Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 89
Found at i:2205816 original size:2 final size:2
Alignment explanation
Indices: 2205809--2205855 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2205799 TAGTTTTTCC
2205809 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
2205851 TA TA T
1 TA TA T
2205856 GGTAAATTAT
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:2219199 original size:2 final size:2
Alignment explanation
Indices: 2219192--2219228 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2219182 TTATTATTAT
2219192 TA 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 TA T
2219229 TTTCTTTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2219394 original size:14 final size:13
Alignment explanation
Indices: 2219377--2219431 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
2219367 TTTATTAATA
2219377 TATTTTTATTTTAT
1 TATTTTTATTTT-T
*
2219391 TATTTTTCCTTTTT
1 TATTTTT-ATTTTT
* *
2219405 TGTTTTTGTTTTT
1 TATTTTTATTTTT
*
2219418 TATTATTATTTTT
1 TATTTTTATTTTT
2219431 T
1 T
2219432 TACCTAACGT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
13 16 0.47
14 14 0.41
15 4 0.12
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.80
Consensus pattern (13 bp):
TATTTTTATTTTT
Found at i:2219421 original size:76 final size:76
Alignment explanation
Indices: 2219252--2219405 Score: 233
Period size: 76 Copynumber: 2.1 Consensus size: 76
2219242 TTGTAATTAA
*
2219252 TTTTT-TTCTCTATTTATTTTATTTATTTAATCTAATATATTTATTTATACATATATATTTTTAT
1 TTTTTCTTCTCTATTTATTTTATTTATTTAATCTAATATATTTATTAATACATATATATTTTTAT
*
2219316 TTTTATTTCTT
66 TTTTATTCCTT
* * *
2219327 TTTTTCTTCTCTATTTATTTTATTTATTTAATCTAATATATTTATTAATATATTTTTA-TTTTAT
1 TTTTTCTTCTCTATTTATTTTATTTATTTAATCTAATATATTTATTAATACATATATATTTTTAT
2219391 TATTT-TTCCTT
66 T-TTTATTCCTT
2219402 TTTT
1 TTTT
2219406 GTTTTTGTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
75 21 0.29
76 51 0.71
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (76 bp):
TTTTTCTTCTCTATTTATTTTATTTATTTAATCTAATATATTTATTAATACATATATATTTTTAT
TTTTATTCCTT
Found at i:2223678 original size:2 final size:2
Alignment explanation
Indices: 2223671--2223716 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
2223661 TAAAGAGAAG
* *
2223671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2223713 AT AT
1 AT AT
2223717 GTGAGGATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2228929 original size:23 final size:23
Alignment explanation
Indices: 2228899--2228948 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
2228889 GCCCGGGGTT
* *
2228899 TGGGTCTGATGACCTCTTGTAAC
1 TGGGTCTGATGACCCCTTATAAC
2228922 TGGGTCTGATGACCCCTTATAAC
1 TGGGTCTGATGACCCCTTATAAC
2228945 TGGG
1 TGGG
2228949 CCCGATTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.32
Consensus pattern (23 bp):
TGGGTCTGATGACCCCTTATAAC
Found at i:2229051 original size:17 final size:17
Alignment explanation
Indices: 2229001--2229077 Score: 68
Period size: 17 Copynumber: 4.6 Consensus size: 17
2228991 TAAGCAATAT
*
2229001 TAATAA-TAATATTA-A
1 TAATAATTATTATTATA
* ** *
2229016 TAATTATTAAAATTTTA
1 TAATAATTATTATTATA
2229033 TAATAATTATTATTATA
1 TAATAATTATTATTATA
* *
2229050 TAGTAATTATTATAATA
1 TAATAATTATTATTATA
*
2229067 TAATATTTATT
1 TAATAATTATT
2229078 TTTCAGATAA
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
