAACAAATTTGAG
Found at i:45562196 original size:2 final size:2
Alignment explanation
Indices: 45562189--45562265 Score: 129
Period size: 2 Copynumber: 38.0 Consensus size: 2
45562179 NNNNNNNNNN
45562189 TA TA TA TA TA GTA TA TA -A TA TA TA CTA 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
45562232 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
45562266 AACAATTCAA
Statistics
Matches: 72, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.01
2 67 0.93
3 4 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:45563248 original size:13 final size:13
Alignment explanation
Indices: 45563230--45563254 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45563220 CAAACGATAA
45563230 AAATTTTCACACG
1 AAATTTTCACACG
45563243 AAATTTTCACAC
1 AAATTTTCACAC
45563255 ATATAAATTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:45565147 original size:21 final size:22
Alignment explanation
Indices: 45565115--45565155 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
45565105 TTATATATAT
*
45565115 TTTTAGATTTTTTTTAAAATTA
1 TTTTAGATTTTTTTAAAAATTA
45565137 TTTTA-ATTTTTTTAAAAAT
1 TTTTAGATTTTTTTAAAAAT
45565156 ATAAATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTAGATTTTTTTAAAAATTA
Found at i:45565189 original size:18 final size:19
Alignment explanation
Indices: 45565168--45565210 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
45565158 AAATTTCAGA
*
45565168 AATTTTATAAA-TACTTTG
1 AATTTTAAAAATTACTTTG
*
45565186 AATTTTAAAAATTATTTTG
1 AATTTTAAAAATTACTTTG
45565205 AATTTT
1 AATTTT
45565211 TTATAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (19 bp):
AATTTTAAAAATTACTTTG
Found at i:45572931 original size:4 final size:4
Alignment explanation
Indices: 45572922--45572946 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
45572912 GGGAGAGAGG
45572922 GGGA GGGA GGGA GGGA GGGA GGGA G
1 GGGA GGGA GGGA GGGA GGGA GGGA G
45572947 AGCAGTGCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (4 bp):
GGGA
Found at i:45574557 original size:6 final size:6
Alignment explanation
Indices: 45574546--45574572 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
45574536 AAACAGCTAA
45574546 AAAACC AAAACC AAAACC AAAACC AAA
1 AAAACC AAAACC AAAACC AAAACC AAA
45574573 CTAAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.30, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACC
Found at i:45585432 original size:44 final size:46
Alignment explanation
Indices: 45585382--45585476 Score: 149
Period size: 47 Copynumber: 2.1 Consensus size: 46
45585372 TTTAAAACCT
*
45585382 CACAAGCTATGCA-T-TAAATGAAACACTTAATATTATATGCGGCA
1 CACAAGCTATGCATTATAAATGAAACACCTAATATTATATGCGGCA
*
45585426 CACAAGCTATGTATTAATAAATGAAACACCTAATATTATATGCGGCA
1 CACAAGCTATGCATT-ATAAATGAAACACCTAATATTATATGCGGCA
45585473 CACA
1 CACA
45585477 TTTATATTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
44 12 0.26
45 1 0.02
47 33 0.72
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (46 bp):
CACAAGCTATGCATTATAAATGAAACACCTAATATTATATGCGGCA
Found at i:45589703 original size:41 final size:42
Alignment explanation
Indices: 45589644--45589739 Score: 108
Period size: 41 Copynumber: 2.3 Consensus size: 42
45589634 TTACTTGATA
* * * * *
45589644 CAATACGCCGGCATAAAGCTTGCTAGGCTCAAGGCCT-AATT
1 CAATACACCGGCATAAAGCCTACTAGGCACAAAGCCTAAATT
45589685 CAATACACCGGC-TCAAAGCCTACTAGGCACAAAGCCTAAATT
1 CAATACACCGGCAT-AAAGCCTACTAGGCACAAAGCCTAAATT
*
45589727 -AATACACTGGCAT
1 CAATACACCGGCAT
45589740 GACGCCTGCT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
40 1 0.02
41 40 0.87
42 5 0.11
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (42 bp):
CAATACACCGGCATAAAGCCTACTAGGCACAAAGCCTAAATT
Found at i:45596771 original size:18 final size:18
Alignment explanation
Indices: 45596750--45596792 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
45596740 ACTTTTATAT
45596750 CAAAAGTAATTTTTGTCC
1 CAAAAGTAATTTTTGTCC
**
45596768 CAAAAGTGCTTTTTGTCC
1 CAAAAGTAATTTTTGTCC
45596786 CAAAAGT
1 CAAAAGT
45596793 GTTTTTTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (18 bp):
CAAAAGTAATTTTTGTCC
Found at i:45596799 original size:18 final size:18
Alignment explanation
Indices: 45596759--45596798 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
45596749 TCAAAAGTAA
45596759 TTTTTGTCCCAAAAGTGC
1 TTTTTGTCCCAAAAGTGC
45596777 TTTTTGTCCCAAAAGTG-
1 TTTTTGTCCCAAAAGTGC
45596794 TTTTT
1 TTTTT
45596799 TAGAAGCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (18 bp):
TTTTTGTCCCAAAAGTGC
Found at i:45599193 original size:28 final size:28
Alignment explanation
Indices: 45599153--45599206 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
45599143 TCATTGAAAG
45599153 TAAAACTCTTTGACTTTGAAGTAAAATA
1 TAAAACTCTTTGACTTTGAAGTAAAATA
45599181 TAAAACTCTTTGACTTTGAAGTAAAA
1 TAAAACTCTTTGACTTTGAAGTAAAA
45599207 GTAAAATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (28 bp):
TAAAACTCTTTGACTTTGAAGTAAAATA
Found at i:45603867 original size:5 final size:5
Alignment explanation
Indices: 45603857--45603907 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
45603847 ATTGAAAAGT
* **
45603857 TTTAA TTTAA -TTAG TTTAA TTTTT TTATAA TTTAA TTTAA TTTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TT-TAA TTTAA TTTAA -TTTAA TTTAA
45603908 AAGTTTCACA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 3 0.08
5 26 0.70
6 8 0.22
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (5 bp):
TTTAA
Found at i:45603892 original size:16 final size:16
Alignment explanation
Indices: 45603857--45603907 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
45603847 ATTGAAAAGT
*
45603857 TTTAATTTAA--TTAG
1 TTTAATTTAATTTTAA
*
45603871 TTTAATTT-TTTTATAA
1 TTTAATTTAATTT-TAA
45603887 TTTAATTTAATTTTAA
1 TTTAATTTAATTTTAA
45603903 TTTAA
1 TTTAA
45603908 AAGTTTCACA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 8 0.27
15 1 0.03
16 18 0.60
17 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTAATTTAATTTTAA
Found at i:45604151 original size:12 final size:12
Alignment explanation
Indices: 45604116--45604151 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
45604106 GTTCAAGAAC
*
45604116 AAGCTCGTTTAA
1 AAGCTCGTTTAT
*
45604128 AAGCTCATTTAT
1 AAGCTCGTTTAT
45604140 AAGCTCGTTTAT
1 AAGCTCGTTTAT
45604152 TGACTCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (12 bp):
AAGCTCGTTTAT
Found at i:45611521 original size:11 final size:10
Alignment explanation
Indices: 45611482--45611546 Score: 57
Period size: 10 Copynumber: 6.8 Consensus size: 10
45611472 TAATATATAA
45611482 AAATTAAAAT
1 AAATTAAAAT
45611492 --ATTAAAAT
1 AAATTAAAAT
*
45611500 AAATTTAAAT
1 AAATTAAAAT
45611510 AAATTAACAAT
1 AAATTAA-AAT
*
45611521 --ATTGAAAT
1 AAATTAAAAT
* *
45611529 AAGTTCAAAT
1 AAATTAAAAT
45611539 AAATTAAA
1 AAATTAAA
45611547 GATGTTAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
8 11 0.26
9 4 0.09
10 25 0.58
11 3 0.07
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (10 bp):
AAATTAAAAT
Found at i:45611521 original size:29 final size:28
Alignment explanation
Indices: 45611441--45611558 Score: 100
Period size: 29 Copynumber: 4.1 Consensus size: 28
45611431 AATGAAATAT
45611441 ATAAATTTAAATATAATTTAAGAA-A-T-AA
1 ATAAATTTAAATA-AA-TTAA-AATATTAAA
*
45611469 ATATAATATATAA-AAATTAAAATATTAAA
1 ATA-AATTTA-AATAAATTAAAATATTAAA
*
45611498 ATAAATTTAAATAAATTAACAATATTGAA
1 ATAAATTTAAATAAATTAA-AATATTAAA
* * *
45611527 ATAAGTTCAAATAAATTAAAGATGTTAAA