15 5 0.10
16 6 0.12
17 38 0.78
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (17 bp):
TAATAATTATTATTATA
Found at i:2229243 original size:39 final size:39
Alignment explanation
Indices: 2229198--2229276 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
2229188 TTTTTAAAAG
* *
2229198 GAAACTAAGCCTAATTTTTAGGGGTTCCTTGACAAGTAA
1 GAAACTAAGCCTAATTTTCAAGGGTTCCTTGACAAGTAA
* * * *
2229237 GAAACTAAGCTTGATTTTCAAGGGTTTCTTGACGAGTAA
1 GAAACTAAGCCTAATTTTCAAGGGTTCCTTGACAAGTAA
2229276 G
1 G
2229277 TCCTTTGGGC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (39 bp):
GAAACTAAGCCTAATTTTCAAGGGTTCCTTGACAAGTAA
Found at i:2229379 original size:41 final size:42
Alignment explanation
Indices: 2229273--2229379 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 42
2229263 TCTTGACGAG
* * ** *
2229273 TAAGTCCTTTGGGCCATCAATAAGTCTTTCGAGCGTGATGCT
1 TAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCAAGATGCA
* ** *
2229315 TAATTCATTCGGGCCATTTATAAGTTTTTCGAGCAAGATG-A
1 TAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCAAGATGCA
*
2229356 TAAGTCATTCGGGCCATCCATAAG
1 TAAGTCATTCGGGCCATCAATAAG
2229380 ACCTTTAGGT
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 21 0.40
42 32 0.60
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (42 bp):
TAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCAAGATGCA
Found at i:2229854 original size:36 final size:36
Alignment explanation
Indices: 2229734--2229885 Score: 130
Period size: 36 Copynumber: 4.2 Consensus size: 36
2229724 TTTTTCTAAG
* * *
2229734 AACAAATTTTGTCTCGCTGGAGACAATTT-TGCTTAA
1 AACAAATTTTGTCTCTCTTGAGACAATTTCT-CTTGA
* ** * *
2229770 AACAAAATTAATCT-TACTTGAGATTATTTTCTCCTTGA
1 AACAAATTTTGTCTCT-CTTGAGA-CAATTTCT-CTTGA
*
2229808 AACAAATTTTGTCTCAT-TTGAGACAGTTTCTCTTGA
1 AACAAATTTTGTCTC-TCTTGAGACAATTTCTCTTGA
* * *
2229844 AACAAGTTTTGTCTCTCTTGAGACAATTTCCCTCGA
1 AACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGA
2229880 AACAAA
1 AACAAA
2229886 ATCTTTGAAT
Statistics
Matches: 91, Mismatches: 19, Indels: 12
0.75 0.16 0.10
Matches are distributed among these distances:
35 1 0.01
36 57 0.63
37 10 0.11
38 22 0.24
40 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (36 bp):
AACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGA
Found at i:2229978 original size:31 final size:31
Alignment explanation
Indices: 2229935--2230047 Score: 86
Period size: 31 Copynumber: 3.5 Consensus size: 31
2229925 CTTGAGACAA
*
2229935 TTTCTCTTGAAACACAAAATCTTTGAATCTG
1 TTTCCCTTGAAACACAAAATCTTTGAATCTG
* *
2229966 TTTCCCTTGAAACA-AAATTTGGTCTCCCTTGAGA-CAG
1 TTTCCCTTGAAACACAAA----ATCT---TTGA-ATCTG
* *
2230003 TTTCTCTTGAAACACAAAATCTTTGAATTTG
1 TTTCCCTTGAAACACAAAATCTTTGAATCTG
*
2230034 TTTCCATTGAAACA
1 TTTCCCTTGAAACA
2230048 AAATTTGGTC
Statistics
Matches: 63, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
30 4 0.06
31 30 0.48
34 6 0.10
37 19 0.30
38 4 0.06
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (31 bp):
TTTCCCTTGAAACACAAAATCTTTGAATCTG
Found at i:2230015 original size:68 final size:68
Alignment explanation
Indices: 2229833--2230205 Score: 461
Period size: 68 Copynumber: 5.5 Consensus size: 68
2229823 ATTTGAGACA
* * * * *
2229833 GTTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAATTTCCCTCG-AA-ACAAAATCTTTGAA
1 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAAATCTTTGAA
*
2229895 TAT
66 TCT
*
2229898 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACACAAAATCTTTGAA
1 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAAATCTTTGAA
2229962 TCT
66 TCT
* *
2229965 GTTTCCCTTGAAACAAAATTTGGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTGAA
1 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAAATCTTTGAA
*
2230030 TTT
66 TCT
* * ** *
2230033 GTTTCCATTGAAACAAAATTTGGTCTCCCTTGAGACTGTTTCTCTTGAAACACAAAAAAACCTTT
1 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAC---AAAATCTTT
2230098 GAAAT-T
63 G-AATCT
* * * *
2230104 GTTTCACTTGAAACAAAATTTTGTCTCCCTTGAGATATTTTCTCTTGAAACACAAAATCTCTGAA
1 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAAATCTTTGAA
*
2230169 CCT
66 TCT
* * *
2230172 ATTTCCCTTGAAACAAAA-TTTATCTCACTTGAGA
1 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGA
2230206 TTGTTTTTCT
Statistics
Matches: 275, Mismatches: 25, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
65 42 0.15
66 2 0.01
67 46 0.17
68 125 0.45
71 57 0.21
72 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (68 bp):
GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAAATCTTTGAA
TCT
Found at i:2230135 original size:139 final size:135
Alignment explanation
Indices: 2229833--2230211 Score: 469
Period size: 139 Copynumber: 2.8 Consensus size: 135
2229823 ATTTGAGACA
* * * * *
2229833 GTTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAATTTCCCTCG-AA-ACAAAATCTTTGAA
1 GTTTCACTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAAATCTTTGAA
* * ** *
2229895 TATGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACACAAAATCTTTG
66 TATGTTTCCCTTGAAACAAAATTTGTCTCACTTGAGACTGTTTCTCTTGAAACACAAAACCTTTG
2229960 AATCT
131 AATCT
* * *
2229965 GTTTCCCTTGAAACAAAATTTGGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTGAA
1 GTTTCACTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAAATCTTTGAA
* * *
2230030 TTTGTTTCCATTGAAACAAAATTTGGTCTCCCTTGAGACTGTTTCTCTTGAAACACAAAAAAACC
66 TATGTTTCCCTTGAAACAAAATTT-GTCTCACTTGAGACTGTTTCTCTTGAAACAC---AAAACC
2230095 TTTGAAAT-T
127 TTTG-AATCT
* * *
2230104 GTTTCACTTGAAACAAAATTTTGTCTCCCTTGAGATATTTTCTCTTGAAACACAAAATCTCTGAA
1 GTTTCACTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAAATCTTTGAA
** * * *
2230169 CCTATTTCCCTTGAAACAAAATTTATCTCACTTGAGATTGTTT
66 TATGTTTCCCTTGAAACAAAATTTGTCTCACTTGAGACTGTTT
2230212 TTCTCAAAAC
Statistics
Matches: 213, Mismatches: 26, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
132 13 0.06
133 26 0.12
134 2 0.01
135 35 0.16
136 28 0.13
138 16 0.08
139 90 0.42
140 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (135 bp):
GTTTCACTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAAATCTTTGAA
TATGTTTCCCTTGAAACAAAATTTGTCTCACTTGAGACTGTTTCTCTTGAAACACAAAACCTTTG
AATCT
Found at i:2230258 original size:36 final size:35
Alignment explanation
Indices: 2230173--2230259 Score: 84
Period size: 36 Copynumber: 2.4 Consensus size: 35
2230163 TCTGAACCTA
* **
2230173 TTTCCCTTGAAACAAAATTTATCTCACTTGAGATTG
1 TTTCCCTTGAAAC-AAATTTATCTCACTGGAGACAG
** ** *
2230209 TTTTTCTCAAAACAAGTTTCATCTCACTGGAGACAG
1 TTTCCCTTGAAACAAATTT-ATCTCACTGGAGACAG
2230245 TTTCCCTTGAAACAA
1 TTTCCCTTGAAACAA
2230260 TAAATTTTAT
Statistics
Matches: 38, Mismatches: 12, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
35 5 0.13