1 ATAAATTTAAATAAATTAAA-ATATTAAA
45611556 ATA
1 ATA
45611559 TTTGAAAGAG
Statistics
Matches: 75, Mismatches: 7, Indels: 15
0.77 0.07 0.15
Matches are distributed among these distances:
26 2 0.03
27 7 0.09
28 19 0.25
29 45 0.60
30 2 0.03
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (28 bp):
ATAAATTTAAATAAATTAAAATATTAAA
Found at i:45611898 original size:3 final size:3
Alignment explanation
Indices: 45611890--45611965 Score: 75
Period size: 3 Copynumber: 25.3 Consensus size: 3
45611880 TATATAAGCA
** * *
45611890 AAT AAT AAT -AT CAAT AAT AGC AAT AAT ACT AAT AAT ACT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
45611935 AAT GAA- AGT AAT AAT AAT AAT AAT AAT AAT A
1 AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT A
45611966 TCAAAATTAT
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
2 3 0.05
3 52 0.88
4 4 0.07
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:45611980 original size:30 final size:29
Alignment explanation
Indices: 45611890--45611994 Score: 83
Period size: 30 Copynumber: 3.7 Consensus size: 29
45611880 TATATAAGCA
*
45611890 AATAATAAT-ATCAATAATAGC--AATAAT
1 AATAATAATAAT-AATAATATCAAAATAAT
* * * *
45611917 ACTAATAATACTAATAATAATGAAAGTAAT
1 AATAATAATAATAATAAT-ATCAAAATAAT
*
45611947 AATAATAATAATAATAATATCAAAATTATT
1 AATAATAATAATAATAATATCAAAA-TAAT
* *
45611977 AATATTAATGATAA-AATA
1 AATAATAATAATAATAATA
45611995 ACCAAACTAA
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
27 14 0.23
28 2 0.03
29 9 0.15
30 36 0.59
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (29 bp):
AATAATAATAATAATAATATCAAAATAAT
Found at i:45612679 original size:3 final size:3
Alignment explanation
Indices: 45612671--45612718 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
45612661 TTGTAAAATG
45612671 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
45612719 GTAAAACAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:45613227 original size:17 final size:17
Alignment explanation
Indices: 45613205--45613243 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
45613195 TATTGGACTT
45613205 TTATTTTTGGTTTTAAA
1 TTATTTTTGGTTTTAAA
45613222 TTA--TTTGGTTTTAAA
1 TTATTTTTGGTTTTAAA
45613237 TT-TTTTT
1 TTATTTTT
45613244 ATTTATGCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 14 0.70
16 3 0.15
17 3 0.15
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (17 bp):
TTATTTTTGGTTTTAAA
Found at i:45613230 original size:15 final size:15
Alignment explanation
Indices: 45613210--45613238 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
45613200 GACTTTTATT
45613210 TTTGGTTTTAAATTA
1 TTTGGTTTTAAATTA
45613225 TTTGGTTTTAAATT
1 TTTGGTTTTAAATT
45613239 TTTTTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (15 bp):
TTTGGTTTTAAATTA
Found at i:45613780 original size:7 final size:7
Alignment explanation
Indices: 45613768--45613797 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
45613758 TTAAGGGAGG
45613768 AAGAAGA
1 AAGAAGA
45613775 AAGAAGA
1 AAGAAGA
45613782 AAGAAG-
1 AAGAAGA
45613788 AAGAAGA
1 AAGAAGA
45613795 AAG
1 AAG
45613798 GACAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:45614912 original size:11 final size:11
Alignment explanation
Indices: 45614877--45614918 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
45614867 AAATGACACC
45614877 AAAACAACAAG
1 AAAACAACAAG
* * *
45614888 AAAACCATAGG
1 AAAACAACAAG
45614899 AAAACAACAAG
1 AAAACAACAAG
45614910 AAAACAACA
1 AAAACAACA
45614919 TATTTCTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.69, C:0.19, G:0.10, T:0.02
Consensus pattern (11 bp):
AAAACAACAAG
Found at i:45615271 original size:2 final size:2
Alignment explanation
Indices: 45615228--45615252 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45615218 ATGATATGTT
45615228 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
45615253 TAATAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45623704 original size:45 final size:44
Alignment explanation
Indices: 45623615--45623707 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 44
45623605 ATTACAACAT
45623615 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
*
45623659 CATTCCATTCAACCAAACA-ATTGAATTACTATTACAGCTT-TATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAG-TTCTATTC
45623704 CATT
1 CATT
45623708 ACACCTCTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
43 1 0.02
44 22 0.49
45 20 0.44
46 2 0.04
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
Found at i:45623710 original size:16 final size:16
Alignment explanation
Indices: 45623689--45623744 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
45623679 TTGAATTACT
*
45623689 ATTACAGCTTTATTCC
1 ATTACAGCTCTATTCC
*
45623705 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
45623721 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
45623737 ATTACAGC
1 ATTACAGC
45623745 GAATCAAACG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:45624137 original size:22 final size:23
Alignment explanation
Indices: 45624099--45624142 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
45624089 TAAATATTCT
*
45624099 AAATTATAATGAAAAT-ATAAAA
1 AAATTAAAATGAAAATAATAAAA
45624121 AAATTAAAAT-AATAATAATAAA
1 AAATTAAAATGAA-AATAATAAA
45624143 GTACAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 2 0.11
22 12 0.63
23 5 0.26
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (23 bp):
AAATTAAAATGAAAATAATAAAA
Found at i:45630268 original size:23 final size:23
Alignment explanation
Indices: 45630241--45630294 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
45630231 AAATTCAAAT
* *
45630241 TTCGAGTTAA-TTGAATCGAGTTA
1 TTCGAGTTAACTTGAAT-AAGTAA
*
45630264 TTCGAGTCAACTTGAATAAGTAA
1 TTCGAGTTAACTTGAATAAGTAA
45630287 TTCGAGTT
1 TTCGAGTT
45630295 TTGAGTTCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.37
Consensus pattern (23 bp):
TTCGAGTTAACTTGAATAAGTAA
Found at i:45630496 original size:20 final size:20
Alignment explanation
Indices: 45630426--45630498 Score: 75
Period size: 19 Copynumber: 3.8 Consensus size: 20
45630416 ACAAAAATTA
45630426 AAAAAGTTTCAAAATATTTT
1 AAAAAGTTTCAAAATATTTT
45630446 AAAAAAGTTT--AAATAATTTT
1 -AAAAAGTTTCAAAAT-ATTTT
*
45630466 TAAAA--TTCAAAATATTTAT
1 AAAAAGTTTCAAAATATTT-T
45630485 AAAAA-TTTCAAAAT
1 AAAAAGTTTCAAAAT
45630499 TTATGTTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
17 2 0.04
18 4 0.09
19 17 0.38
20 13 0.29
21 9 0.20
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (20 bp):
AAAAAGTTTCAAAATATTTT
Found at i:45632131 original size:15 final size:15
Alignment explanation
Indices: 45632111--45632162 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 15
45632101 TAGTTTCTTC
*
45632111 AAAAAAAAACTCG-A
1 AAAAAAAAATTCGAA
*
45632125 AAAAAAAATTTC-AA
1 AAAAAAAAATTCGAA
45632139 AAAAAAAAATTTCGAA
1 AAAAAAAAA-TTCGAA
45632155 AAAAAAAA
1 AAAAAAAA
45632163 CTAGTTTCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 19 0.59
15 3 0.09
16 10 0.31
ACGTcount: A:0.75, C:0.08, G:0.04, T:0.13
Consensus pattern (15 bp):
AAAAAAAAATTCGAA
Found at i:45632170 original size:19 final size:15
Alignment explanation
Indices: 45632124--45632162 Score: 69
Period size: 15 Copynumber: 2.5 Consensus size: 15
45632114 AAAAAACTCG
45632124 AAAAAAAAATTTCAA
1 AAAAAAAAATTTCAA
45632139 AAAAAAAAATTTCGAA
1 AAAAAAAAATTTC-AA
45632155 AAAAAAAA
1 AAAAAAAA
45632163 CTAGTTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (15 bp):
AAAAAAAAATTTCAA
Found at i:45632221 original size:13 final size:13
Alignment explanation
Indices: 45632203--45632254 Score: 86
Period size: 14 Copynumber: 3.8 Consensus size: 13
45632193 TATCAAGTTG
45632203 TGAAAAAAAAATT
1 TGAAAAAAAAATT
45632216 TGAAAAAAAAAATT
1 TG-AAAAAAAAATT
45632230 TGAAAAAAAAATT
1 TGAAAAAAAAATT
45632243 GTGAAAAAAAAA
1 -TGAAAAAAAAA
45632255 GTGAGAGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
13 13 0.35
14 24 0.65
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (13 bp):
TGAAAAAAAAATT
Found at i:45633230 original size:24 final size:24
Alignment explanation
Indices: 45633202--45633256 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
45633192 AAGAAAAATG
45633202 AAAGAAAAAGAAATAGAAATCGAA
1 AAAGAAAAAGAAATAGAAATCGAA
* * * * *
45633226 AAAGAAAATGAGATTGAAATTGCA
1 AAAGAAAAAGAAATAGAAATCGAA
45633250 AAAGAAA
1 AAAGAAA
45633257 GTATGGAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.65, C:0.04, G:0.18, T:0.13
Consensus pattern (24 bp):
AAAGAAAAAGAAATAGAAATCGAA
Found at i:45638195 original size:19 final size:20
Alignment explanation
Indices: 45638160--45638200 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
45638150 AACTATTTAA
* *
45638160 ATAATATTATTTGAATAGTT
1 ATAATATTATATGAATAATT
45638180 ATAATATTA-ATGAATAATT
1 ATAATATTATATGAATAATT
45638199 AT
1 AT
45638201 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (20 bp):
ATAATATTATATGAATAATT
Found at i:45644954 original size:23 final size:23
Alignment explanation
Indices: 45644922--45645038 Score: 164
Period size: 23 Copynumber: 5.1 Consensus size: 23
45644912 ATGCTAATAT
*
45644922 TGTTATCGAACTGATTTTGATAC
1 TGTTACCGAACTGATTTTGATAC
*
45644945 TGTTACCGAATTGATTTTGATAC
1 TGTTACCGAACTGATTTTGATAC
*
45644968 TGCTACC-ATACTGATTTTGATAC
1 TGTTACCGA-ACTGATTTTGATAC
* * *
45644991 TGTTACCAAACTAATTTTGATAT
1 TGTTACCGAACTGATTTTGATAC
45645014 TGTTACCGAACTGATTTTGATAC
1 TGTTACCGAACTGATTTTGATAC
45645037 TG
1 TG
45645039 AAATGCATGA
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
22 1 0.01
23 80 0.98
24 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (23 bp):
TGTTACCGAACTGATTTTGATAC
Found at i:45645895 original size:17 final size:16
Alignment explanation
Indices: 45645861--45645891 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
45645851 CCTATTTACT
*
45645861 TTCCCTCAAACTTTTA
1 TTCCCTAAAACTTTTA
45645877 TTCCCTAAAACTTTT
1 TTCCCTAAAACTTTT
45645892 TATTTTCCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (16 bp):
TTCCCTAAAACTTTTA
Found at i:45646535 original size:5 final size:5
Alignment explanation
Indices: 45646525--45646550 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
45646515 CTCGAAAATT
45646525 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
45646551 CGAATGTTCA
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:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:45647386 original size:14 final size:14
Alignment explanation
Indices: 45647367--45647393 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45647357 TTATATAATA
45647367 ATTAATTCCAAATT
1 ATTAATTCCAAATT
45647381 ATTAATTCCAAAT
1 ATTAATTCCAAAT
45647394 ACATTATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTAATTCCAAATT
Found at i:45650588 original size:20 final size:20
Alignment explanation
Indices: 45650490--45650593 Score: 65
Period size: 20 Copynumber: 5.1 Consensus size: 20
45650480 ATAAAGTAGG
45650490 TTATATATTATTTT-TTAACA
1 TTATATATTATTTTATTAA-A
45650510 TTATATATTATGATTT-TTATTAA
1 TTATATATTAT--TTTATTA--AA
* *
45650533 TT-TATA-T-TTTAATAATAA
1 TTATATATTATTTTATTA-AA
** *
45650551 TTATATTAAAAATTTATTAAA
1 TTATA-TATTATTTTATTAAA
45650572 TTATATATTATTTTATTAAA
1 TTATATATTATTTTATTAAA
45650592 TT
1 TT
45650594 TTATTTAATA
Statistics
Matches: 66, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
18 7 0.11
19 4 0.06
20 28 0.42
21 8 0.12
22 15 0.23
23 3 0.05
24 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (20 bp):
TTATATATTATTTTATTAAA
Found at i:45650617 original size:57 final size:60
Alignment explanation
Indices: 45650504--45650667 Score: 203
Period size: 57 Copynumber: 2.7 Consensus size: 60
45650494 ATATTATTTT
* *
45650504 TTAACATTATATATTATGATTTTTATT-AATTTATATTTTAATAATAATTATATTAAAA-ATTTA
1 TTAA-ATTAT-TATTATTATTTTTATTAAATTT-TA-TTTAATAATAATTATATTAAAATA-TGA
*
45650567 TTAAATTA-TA-TATTA-TTTTATTAAATTTTATTTAATAATAATTATGTTAAAATATGA
1 TTAAATTATTATTATTATTTTTATTAAATTTTATTTAATAATAATTATATTAAAATATGA
*
45650624 TTAAATTATTTATTATTATTTTTATTAAATTATATTTAATAATA
1 TTAAATTA-TTATTATTATTTTTATTAAATTTTATTTAATAATA
45650668 TTAATAATCA
Statistics
Matches: 91, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
57 31 0.34
58 10 0.11
59 11 0.12
60 7 0.08
61 24 0.26
62 4 0.04
63 4 0.04
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (60 bp):
TTAAATTATTATTATTATTTTTATTAAATTTTATTTAATAATAATTATATTAAAATATGA
Found at i:45650798 original size:44 final size:46
Alignment explanation
Indices: 45650748--45650835 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 46
45650738 TACAACATCT
*
45650748 ATTCCATTAAACCAAAC-ACAAGAA-TA-TTATTACAGCTCTATTTC
1 ATTCCATTAAACCAAACAAC-AGAATTACTGATTACAGCTCTATTTC
* *
45650792 ATTCCATTCAACCAAACAACTGAATTACTGATTACAGCTCTATT
1 ATTCCATTAAACCAAACAACAGAATTACTGATTACAGCTCTATT
45650836 CCACTACAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 19 0.50
45 4 0.11
46 15 0.39
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.32
Consensus pattern (46 bp):
ATTCCATTAAACCAAACAACAGAATTACTGATTACAGCTCTATTTC
Found at i:45652256 original size:17 final size:17
Alignment explanation
Indices: 45652234--45652284 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
45652224 TTTTTATGTT
*
45652234 TTATATATATTATTTTA
1 TTATATATATTATTATA
45652251 TTATATA-ATATATTATA
1 TTATATATAT-TATTATA
45652268 TTATAT-TA-TATTATA
1 TTATATATATTATTATA
45652283 TT
1 TT
45652285 GTTTTATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 9 0.29
16 2 0.06
17 20 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATATATTATTATA
Found at i:45652261 original size:5 final size:5
Alignment explanation
Indices: 45652234--45652298 Score: 73
Period size: 5 Copynumber: 13.2 Consensus size: 5
45652224 TTTTTATGTT
45652234 TTATA -TATA TTAT- TT-TA TTATA TAATATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
* *
45652283 TTGTT TTATA TTATA T
1 TTATA TTATA TTATA T
45652299 AAATTAAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
3 1 0.02
4 8 0.16
5 37 0.73
7 5 0.10
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:45652476 original size:8 final size:8
Alignment explanation
Indices: 45652465--45652503 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
45652455 AAATAAAGTA
45652465 AAAGAAAC
1 AAAGAAAC
45652473 AAAGAAAC
1 AAAGAAAC
45652481 AAAGAAGA-
1 AAAGAA-AC
45652489 AAAGAAAC
1 AAAGAAAC
*
45652497 AGAGAAA
1 AAAGAAA
45652504 GAGACGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 1 0.04
8 26 0.93
9 1 0.04
ACGTcount: A:0.74, C:0.08, G:0.18, T:0.00
Consensus pattern (8 bp):
AAAGAAAC
Found at i:45653111 original size:3 final size:3
Alignment explanation
Indices: 45653103--45653130 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
45653093 TAAAAATTTA
45653103 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
45653131 ATGATTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:45658814 original size:20 final size:19
Alignment explanation
Indices: 45658781--45658828 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