36 33 0.87
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (35 bp):
TTTCCCTTGAAACAAATTTATCTCACTGGAGACAG
Found at i:2230348 original size:78 final size:74
Alignment explanation
Indices: 2230173--2230354 Score: 208
Period size: 78 Copynumber: 2.4 Consensus size: 74
2230163 TCTGAACCTA
* *
2230173 TTTCCCTTGAAAC-AAAA-TTTATCTCACTTGAGATTGTTTTTCTCAAAACAAGTTTCATCTCAC
1 TTTCCCTTGAAACAAAAATTTTATCTCACTCGAGATTGTTTTTCTCAAAACAAGCTTCATCTCAC
2230236 TGGAGACAG
66 TGGAGACAG
* * *
2230245 TTTCCCTTGAAACAATAAATTTTATCTCACTCGAGATGATTTTTTTCTTAAAACTAA-CTTCGTC
1 TTTCCCTTGAAACAA-AAATTTTATCTCACTCGAGAT--TGTTTTTCTCAAAAC-AAGCTTCATC
* * *
2230309 TCGCTTGAGACAAT
62 TCACTGGAGAC-AG
*
2230323 TTTCCCTTGAAGCAAGAAATTTTATCTCACTC
1 TTTCCCTTGAAACAA-AAATTTTATCTCACTC
2230355 AAGAGAGCTT
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
72 13 0.14
73 1 0.01
74 3 0.03
75 16 0.17
77 27 0.29
78 33 0.35
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (74 bp):
TTTCCCTTGAAACAAAAATTTTATCTCACTCGAGATTGTTTTTCTCAAAACAAGCTTCATCTCAC
TGGAGACAG
Found at i:2230671 original size:91 final size:91
Alignment explanation
Indices: 2230562--2230815 Score: 402
Period size: 91 Copynumber: 2.8 Consensus size: 91
2230552 TTCCAGCGAG
2230562 GAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* ** *
2230627 GACCTTGCTTTGACGATT-TTAATTGA
66 GACCTTGCCTTGAC-ATTACCAATGGA
**
2230653 GAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
2230718 GACCTTGCCTTGACATTACCAGTGGA
66 GACCTTGCCTTGACATTACCAATGGA
* *
2230744 GAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
2230809 AACCTTG
66 GACCTTG
2230816 GCTCAACATT
Statistics
Matches: 150, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
90 3 0.02
91 147 0.98
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.25
Consensus pattern (91 bp):
GAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
GACCTTGCCTTGACATTACCAATGGA
Found at i:2230960 original size:42 final size:42
Alignment explanation
Indices: 2230913--2231071 Score: 147
Period size: 42 Copynumber: 3.5 Consensus size: 42
2230903 ATTGTTTGAT
*
2230913 TCCATCACATACAGAGTTGGAACAACACCAATACTTGGCTCA
1 TCCATCACATACGGAGTTGGAACAACACCAATACTTGGCTCA
* * *
2230955 TCCATCACATACGGAGTTGGATCAACATCATCAACGTTGTCATTCTTGCCTGA
1 TCCATCACATACGGAGTTGGAACAACA-C--CAA-----T-A--CTTGGCTCA
* * *
2231008 TTCCATCACGTACGGAGTTAGAACAACACCAAAACTTGGCTCA
1 -TCCATCACATACGGAGTTGGAACAACACCAATACTTGGCTCA
2231051 TCCATCACATACGGAGTTGGA
1 TCCATCACATACGGAGTTGGA
2231072 TCAGCATCTT
Statistics
Matches: 93, Mismatches: 12, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
42 44 0.47
43 8 0.09
45 4 0.04
50 1 0.01
51 4 0.04
53 8 0.09
54 24 0.26
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (42 bp):
TCCATCACATACGGAGTTGGAACAACACCAATACTTGGCTCA
Found at i:2231009 original size:96 final size:95
Alignment explanation
Indices: 2230840--2231113 Score: 415
Period size: 96 Copynumber: 2.9 Consensus size: 95
2230830 ATTGCTCGAT
* * *
2230840 AACACCAATACTTGGCTCATCCATCACATTCGGAGTTGGATCAACATCATCAACATTGCCATTAT
1 AACACCAATACTTGGCTCATCCATCACATACGGAGTTGGATCAACATCATCAACATTGTCATTCT
* *
2230905 TGTTTGATTCCATCACATACAGAGTTGGAAC
66 TG-CTGATTCCATCACATACAGAGTTAGAAC
*
2230936 AACACCAATACTTGGCTCATCCATCACATACGGAGTTGGATCAACATCATCAACGTTGTCATTCT
1 AACACCAATACTTGGCTCATCCATCACATACGGAGTTGGATCAACATCATCAACATTGTCATTCT
* *