45658771 AAATAGTTTT
*
45658781 TTTTTTTAAATTTTAATAC
1 TTTTTTTAAATTTTAATAA
* *
45658800 TTTTTTTATAGTTTTTATAA
1 TTTTTTTA-AATTTTAATAA
45658820 TTTTTTTAA
1 TTTTTTTAA
45658829 TTATATGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTTTTAAATTTTAATAA
Found at i:45658863 original size:18 final size:18
Alignment explanation
Indices: 45658842--45658884 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
45658832 TATGGATTGG
45658842 TTTATAATTCA-AAATATA
1 TTTATAATT-ATAAATATA
*
45658860 TTTAAAATTATAAATATA
1 TTTATAATTATAAATATA
45658878 TTTATAA
1 TTTATAA
45658885 ATTTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTATAATTATAAATATA
Found at i:45658891 original size:18 final size:18
Alignment explanation
Indices: 45658853--45658892 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
45658843 TTATAATTCA
45658853 AAATATATTTAAAATTAT
1 AAATATATTTAAAATTAT
45658871 AAATATATTTATAAATT-T
1 AAATATATTTA-AAATTAT
45658889 AAAT
1 AAAT
45658893 TAATATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATATATTTAAAATTAT
Found at i:45658911 original size:20 final size:20
Alignment explanation
Indices: 45658853--45658911 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 20
45658843 TTATAATTCA
*
45658853 AAATATATTT-AAAAT-TAT
1 AAATATATTTAAAAATAAAT
*
45658871 AAATATATTTATAAATTTAAAT
1 AAATATATTTA-AAA-ATAAAT
*
45658893 TAATATATTTAAAAATAAA
1 AAATATATTTAAAAATAAA
45658912 AATTTGAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 10 0.30
20 7 0.21
21 4 0.12
22 12 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATATATTTAAAAATAAAT
Found at i:45658914 original size:22 final size:22
Alignment explanation
Indices: 45658872--45658915 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
45658862 TAAAATTATA
* **
45658872 AATATATTTATAAATTTAAATT
1 AATATATTTAAAAATAAAAATT
45658894 AATATATTTAAAAATAAAAATT
1 AATATATTTAAAAATAAAAATT
45658916 TGAAGAATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATATATTTAAAAATAAAAATT
Found at i:45660204 original size:10 final size:9
Alignment explanation
Indices: 45660165--45660304 Score: 62
Period size: 9 Copynumber: 15.4 Consensus size: 9
45660155 ACATGTGGCA
*
45660165 AAAAATGAT
1 AAAAATTAT
45660174 AAAAA--AT
1 AAAAATTAT
*
45660181 AAAAATAAAT
1 AAAAAT-TAT
*
45660191 AAAAGTTAT
1 AAAAATTAT
45660200 AAAAATTAT
1 AAAAATTAT
* *
45660209 TAAATTCTAAT
1 AAAAAT-T-AT
**
45660220 AAAAACAAT
1 AAAAATTAT
45660229 AAAAA-TATT
1 AAAAATTA-T
*
45660238 AAAAAATTAGA
1 -AAAAATTA-T
45660249 AAAAATTAT
1 AAAAATTAT
45660258 --AAATCT-T
1 AAAAAT-TAT
45660265 AAAAATTAT
1 AAAAATTAT
45660274 -AAAA-TAT
1 AAAAATTAT
*
45660281 AGAAAATATAG
1 A-AAAAT-TAT
45660292 AAAAATTAT
1 AAAAATTAT
45660301 AAAA
1 AAAA
45660305 TTTTATAAAG
Statistics
Matches: 100, Mismatches: 15, Indels: 32
0.68 0.10 0.22
Matches are distributed among these distances:
7 15 0.15
8 7 0.07
9 42 0.42
10 26 0.26
11 10 0.10
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (9 bp):
AAAAATTAT
Found at i:45660281 original size:7 final size:8
Alignment explanation
Indices: 45660250--45660373 Score: 52
Period size: 9 Copynumber: 14.0 Consensus size: 8
45660240 AAAATTAGAA
45660250 AAAATTAT
1 AAAATTAT
*
45660258 AAATCTTA-
1 AAA-ATTAT
45660266 AAAATTAT
1 AAAATTAT
*
45660274 AAAATATAG
1 AAAAT-TAT
*
45660283 AAAATATAGA
1 AAAAT-TA-T
45660293 AAAATTAT
1 AAAATTAT
45660301 AAAATTTTAT
1 AAAA--TTAT
* *
45660311 AAAGTCGTAAG
1 AAAAT--T-AT
45660322 AAAATTAT
1 AAAATTAT
* *
45660330 AAAAATGT
1 AAAATTAT
*
45660338 GAAGAAATAT
1 -AA-AATTAT
45660348 AAAATTCAT
1 AAAATT-AT
45660357 AAAAGTTAT
1 AAAA-TTAT
45660366 AAAATTAT
1 AAAATTAT
45660374 TGTATTAAAA
Statistics
Matches: 90, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
7 3 0.03
8 30 0.33
9 32 0.36
10 20 0.22
11 5 0.06
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.31
Consensus pattern (8 bp):
AAAATTAT
Found at i:45660606 original size:17 final size:17
Alignment explanation
Indices: 45660580--45660630 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
45660570 TTTTATAAAA
*
45660580 TTTTACAATTTTTTATT
1 TTTTATAATTTTTTATT
*
45660597 TTTTATAATTTTTTCTAT
1 TTTTATAATTTTTTAT-T
45660615 TTTT-TAATTTTTTATT
1 TTTTATAATTTTTTATT
45660631 AAATTTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 1 0.03
17 24 0.80
18 5 0.17
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTATAATTTTTTATT
Found at i:45660610 original size:27 final size:26
Alignment explanation
Indices: 45660559--45660647 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 26
45660549 GCATTTGATT
45660559 TTTTTTATGATTTTTATAAAATTTTACAA
1 TTTTTTAT--TTTTTATAAAATTTT-CAA
** *
45660588 TTTTTTATTTTTTATAATTTTTTCTA
1 TTTTTTATTTTTTATAAAATTTTCAA
*
45660614 TTTTTTAATTTTTTATTAAATTTT-AA
1 TTTTTT-ATTTTTTATAAAATTTTCAA
*
45660640 TATTTTAT
1 TTTTTTAT
45660648 AACTTTTGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
25 2 0.04
26 14 0.27
27 27 0.53
29 8 0.16
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (26 bp):
TTTTTTATTTTTTATAAAATTTTCAA
Found at i:45660626 original size:9 final size:9
Alignment explanation
Indices: 45660588--45660678 Score: 55
Period size: 10 Copynumber: 9.8 Consensus size: 9
45660578 AATTTTACAA
45660588 TTTTT-TAT
1 TTTTTATAT
45660596 TTTTTATAAT
1 TTTTTAT-AT
*
45660606 TTTTTCTAT
1 TTTTTATAT
45660615 TTTTTA-AT
1 TTTTTATAT
*
45660623 TTTTTATTAA
1 TTTTTA-TAT
*
45660633 ATTTTA-AT
1 TTTTTATAT
*
45660641 ATTTTATAACT
1 TTTTTAT-A-T
45660652 TTTGTTGAT-T
1 TTT-TT-ATAT
45660662 TTTTTATAT
1 TTTTTATAT
45660671 ATTTTTAT
1 -TTTTTAT
45660679 TGCCACATGT
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
8 22 0.33
9 11 0.17
10 26 0.39
11 3 0.05
12 2 0.03
13 2 0.03
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTTATAT
Found at i:45660628 original size:8 final size:8
Alignment explanation
Indices: 45660586--45660628 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
45660576 AAAATTTTAC
45660586 AATTTTTT
1 AATTTTTT
*
45660594 ATTTTTTAT
1 AATTTTT-T
45660603 AATTTTTT
1 AATTTTTT
*
45660611 CTATTTTTT
1 -AATTTTTT
45660620 AATTTTTT
1 AATTTTTT
45660628 A
1 A
45660629 TTAAATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 15 0.52
9 14 0.48
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (8 bp):
AATTTTTT
Found at i:45660637 original size:18 final size:18
Alignment explanation
Indices: 45660569--45660647 Score: 56
Period size: 18 Copynumber: 4.4 Consensus size: 18
45660559 TTTTTTATGA
*
45660569 TTTTTATAAAATTTTACAAT
1 TTTTTATTAAATTTT--AAT
*
45660589 TTTTTATT--TTTTATAAT
1 TTTTTATTAAATTT-TAAT
* **
45660606 TTTTT-CTATTTTTTAAT
1 TTTTTATTAAATTTTAAT
45660623 TTTTTATTAAATTTTAAT
1 TTTTTATTAAATTTTAAT
*
45660641 ATTTTAT
1 TTTTTAT
45660648 AACTTTTGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
16 1 0.02
17 17 0.35
18 22 0.46
19 1 0.02
20 7 0.15
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTATTAAATTTTAAT
Found at i:45661551 original size:18 final size:17
Alignment explanation
Indices: 45661499--45661552 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
45661489 ACTCCCCCTA
45661499 TTTACTTTCCCTCAAAC-T
1 TTTA-TTTCCCT-AAACTT
* *
45661517 TTTATTCCCCAAAACTT
1 TTTATTTCCCTAAACTT
45661534 TTTATTTTCCCTAAACTT
1 TTTA-TTTCCCTAAACTT
45661552 T
1 T
45661553 ACTTCTCACC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.13
17 10 0.33
18 16 0.53
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTATTTCCCTAAACTT
Found at i:45662732 original size:32 final size:33
Alignment explanation
Indices: 45662690--45662755 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
45662680 TCTCGACACA
* * *
45662690 TTAAATAATAATTATGTTGTTTT-AAGTTTTTT
1 TTAAATAATAAATATATTGTTTTCAAGTTGTTT
* *
45662722 TTAATTAATAAATATATTTTTTTCAAGTTGTTT
1 TTAAATAATAAATATATTGTTTTCAAGTTGTTT
45662755 T
1 T
45662756 ATTTTTAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 19 0.68
33 9 0.32
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.59
Consensus pattern (33 bp):
TTAAATAATAAATATATTGTTTTCAAGTTGTTT
Found at i:45662797 original size:22 final size:23
Alignment explanation
Indices: 45662769--45662818 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
45662759 TTTAATTCAT
*
45662769 CTTTTTATAAA-ATCAAATATTA
1 CTTTTTAAAAACATCAAATATTA
* *
45662791 CTTTTTAAAAACATCAACTATTT
1 CTTTTTAAAAACATCAAATATTA
45662814 CTTTT
1 CTTTT
45662819 GATATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (23 bp):
CTTTTTAAAAACATCAAATATTA
Found at i:45667055 original size:19 final size:19
Alignment explanation
Indices: 45667031--45667068 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
45667021 TATGATATGC
45667031 AAAATTAT-AAGTATATTAT
1 AAAATTATCAAGTA-ATTAT
*
45667050 AAAATTGTCAAGTAATTAT
1 AAAATTATCAAGTAATTAT
45667069 CAATTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (19 bp):
AAAATTATCAAGTAATTAT
Found at i:45668284 original size:18 final size:18
Alignment explanation
Indices: 45668234--45668284 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
45668224 AACTTATAAA
* *
45668234 AATAATTAAAAT-ATTAT
1 AATAATTATAATAATTCT
*
45668251 AATAATTCTAATAATTCT
1 AATAATTATAATAATTCT
45668269 AATAGATTATAA-AATT
1 AATA-ATTATAATAATT
45668285 AATAAAGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 10 0.36
18 12 0.43
19 6 0.21
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (18 bp):
AATAATTATAATAATTCT
Found at i:45668322 original size:20 final size:18
Alignment explanation
Indices: 45668299--45668349 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
45668289 AAGCATATTT
45668299 AAAATAATTAAAATCCTATA
1 AAAATAATTAAAAT--TATA
* *
45668319 AAAATCATAAAAATTATA
1 AAAATAATTAAAATTATA
45668337 AAAA-AATATAAAA
1 AAAATAAT-TAAAA
45668350 AAGTATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 12 0.46
20 12 0.46
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATAATTAAAATTATA
Found at i:45668360 original size:20 final size:20
Alignment explanation
Indices: 45668318--45668360 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
45668308 AAAATCCTAT
*
45668318 AAAAATCATAAAAATTATAA
1 AAAAATCATAAAAAGTATAA
45668338 AAAAAT-ATAAAAAAGTATTAA
1 AAAAATCAT-AAAAAGTA-TAA
45668359 AA
1 AA
45668361 TTGATATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 13 0.65
21 5 0.25
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAAATCATAAAAAGTATAA
Found at i:45669100 original size:12 final size:12
Alignment explanation
Indices: 45669085--45669111 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
45669075 TTAAATTTTC
45669085 TATTAATATACA
1 TATTAATATACA
45669097 TATTAATATACA
1 TATTAATATACA
45669109 TAT
1 TAT
45669112 ATGATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (12 bp):
TATTAATATACA
Found at i:45672553 original size:13 final size:13
Alignment explanation
Indices: 45672535--45672559 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45672525 GTGAGCTAAC
45672535 GTACTTAGTAAGT
1 GTACTTAGTAAGT
45672548 GTACTTAGTAAG
1 GTACTTAGTAAG
45672560 AGCTCAAAGC
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:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (13 bp):
GTACTTAGTAAGT
Found at i:45673906 original size:2 final size:2
Alignment explanation
Indices: 45673901--45673930 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
45673891 AAAAAAATTG
45673901 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
45673931 TAGGGTTTAC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45674615 original size:8 final size:8
Alignment explanation
Indices: 45674598--45674701 Score: 52
Period size: 8 Copynumber: 12.1 Consensus size: 8
45674588 TCATTAGATT
45674598 TTTTAT-A
1 TTTTATAA
45674605 TTTTATAA
1 TTTTATAA
*
45674613 TTTTATAG
1 TTTTATAA
45674621 TTTTAATAA
1 TTTT-ATAA
45674630 GTTTATATCAA
1 -TTT-TAT-AA
*
45674641 TTTTAATAT
1 TTTT-ATAA
*
45674650 TTTTATTA
1 TTTTATAA
*
45674658 TATTATTAA
1 TTTTA-TAA
45674667 TATTTA-ATA
1 T-TTTATA-A
45674676 TTTTATAA
1 TTTTATAA
*
45674684 CGTTTTATGA
1 --TTTTATAA
45674694 TTTT-TAA
1 TTTTATAA
45674701 T
1 T
45674702 CATTTTTTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
7 9 0.12
8 28 0.37
9 15 0.20
10 20 0.27
11 3 0.04
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (8 bp):
TTTTATAA
Found at i:45674629 original size:17 final size:16
Alignment explanation
Indices: 45674598--45674707 Score: 62
Period size: 18 Copynumber: 6.2 Consensus size: 16
45674588 TCATTAGATT
45674598 TTTTATATTTT-ATAA
1 TTTTATATTTTAATAA
45674613 TTTTATAGTTTTAATAA
1 TTTTATA-TTTTAATAA
*
45674630 GTTTATATCAATTTTAATAT
1 -TTT-TAT--ATTTTAATAA
* *
45674650 TTTTATTATATTATTAA
1 TTTTA-TATTTTAATAA
45674667 TATTTAATATTTT-ATAA
1 T-TTT-ATATTTTAATAA
*
45674684 CGTTTTATGATTTTTAATCA
1 --TTTTAT-A-TTTTAATAA
45674704 TTTT
1 TTTT
45674708 TTATGGAAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 25
0.70 0.07 0.24
Matches are distributed among these distances:
15 7 0.09
16 4 0.05
17 17 0.23
18 21 0.28
19 13 0.18
20 11 0.15
21 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.61
Consensus pattern (16 bp):
TTTTATATTTTAATAA
Found at i:45674652 original size:28 final size:26
Alignment explanation
Indices: 45674608--45674707 Score: 73
Period size: 27 Copynumber: 3.7 Consensus size: 26
45674598 TTTTATATTT
45674608 TATAATTTT-ATAGTTTTAATAAGTTTA
1 TATAATTTTAATA-TTTT-ATAAGTTTA
*
45674635 TATCAATTTTAATATTTTTATTA-TATTA
1 TAT-AATTTTAATA-TTTTATAAGT-TTA
45674663 T-TAATATTTAATATTTTATAACGTTT-
1 TATAAT-TTTAATATTTTATAA-GTTTA
*
45674689 TATGATTTTTAATCATTTT
1 TAT-AATTTTAAT-ATTTT
45674708 TTATGGAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
26 11 0.18
27 21 0.35
28 21 0.35
29 7 0.12
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (26 bp):
TATAATTTTAATATTTTATAAGTTTA
Found at i:45675691 original size:22 final size:21
Alignment explanation
Indices: 45675646--45675699 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
45675636 TTGCTCCCTA
**
45675646 AATAATAATAATAATCTAAATT
1 AATAATAA-AATAAGATAAATT
45675668 AATAATAAAATAAGATAAACTT
1 AATAATAAAATAAGATAAA-TT
*
45675690 AAAAATAAAA
1 AATAATAAAA
45675700 AAGTCTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (21 bp):
AATAATAAAATAAGATAAATT
Found at i:45678474 original size:15 final size:15
Alignment explanation
Indices: 45678454--45678487 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
45678444 GAACAATGTT
*
45678454 AATAAATAATAAATA
1 AATAAACAATAAATA
45678469 AATAAACAATAAATA
1 AATAAACAATAAATA
45678484 AATA
1 AATA
45678488 CACACACACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAAACAATAAATA
Found at i:45692322 original size:25 final size:25
Alignment explanation
Indices: 45692267--45692327 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
45692257 CAATTAGATC
* *
45692267 CATTTTATGATAAAATTATTTACTAT
1 CATTTT-TGATAAAATTATTAAATAT
45692293 C-TTTTTGATAGAAATTATTAAAT-T
1 CATTTTTGATA-AAATTATTAAATAT
45692317 CATTTTT-ATAA
1 CATTTTTGATAA