2231001 TGCCTGATTCCATCACGTACGGAGTTAGAAC
66 TG-CTGATTCCATCACATACAGAGTTAGAAC
* * *
2231032 AACACCAAAACTTGGCTCATCCATCACATACGGAGTTGGATCAGCATCTTCAACATTGTCATTCT
1 AACACCAATACTTGGCTCATCCATCACATACGGAGTTGGATCAACATCATCAACATTGTCATTCT
2231097 TGCTCGA-TCCATCACAT
66 TGCT-GATTCCATCACAT
2231114 GTGGAGTTGA
Statistics
Matches: 163, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
95 11 0.07
96 152 0.93
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (95 bp):
AACACCAATACTTGGCTCATCCATCACATACGGAGTTGGATCAACATCATCAACATTGTCATTCT
TGCTGATTCCATCACATACAGAGTTAGAAC
Found at i:2233641 original size:21 final size:20
Alignment explanation
Indices: 2233626--2233675 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
2233616 TTTTTACTTT
*
2233626 TTTTATTTATTGTTTTAATTA
1 TTTTAATTA-TGTTTTAATTA
*
2233647 TTTTAATTATGTTTATTAATTT
1 TTTTAATTATG-TT-TTAATTA
2233669 TTTTAAT
1 TTTTAAT
2233676 ATTTTATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 10 0.40
22 13 0.52
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTTAATTATGTTTTAATTA
Found at i:2233641 original size:22 final size:21
Alignment explanation
Indices: 2233616--2233675 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
2233606 TATGTTGTTT
* *
2233616 TTTTTACTTTTTTTATTTAT-
1 TTTTTAATTTTTTTAATTATG
*
2233636 TGTTTTAATTATTTTAATTATG
1 T-TTTTAATTTTTTTAATTATG
2233658 TTTATTAATTTTTTTAAT
1 TTT-TTAATTTTTTTAAT
2233676 ATTTTATAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 18 0.55
22 14 0.42
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTTTAATTTTTTTAATTATG
Found at i:2233688 original size:19 final size:22
Alignment explanation
Indices: 2233623--2233682 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
2233613 TTTTTTTTAC
*
2233623 TTTTTTTATTTAT-TGTT-TTAA
1 TTTTTTTAATTATGT-TTATTAA
*
2233644 TTATTTTAATTATGTTTATTAA
1 TTTTTTTAATTATGTTTATTAA
2233666 TTTTTTTAA-TAT-TTTAT
1 TTTTTTTAATTATGTTTAT
2233683 AGTTTTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 5 0.15
21 16 0.47
22 13 0.38
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (22 bp):
TTTTTTTAATTATGTTTATTAA
Found at i:2234992 original size:22 final size:22
Alignment explanation
Indices: 2234967--2235008 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2234957 TTTATTAACG
*
2234967 GTGTCAATTCTAAAATTTTATT
1 GTGTCAATCCTAAAATTTTATT
* *
2234989 GTGTCCATCCTGAAATTTTA
1 GTGTCAATCCTAAAATTTTA
2235009 ATTTTCTTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (22 bp):
GTGTCAATCCTAAAATTTTATT
Found at i:2242288 original size:36 final size:36
Alignment explanation
Indices: 2242241--2242312 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
2242231 CCTAGCATTC
* *
2242241 GCCAAGAACCAGATTCGGATCTTGTTGCCTCTGAAA
1 GCCAAGAACCAGATTCGGATCCTGTTGCATCTGAAA
2242277 GCCAAGAACCAGATTCGGATCCTGTTGCATCTGAAA
1 GCCAAGAACCAGATTCGGATCCTGTTGCATCTGAAA
2242313 CAGAAGGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (36 bp):
GCCAAGAACCAGATTCGGATCCTGTTGCATCTGAAA
Found at i:2245018 original size:72 final size:72
Alignment explanation
Indices: 2244901--2245037 Score: 247
Period size: 72 Copynumber: 1.9 Consensus size: 72
2244891 TTTGGTGATA
*
2244901 ATGTTTGGTAAGACTGAAGATTTAACCAGCTGCTTTGTGTAATTGTTACTATTGTAATTTATGCC
1 ATGTTTGGTAAGACTGAAGATTTAACCAGCTGCTTTGTGTAATTGTTACTATAGTAATTTATGCC
2244966 CACAAAT
66 CACAAAT
* *
2244973 ATGTTTGGTAAGACTGAAGATTTAACCAGTTGCTTTGTGTAATTGTTTCTATAGTAATTTATGCC
1 ATGTTTGGTAAGACTGAAGATTTAACCAGCTGCTTTGTGTAATTGTTACTATAGTAATTTATGCC
2245038 TTTTTAATAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (72 bp):
ATGTTTGGTAAGACTGAAGATTTAACCAGCTGCTTTGTGTAATTGTTACTATAGTAATTTATGCC
CACAAAT
Found at i:2265190 original size:39 final size:39
Alignment explanation
Indices: 2265136--2265211 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 39
2265126 GGTATTTTTA
*
2265136 ATGATTATTTAATTATGCACATTTTCT-AAACTTATGCCG
1 ATGATTATTTAATTATACACATTTT-TAAAACTTATGCCG
2265175 ATGATTATTTAATTATACACATTTTTAAAACTTATGC
1 ATGATTATTTAATTATACACATTTTTAAAACTTATGC
2265212 AGGTGGCTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 1 0.03
39 34 0.97
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (39 bp):
ATGATTATTTAATTATACACATTTTTAAAACTTATGCCG
Found at i:2269412 original size:12 final size:12
Alignment explanation
Indices: 2269395--2269419 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2269385 ATGAAATTAT
2269395 AAAAAAACTAAA
1 AAAAAAACTAAA
2269407 AAAAAAACTAAA
1 AAAAAAACTAAA
2269419 A
1 A
2269420 TATCTCATTT
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:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAAAACTAAA
Found at i:2274548 original size:35 final size:35
Alignment explanation
Indices: 2274508--2274576 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
2274498 AGAGAATGAC
2274508 CTTACTTTACTAATTTTTAAACTAAAAGAGACCTT
1 CTTACTTTACTAATTTTTAAACTAAAAGAGACCTT
2274543 CTTACTTTACTAATTTTTAAACTAAAAGAGACCT
1 CTTACTTTACTAATTTTTAAACTAAAAGAGACCT
2274577 AAAATGTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (35 bp):
CTTACTTTACTAATTTTTAAACTAAAAGAGACCTT
Found at i:2287090 original size:45 final size:45
Alignment explanation
Indices: 2287026--2287145 Score: 195
Period size: 45 Copynumber: 2.7 Consensus size: 45
2287016 CATATTTTCG
** *
2287026 CGTAGTTCAATATCACATAGTTTATATCATATGTTCACATGTTCA
1 CGTAGTTCGGTATCACATAGTTTATATCATATGTTAACATGTTCA
2287071 CGTAGTTCGGTATCACATAGTTTATATCATATGTTAACATGTTCA
1 CGTAGTTCGGTATCACATAGTTTATATCATATGTTAACATGTTCA
**
2287116 CGTAGTTCGGTATCACATAACTTATATCAT
1 CGTAGTTCGGTATCACATAGTTTATATCAT
2287146 TTTCTCATAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (45 bp):
CGTAGTTCGGTATCACATAGTTTATATCATATGTTAACATGTTCA
Found at i:2291912 original size:17 final size:18
Alignment explanation
Indices: 2291867--2291915 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
2291857 TTTTCATAAT
2291867 AACAATATAATTTGATCAA
1 AACAATATAATTTGA-CAA
2291886 AACACA-ATAATTTGA-AA
1 AACA-ATATAATTTGACAA
*
2291903 AATAATATAATTT
1 AACAATATAATTT
2291916 TTTTTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 1 0.04
17 12 0.44
19 13 0.48
20 1 0.04
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (18 bp):
AACAATATAATTTGACAA
Found at i:2292341 original size:21 final size:21
Alignment explanation
Indices: 2292315--2292397 Score: 62
Period size: 21 Copynumber: 3.8 Consensus size: 21
2292305 CAGATCCCCA
*
2292315 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2292336 GGGGGGAATCGGTTCCCCT-T
1 GGGGGGAATCGATTCCCCTGT
* * *
2292356 CAAAGGGGGAATCGGTTCCCTCAG-
1 ---GGGGGGAATCGATTCCC-CTGT
2292380 GGGGAGGAATCGATTCCC
1 GGGG-GGAATCGATTCCC
2292398 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
20 1 0.02
21 20 0.40
22 12 0.24