45692328 TTCCTGTGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
23 1 0.03
24 10 0.32
25 19 0.61
26 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.51
Consensus pattern (25 bp):
CATTTTTGATAAAATTATTAAATAT
Found at i:45695046 original size:20 final size:20
Alignment explanation
Indices: 45695017--45695062 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
45695007 TAAATAGAAC
45695017 AAGACACAATTAATTAAGTT
1 AAGACACAATTAATTAAGTT
* **
45695037 AAGACCCAATTAATTTGGTT
1 AAGACACAATTAATTAAGTT
45695057 AAGACA
1 AAGACA
45695063 AGACACATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (20 bp):
AAGACACAATTAATTAAGTT
Found at i:45700534 original size:19 final size:18
Alignment explanation
Indices: 45700493--45700535 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
45700483 TTTTTTTCTC
45700493 TTTTTTTTTAATTCACGAA
1 TTTTTTTTTAATTCACG-A
*
45700512 TTTTTTTTCAATTCAC--
1 TTTTTTTTTAATTCACGA
45700528 TTTTTTTT
1 TTTTTTTT
45700536 AAAATTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 8 0.35
19 15 0.65
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTTTTTTAATTCACGA
Found at i:45701912 original size:20 final size:20
Alignment explanation
Indices: 45701883--45701928 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
45701873 TAAATAGAAC
45701883 AAGACACAATTAATTAAGTT
1 AAGACACAATTAATTAAGTT
* **
45701903 AAGACCCAATTAATTTGGTT
1 AAGACACAATTAATTAAGTT
45701923 AAGACA
1 AAGACA
45701929 AGACACATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (20 bp):
AAGACACAATTAATTAAGTT
Found at i:45705906 original size:43 final size:43
Alignment explanation
Indices: 45705853--45706081 Score: 314
Period size: 43 Copynumber: 5.3 Consensus size: 43
45705843 ACAAATGCTA
45705853 CTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
1 CTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
* * *
45705896 CTAAATACCAAGACCTTTAGCGGTGCTTTTCCTACAAACGCCG
1 CTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
* *
45705939 CTAAAGACCAGGACCTTTAGTGGCGCTTTTCCCACAAACGCCG
1 CTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
* * *
45705982 CTAAAGACCAGGACCTTTAGCGACGCTTTTCCCACAAACGCTG
1 CTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
* * ** * **
45706025 CTAAAAACCAAAACCTTTAGCGGCAATTTTCCCACAAATGCTT
1 CTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
*
45706068 CTAAAGACCCAGAC
1 CTAAAGACCAAGAC
45706082 ACTATAGCTC
Statistics
Matches: 164, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 164 1.00
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (43 bp):
CTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
Found at i:45706393 original size:15 final size:15
Alignment explanation
Indices: 45706373--45706403 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
45706363 AGGGATATGG
45706373 ATCATCTTCATCTTC
1 ATCATCTTCATCTTC
*
45706388 ATCATCTTCTTCTTC
1 ATCATCTTCATCTTC
45706403 A
1 A
45706404 CTTTCAACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.32, G:0.00, T:0.48
Consensus pattern (15 bp):
ATCATCTTCATCTTC
Found at i:45710556 original size:21 final size:21
Alignment explanation
Indices: 45710532--45710585 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
45710522 ATAAAACATA
45710532 AACCCTAAACCCCTAACCCTT
1 AACCCTAAACCCCTAACCCTT
**
45710553 AACCACT-AACATCTAACCCTT
1 AACC-CTAAACCCCTAACCCTT
45710574 AACCCCTAAACC
1 AA-CCCTAAACC
45710586 TTAAACCCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.37, C:0.44, G:0.00, T:0.19
Consensus pattern (21 bp):
AACCCTAAACCCCTAACCCTT
Found at i:45710598 original size:21 final size:21
Alignment explanation
Indices: 45710574--45710613 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
45710564 TCTAACCCTT
*
45710574 AACCCCTAAACCTTAAACCCC
1 AACCCCTAAACCATAAACCCC
*
45710595 AACCCTTAAACCATAAACC
1 AACCCCTAAACCATAAACC
45710614 ATAATCTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.15
Consensus pattern (21 bp):
AACCCCTAAACCATAAACCCC
Found at i:45711667 original size:41 final size:41
Alignment explanation
Indices: 45711573--45711780 Score: 238
Period size: 41 Copynumber: 5.1 Consensus size: 41
45711563 TAAATTATTT
** * **
45711573 TAAATCCGTGAGCATTAGCGACGCTTTTTAAAAAACGCCGC
1 TAAATCCCAGAGCATTAGCGGCGCTTCCTAAAAAACGCCGC
*** * * * *
45711614 TAAA-AATAGAGCACTAGCGGCGCTACTTCAAAAACGCCGC
1 TAAATCCCAGAGCATTAGCGGCGCTTCCTAAAAAACGCCGC
* * *
45711654 TAAAGCCCCGAGCATTAGCGGTGCTTCCTAAAAAACGCCGC
1 TAAATCCCAGAGCATTAGCGGCGCTTCCTAAAAAACGCCGC
45711695 TAAATCCCAGAGCATTAGCGGCGCTTCCTAAAAAACGCCGC
1 TAAATCCCAGAGCATTAGCGGCGCTTCCTAAAAAACGCCGC
* * * *
45711736 TAAATCCCAGAGCATTAGCCGCGCTTTCTCAAAAACACCGC
1 TAAATCCCAGAGCATTAGCGGCGCTTCCTAAAAAACGCCGC
45711777 TAAA
1 TAAA
45711781 ACCCCGAAAG
Statistics
Matches: 141, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
40 31 0.22
41 110 0.78
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (41 bp):
TAAATCCCAGAGCATTAGCGGCGCTTCCTAAAAAACGCCGC
Found at i:45711868 original size:39 final size:39
Alignment explanation
Indices: 45711825--45711948 Score: 126
Period size: 40 Copynumber: 3.1 Consensus size: 39
45711815 TAGGTTTTTT
* * *
45711825 GCGGCGCTTTTTGAAAAACGCCGCTAATTCT-TATTTTTA
1 GCGGCG-TTTTTGAAAAGCGCCGCTAATTCTCAATCTTTA
** *
45711864 GCGGCGTTTTCCATAAAGCGCCGCTAATGT-TCGATCTTTA
1 GCGGCGTTTTTGA-AAAGCGCCGCTAAT-TCTCAATCTTTA
* *
45711904 GCGGCATTTTCTGAATAGCGCCGCTAATTCTCAATCTTTA
1 GCGGCGTTTT-TGAAAAGCGCCGCTAATTCTCAATCTTTA
45711944 GCGGC
1 GCGGC
45711949 ATTTGGATAA
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
38 5 0.07
39 21 0.30
40 43 0.61
41 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (39 bp):
GCGGCGTTTTTGAAAAGCGCCGCTAATTCTCAATCTTTA
Found at i:45711914 original size:40 final size:40
Alignment explanation
Indices: 45711843--45711952 Score: 129
Period size: 40 Copynumber: 2.8 Consensus size: 40
45711833 TTTTGAAAAA
* * *
45711843 CGCCGCTAATTCT-TATTTTTAGCGGCGTTTTCCAT-AA-AG
1 CGCCGCTAATTCTCAATCTTTAGCGGCATTTT-C-TGAATAG
*
45711882 CGCCGCTAATGT-TCGATCTTTAGCGGCATTTTCTGAATAG
1 CGCCGCTAAT-TCTCAATCTTTAGCGGCATTTTCTGAATAG
45711922 CGCCGCTAATTCTCAATCTTTAGCGGCATTT
1 CGCCGCTAATTCTCAATCTTTAGCGGCATTT
45711953 GGATAAAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
38 1 0.02
39 15 0.24
40 46 0.74
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (40 bp):
CGCCGCTAATTCTCAATCTTTAGCGGCATTTTCTGAATAG
Found at i:45714056 original size:22 final size:22
Alignment explanation
Indices: 45714012--45714056 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
45714002 TTTTATATTT
* *
45714012 TTTTTATTTATAGAATTTAAAA
1 TTTTTATTTATAGAAGTAAAAA
45714034 TTTTTATTTATA-AAGTAACAAA
1 TTTTTATTTATAGAAGTAA-AAA
45714056 T
1 T
45714057 GTTAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (22 bp):
TTTTTATTTATAGAAGTAAAAA
Found at i:45722369 original size:6 final size:6
Alignment explanation
Indices: 45722348--45722380 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
45722338 TTTATATATT
45722348 TTTATAA TTT-AA TTTAAA TTTAAA TTTAAA TTT
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTT
45722381 TTTTACTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.20
6 17 0.68
7 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:45726667 original size:54 final size:54
Alignment explanation
Indices: 45726585--45726718 Score: 216
Period size: 54 Copynumber: 2.5 Consensus size: 54
45726575 CCTATCACCA
*
45726585 TGGTCC-AGTTGCAAAGCCACCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