23 16 0.32
24 1 0.02
ACGTcount: A:0.17, C:0.24, G:0.37, T:0.22
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:2292376 original size:22 final size:22
Alignment explanation
Indices: 2292337--2292398 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
2292327 TTCCCCTGTG
2292337 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCCTTCAAA
**
2292360 GGGGGAATCGGTTCCC-TCAGG
1 GGGGGAATCGGTTCCCTTCAAA
*
2292381 GGGAGGAATCGATTCCCT
1 GGG-GGAATCGGTTCCCT
2292399 CTGCACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.18
22 15 0.44
23 13 0.38
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.21
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCTTCAAA
Found at i:2300229 original size:71 final size:71
Alignment explanation
Indices: 2300108--2300267 Score: 203
Period size: 71 Copynumber: 2.2 Consensus size: 71
2300098 TTAAATGACT
* * * *
2300108 AAGGGTATCGATATCTCTAGGGGGTATCGATACTCATTGGGCATTCTGTTTTTCTCGGAGTCAAA
1 AAGGGTATCGGTA-C-CTAGGGGGTATCGATACCCATTGGACATTCTGTTTTTCTCGGAGCCAAA
*
2300173 ATTAACAC
64 ATCAACAC
* * * * *
2300181 AAGGGTATCGGTACCTATGGGGTATCGGTACCCGTTTGACATTTTGTTTTTCTCGGAGCCAAAAT
1 AAGGGTATCGGTACCTAGGGGGTATCGATACCCATTGGACATTCTGTTTTTCTCGGAGCCAAAAT
*
2300246 CAACAT
66 CAACAC
2300252 AAGGGTATCGGTACCT
1 AAGGGTATCGGTACCT
2300268 CCTTATTTAA
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
71 63 0.83
72 1 0.01
73 12 0.16
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (71 bp):
AAGGGTATCGGTACCTAGGGGGTATCGATACCCATTGGACATTCTGTTTTTCTCGGAGCCAAAAT
CAACAC
Found at i:2300697 original size:12 final size:12
Alignment explanation
Indices: 2300680--2300705 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2300670 CTTGATGCAG
2300680 AGTCTCGGGTTA
1 AGTCTCGGGTTA
2300692 AGTCTCGGGTTA
1 AGTCTCGGGTTA
2300704 AG
1 AG
2300706 GAGTTCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.15, G:0.35, T:0.31
Consensus pattern (12 bp):
AGTCTCGGGTTA
Found at i:2303973 original size:22 final size:24
Alignment explanation
Indices: 2303934--2303982 Score: 75
Period size: 22 Copynumber: 2.1 Consensus size: 24
2303924 AACTGTCATC
2303934 TTTGGTTAATGCATCTTATTT-TTG
1 TTTGGTTAA-GCATCTTATTTATTG
2303958 TTTGGTTAA-CATCTTATTTATTG
1 TTTGGTTAAGCATCTTATTTATTG
2303981 TT
1 TT
2303983 CTTTATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 10 0.42
23 5 0.21
24 9 0.38
ACGTcount: A:0.18, C:0.08, G:0.14, T:0.59
Consensus pattern (24 bp):
TTTGGTTAAGCATCTTATTTATTG
Found at i:2305259 original size:31 final size:31
Alignment explanation
Indices: 2305214--2305294 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
2305204 ATCGATAAAG
2305214 TTAATGACCAATTTGTTATAAAT-AGATAACA
1 TTAATGACCAATTTGTTATAAATCA-ATAACA
* ** *
2305245 TTAGTGACTGATTTGTTATAAATCAATAATA
1 TTAATGACCAATTTGTTATAAATCAATAACA
2305276 TTAATGACCAATTTGTTAT
1 TTAATGACCAATTTGTTAT
2305295 TTTTGAAACT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 41 0.98
32 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.41
Consensus pattern (31 bp):
TTAATGACCAATTTGTTATAAATCAATAACA
Found at i:2308910 original size:7 final size:7
Alignment explanation
Indices: 2308898--2308931 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
2308888 CCTTATCATC
2308898 TCACAAG
1 TCACAAG
2308905 TCACAAG
1 TCACAAG
2308912 TCACAAG
1 TCACAAG
2308919 TCACAAG
1 TCACAAG
2308926 TCACAA