1 TGGTCCTA-TTGCAAAGCCTCCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
45726639 TGGTCCTATTGCAAAGCCTCCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
1 TGGTCCTATTGCAAAGCCTCCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
* * *
45726693 TGGTCCTATTGCGAAGTCTCCTACAG
1 TGGTCCTATTGCAAAGCCTCCCACAG
45726719 CATTAACTCC
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
54 74 0.99
55 1 0.01
ACGTcount: A:0.16, C:0.35, G:0.22, T:0.27
Consensus pattern (54 bp):
TGGTCCTATTGCAAAGCCTCCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
Found at i:45726747 original size:54 final size:54
Alignment explanation
Indices: 45726585--45726747 Score: 150
Period size: 54 Copynumber: 3.0 Consensus size: 54
45726575 CCTATCACCA
* * * * * *
45726585 TGGTCC-AGTTGCAAAGCCACCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
1 TGGTCCTA-TTGCAAAGCCTCCCACAGCATCAACTCCGGTTCCAGCACAGGCTCC
* * * * *
45726639 TGGTCCTATTGCAAAGCCTCCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
1 TGGTCCTATTGCAAAGCCTCCCACAGCATCAACTCCGGTTCCAGCACAGGCTCC
* * * * *
45726693 TGGTCCTATTGCGAAGTCTCCTACAGCATTAACTCCAGG-TCCAGCACAGTCTCC
1 TGGTCCTATTGCAAAGCCTCCCACAGCATCAACTCC-GGTTCCAGCACAGGCTCC
45726747 T
1 T
45726748 TATCACCATG
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
54 93 0.97
55 3 0.03
ACGTcount: A:0.18, C:0.36, G:0.20, T:0.26
Consensus pattern (54 bp):
TGGTCCTATTGCAAAGCCTCCCACAGCATCAACTCCGGTTCCAGCACAGGCTCC
Found at i:45729927 original size:30 final size:29
Alignment explanation
Indices: 45729893--45729954 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
45729883 AATGTCAGGC
* *
45729893 AAAAATTATGTGAATAGGTTAATTTTAGAA
1 AAAAATTACGGGAATAGGTT-ATTTTAGAA
* *
45729923 AAAAATTGCGGGAATAGGTTATTTTTGAA
1 AAAAATTACGGGAATAGGTTATTTTAGAA
45729952 AAA
1 AAA
45729955 CACTTCTAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.45, C:0.02, G:0.19, T:0.34
Consensus pattern (29 bp):
AAAAATTACGGGAATAGGTTATTTTAGAA
Found at i:45730279 original size:13 final size:13
Alignment explanation
Indices: 45730261--45730286 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45730251 ATTATTTATC
45730261 ATTTAAATATATA
1 ATTTAAATATATA
45730274 ATTTAAATATATA
1 ATTTAAATATATA
45730287 TAAATTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTAAATATATA
Found at i:45730287 original size:15 final size:14
Alignment explanation
Indices: 45730265--45730301 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
45730255 TTTATCATTT
*
45730265 AAATATATAATTTA
1 AAATATATAAATTA
45730279 AATATATATAAATTA
1 AA-ATATATAAATTA
45730294 AAATATAT
1 AAATATAT
45730302 TAATAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATATAAATTA
Found at i:45730311 original size:11 final size:11
Alignment explanation
Indices: 45730290--45730331 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
45730280 ATATATATAA
45730290 ATTAA-AATAT
1 ATTAATAATAT
45730300 ATTAATAATAT
1 ATTAATAATAT
*
45730311 ATAAAT-A-AT
1 ATTAATAATAT
45730320 ATTAATAATAT
1 ATTAATAATAT
45730331 A
1 A
45730332 GAATTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 7 0.26
10 7 0.26
11 13 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTAATAATAT
Found at i:45730321 original size:20 final size:19
Alignment explanation
Indices: 45730294--45730331 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
45730284 ATATAAATTA
45730294 AAATATATTAATAATATAT
1 AAATATATTAATAATATAT
45730313 AAATAATATTAATAATATA
1 AAAT-ATATTAATAATATA
45730332 GAATTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATATATTAATAATATAT
Found at i:45732479 original size:14 final size:14
Alignment explanation
Indices: 45732462--45732494 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
45732452 TTTTTATTGA
45732462 TTTTTCTTC-GTATC
1 TTTTT-TTCAGTATC
45732476 TTTTTTTCAGTATC
1 TTTTTTTCAGTATC
45732490 TTTTT
1 TTTTT
45732495 GGTACTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.09, C:0.15, G:0.06, T:0.70
Consensus pattern (14 bp):
TTTTTTTCAGTATC
Found at i:45733461 original size:44 final size:43
Alignment explanation
Indices: 45733243--45733485 Score: 191
Period size: 44 Copynumber: 5.5 Consensus size: 43
45733233 CTACTCTCTA
** * ** *
45733243 CAACTTCAAAGAGATAAGATCTATTATTTTAATCCGCTCTGCTA
1 CAACTTCAGGGAGATAAGAT-TATTATTTTAATCTGCTCCACTG
* *
45733287 CAACTTTAGGGAGATATGATTATTAACTTTTAATCTGCTCCACTG
1 CAACTTCAGGGAGATAAGATTATT-A-TTTTAATCTGCTCCACTG
* *** * *
45733332 CAATTTCAGGGAGATAAGATTCGCCATCTTGAATCTGCCCCACTG
1 CAACTTCAGGGAGATAAGATT-ATTAT-TTTAATCTGCTCCACTG
* * * * *
45733377 CAACTTCAGGGGGATTAGATTTATT-TATTCAGTCTACTCCACTG
1 CAACTTCAGGGAGATAAGA-TTATTAT-TTTAATCTGCTCCACTG
* * *
45733421 CAACTTCAGGGAGATAGGATTATTGGTTTTAATCTGCTCCATTG
1 CAACTTCAGGGAGATAAGATTATT-ATTTTAATCTGCTCCACTG
* *
45733465 TAACTTCAAGGAGATAAGATT
1 CAACTTCAGGGAGATAAGATT
45733486 CGCCATCTTC
Statistics
Matches: 155, Mismatches: 37, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
43 9 0.06
44 79 0.51
45 65 0.42
46 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (43 bp):
CAACTTCAGGGAGATAAGATTATTATTTTAATCTGCTCCACTG
Found at i:45733817 original size:51 final size:51
Alignment explanation
Indices: 45733715--45733837 Score: 138
Period size: 51 Copynumber: 2.4 Consensus size: 51
45733705 TCCAAGTCTT
* * * *
45733715 AACGCTAGGGAGATAAGATTCGCTGCCCTCAGCTTTTATCTACTCCGCTGC
1 AACGCTAGGGAAATAAGATTCGCTACCCTCAGCTTTAATCTACTCCACTGC
* * * * **
45733766 AACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGC
1 AACGCTAGGGAAATAAGATTCGCTACCCTCAGCTTTAATCTACTCCACTGC
* *
45733817 AACACTAGGGAAGTAAGATTC
1 AACGCTAGGGAAATAAGATTC
45733838 ACTATCGTAG
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (51 bp):
AACGCTAGGGAAATAAGATTCGCTACCCTCAGCTTTAATCTACTCCACTGC
Found at i:45733989 original size:89 final size:88
Alignment explanation
Indices: 45733859--45734109 Score: 256
Period size: 89 Copynumber: 2.8 Consensus size: 88
45733849 TTCAATATAT
* * ** *
45733859 TCCATTGCCAACTC-AGAGAGGCAAGGTTGGTGT-TGTCGATCTGCTTCGCTGCCAGTACAGGAA
1 TCCACTGCAAACTCAAG-GAGGCAAGACTGGTGTCT-TCGATCTACTTCGCTGCCAGTACAGGAA
45733922 GACAAGATCTATTATCTTCAGTCTAC
64 GACAA-ATCTATTATCTTCAGTCTAC
* * * *
45733948 TCCGCTGCAAACTCAAGGAGGTC-AGGCTGGTGTCTTTGATCTACTTCACTGCCAGTACAGGAAG
1 TCCACTGCAAACTCAAGGAGG-CAAGACTGGTGTCTTCGATCTACTTCGCTGCCAGTACAGGAAG
* * * *
45734012 GCGAAATATTTTATCTTCAGTCTGC
65 AC-AAATCTATTATCTTCAGTCTAC
* * * * * *
45734037 TCCACTGCAAAGTTAGGGAGGCAAGACTTGTGTCTTCGATCTACTTTGCTGCCAGTATAGGAAGA
1 TCCACTGCAAACTCAAGGAGGCAAGACTGGTGTCTTCGATCTACTTCGCTGCCAGTACAGGAAGA
45734102 CAATATCT
66 CAA-ATCT
45734110 GCTATTTTCG
Statistics
Matches: 133, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
88 3 0.02
89 124 0.93
90 6 0.05
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.29
Consensus pattern (88 bp):
TCCACTGCAAACTCAAGGAGGCAAGACTGGTGTCTTCGATCTACTTCGCTGCCAGTACAGGAAGA
CAAATCTATTATCTTCAGTCTAC
Found at i:45734144 original size:45 final size:45
Alignment explanation
Indices: 45734069--45734876 Score: 1000
Period size: 45 Copynumber: 18.0 Consensus size: 45
45734059 AAGACTTGTG
* * * *
45734069 TCTTCGATCTACTTTGCTGCCAGTATAGGAAGACAATATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * * *
45734114 TTTTCGATCTACTTCGTTGCTATTACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
45734159 TCTTCGATTTACTTCGCTGCCATTACAAGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
** * * *
45734204 TCTTCGATCTACTTTACTGCCAGTACAGGAAGACTAGATCTACTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
45734249 TCTTCGATCTA-TATCACTGCCAATACAGAAAGACAAGATTTGCTA
1 TCTTCGATCTACT-TCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * * * *
45734294 TATTCGATTTAC-TCGCTGCTAGTACAGGAAGATAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
45734338 TCTTCGATCTATTTCGCTACCAATAAAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * * *
45734383 TCTTTGATCTACTTCGCTGCCAATATAAGAAGACAAGATCCGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
45734428 TCTTCGATCTACTTCGCTTACCAATACA-GAAGATAAGATCTGTTA
1 TCTTCGATCTACTTCGC-TGCCAATACAGGAAGACAAGATCTGCTA
* ** * *** * * *
45734473 TTTTTAACCTAC-TCTGCTGCTGCT-CAGGGAA-ATAAG-GCTGGTA
1 TCTTCGATCTACTTC-GCTGCCAATACA-GGAAGACAAGATCTGCTA
*
45734516 TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
*
45734561 TCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* ** *
45734606 TCTTCGATCTATTTCGCTGCCTTTACAGGAAGACAAGATCTACTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* *
45734651 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATTTTCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * * *
45734696 TCTTTGATCTACTTTGCTGCCAATACAGGAAGATAAGATCTGTTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
*
45734741 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATATGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
45734786 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* *
45734831 TCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTACTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
45734876 T
1 T
45734877 TTTTTTAACC
Statistics
Matches: 653, Mismatches: 99, Indels: 22
0.84 0.13 0.03
Matches are distributed among these distances:
43 25 0.04
44 54 0.08
45 566 0.87
46 8 0.01
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (45 bp):
TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
Found at i:45740036 original size:21 final size:21
Alignment explanation
Indices: 45740010--45740065 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
45740000 AACAACGGTG
*
45740010 GTGGTGAGATTAGTTACTATA
1 GTGGTGAGATTAGATACTATA
* * * *
45740031 GTGGTGTGATTGGATATTGTA
1 GTGGTGAGATTAGATACTATA
45740052 GTGGTGAGATTAGA
1 GTGGTGAGATTAGA
45740066 AACAGCGGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.02, G:0.36, T:0.38
Consensus pattern (21 bp):
GTGGTGAGATTAGATACTATA
Found at i:45743210 original size:22 final size:22
Alignment explanation
Indices: 45743168--45743211 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
45743158 ATTTTAACTA
*
45743168 ATAATATTTCTAAATTATAATT
1 ATAATATTTCTAAAGTATAATT
*
45743190 ATAATCATTTTTAAAGT-TAATT
1 ATAAT-ATTTCTAAAGTATAATT
45743212 TAAATGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (22 bp):
ATAATATTTCTAAAGTATAATT
Found at i:45747432 original size:2 final size:2
Alignment explanation
Indices: 45747425--45747458 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
45747415 AAACAAAAAC
*
45747425 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45747459 CATGATTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:45750174 original size:24 final size:26
Alignment explanation
Indices: 45750142--45750192 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 26
45750132 TATATGGGTC
45750142 TCACATATTTTTAGTA-TACT-TAATT
1 TCACATATTTTTA-TACTACTATAATT
45750167 TCAC-TATTTTTATACTACTATAATT
1 TCACATATTTTTATACTACTATAATT
45750192 T
1 T
45750193 GTTTTTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 2 0.08
24 12 0.50
25 10 0.42
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.53
Consensus pattern (26 bp):
TCACATATTTTTATACTACTATAATT
Found at i:45750326 original size:44 final size:46
Alignment explanation
Indices: 45750243--45750331 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 46
45750233 CGCTGTAATG
*
45750243 GAATAGAGACGTAATATGTAATCCTTTTGTTTGGTTGAATGGAATA
1 GAATAGAGACGTAATATGTAATCCTTGTGTTTGGTTGAATGGAATA
*
45750289 GAATAGA-ACTGTAATA-GT-ATTCTTGTGTTTGGTTGAATGGAAT
1 GAATAGAGAC-GTAATATGTAATCCTTGTGTTTGGTTGAATGGAAT
45750332 GATGTTGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 23 0.57
45 4 0.10
46 13 0.32
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (46 bp):
GAATAGAGACGTAATATGTAATCCTTGTGTTTGGTTGAATGGAATA
Found at i:45750499 original size:26 final size:26
Alignment explanation
Indices: 45750470--45750584 Score: 77
Period size: 26 Copynumber: 4.3 Consensus size: 26
45750460 TTAATCATAT
45750470 TTTAACATAATTATTATTAAATATAA
1 TTTAACATAATTATTATTAAATATAA
* * ** * * *
45750496 TTTAATAAAATATACGAATTTACTAAAA
1 TTTAACATAAT-TA-TTATTAAATATAA
* * * * *
45750524 TCATAATATATAATACTATAAAATATAA
1 T-TTAACATA-ATTATTATTAAATATAA
*
45750552 TTTAAAATAATTATTATTAAATATAA
1 TTTAACATAATTATTATTAAATATAA
45750578 TTTAACA
1 TTTAACA
45750585 AAAATATATA
Statistics
Matches: 63, Mismatches: 22, Indels: 8
0.68 0.24 0.09
Matches are distributed among these distances:
26 29 0.46
27 8 0.13
28 17 0.27
29 8 0.13
30 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (26 bp):
TTTAACATAATTATTATTAAATATAA
Found at i:45750652 original size:120 final size:120
Alignment explanation
Indices: 45750506--45750748 Score: 459
Period size: 120 Copynumber: 2.0 Consensus size: 120
45750496 TTTAATAAAA
45750506 TATACGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
1 TATACGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
45750571 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
66 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
* *
45750626 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTGAAATAATTATTATTA
1 TATACGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
*
45750691 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTGTTAAATATTCT
66 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
45750746 TAT
1 TAT
45750749 GATTGTATCA
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 120 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (120 bp):
TATACGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
Found at i:45750724 original size:59 final size:60
Alignment explanation
Indices: 45750528--45750726 Score: 198
Period size: 59 Copynumber: 3.4 Consensus size: 60
45750518 CTAAAATCAT
* *
45750528 AATATATAATACT-ATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAA
1 AATATATAATATTAATAAAATATAATTTGAAATAATTATTATTAAATATAATTTAACAAA
* * * * * * *
45750587 AATATATAAT-TTAATAAAAT-T-CTTAGTATTAAATATTCTT--ATATGAATTT-ACTAA
1 AATATATAATATTAATAAAATATAATTTGAAATAATTATTATTAAATAT-AATTTAACAAA
*
45750642 AATCATAATATATAATACTATAAAATATAATTTGAAATAATTATTATTAAATATAATTTAACAAA
1 AAT-AT-ATA-ATATTA--ATAAAATATAATTTGAAATAATTATTATTAAATATAATTTAACAAA
45750707 AATATATAAT-TTAATAAAAT
1 AATATATAATATTAATAAAAT
45750727 TCTTAGTGTT
Statistics
Matches: 109, Mismatches: 18, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
55 11 0.10
56 7 0.06
57 15 0.14
58 4 0.04
59 26 0.24
61 9 0.08
62 3 0.03
63 16 0.15
64 7 0.06
65 11 0.10
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (60 bp):
AATATATAATATTAATAAAATATAATTTGAAATAATTATTATTAAATATAATTTAACAAA
Found at i:45762399 original size:12 final size:12
Alignment explanation
Indices: 45762382--45762406 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45762372 CTTGAAATGC
45762382 CTTCTCTTCACT
1 CTTCTCTTCACT
45762394 CTTCTCTTCACT
1 CTTCTCTTCACT
45762406 C
1 C
45762407 CTTTCTGCTG
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:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (12 bp):
CTTCTCTTCACT
Done.