1 TCACAA
2308932 TAAAGCAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.29, G:0.12, T:0.15
Consensus pattern (7 bp):
TCACAAG
Found at i:2309542 original size:14 final size:14
Alignment explanation
Indices: 2309512--2309555 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2309502 CTGAAGTGGA
*
2309512 AGAAATGAT-GAGTG
1 AGAAA-GATAGAGAG
2309526 AGAAAGATAGAGAG
1 AGAAAGATAGAGAG
*
2309540 AGAAAGAGAGAGAG
1 AGAAAGATAGAGAG
2309554 AG
1 AG
2309556 TGACAGGTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 3 0.11
14 24 0.89
ACGTcount: A:0.52, C:0.00, G:0.39, T:0.09
Consensus pattern (14 bp):
AGAAAGATAGAGAG
Found at i:2326304 original size:101 final size:102
Alignment explanation
Indices: 2326116--2326309 Score: 239
Period size: 101 Copynumber: 1.9 Consensus size: 102
2326106 TCTGCGATGC
* * * * *
2326116 CGATATTTAGGTCGAACAAACTGGTAGTTGAATGTATTCCCCTTGAACTTGAAGGCATCATGTCA
1 CGATATTGAGGTCGAACAAACTCGCAGTTGAATGTACTCCCCTAGAACTTGAAGGCATCATGTCA
* ** *
2326181 TATGGGTTTTGGACTAAGTGTTGTGTCGTAGGCATCT
66 AATGGGTACTGAACTAAGTGTTGTGTCGTAGGCATCT
* * *
2326218 CGATATTGAGGTCGAAGAAGCTCGCAGTTGAATG-CCTCCCCTAGAACTTGAAGGCATCATGTCA
1 CGATATTGAGGTCGAACAAACTCGCAGTTGAATGTACTCCCCTAGAACTTGAAGGCATCATGTCA
* *
2326282 AATTGGTACTGAAC-AGATTGTTGTGTCG
66 AATGGGTACTGAACTA-AGTGTTGTGTCG
2326310 ATGACATCCC
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
100 1 0.01
101 47 0.61
102 29 0.38
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (102 bp):
CGATATTGAGGTCGAACAAACTCGCAGTTGAATGTACTCCCCTAGAACTTGAAGGCATCATGTCA
AATGGGTACTGAACTAAGTGTTGTGTCGTAGGCATCT
Found at i:2326337 original size:101 final size:101
Alignment explanation
Indices: 2326153--2326337 Score: 212
Period size: 101 Copynumber: 1.8 Consensus size: 101
2326143 TTGAATGTAT
* * ** * * *
2326153 TCCCCTTGAACTTGAAGGCATCATGTCATATGGGTTTTGGACTAAGTGTTGTGTCGTAGGCATCT
1 TCCCCTAGAACTTGAAGGCATCATGTCAAATGGGTACTGAACTAAGTGTTGTGTCGTAGACATCC
* * * *
2326218 CGATATTGAGGTCGAAGAAGCTCGCAGTTGAATGCC
66 CCATATTCAAGTCAAAGAAGCTCGCAGTTGAATGCC
* *
2326254 TCCCCTAGAACTTGAAGGCATCATGTCAAATTGGTACTGAAC-AGATTGTTGTGTCG-ATGACAT
1 TCCCCTAGAACTTGAAGGCATCATGTCAAATGGGTACTGAACTA-AGTGTTGTGTCGTA-GACAT
*
2326317 CCCCATATTCAAGTTAAAGAA
64 CCCCATATTCAAGTCAAAGAA
2326338 ATTGGCAGAT
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
100 2 0.03
101 66 0.97
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (101 bp):
TCCCCTAGAACTTGAAGGCATCATGTCAAATGGGTACTGAACTAAGTGTTGTGTCGTAGACATCC
CCATATTCAAGTCAAAGAAGCTCGCAGTTGAATGCC
Found at i:2328641 original size:4 final size:4
Alignment explanation
Indices: 2328632--2328660 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2328622 AATACGTTAA
2328632 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
2328661 TGATGTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2329331 original size:21 final size:21
Alignment explanation
Indices: 2329285--2329340 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
2329275 GATTCTGACT
2329285 ATCGCATTGCGA-TTTCCCAA
1 ATCGCATTGCGATTTTCCCAA
* *
2329305 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGATTTTCCCAA
*
2329327 ATCGCAATGCGATT
1 ATCGCATTGCGATT
2329341 ACGTAAATCG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 21 0.70
22 8 0.27
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (21 bp):
ATCGCATTGCGATTTTCCCAA
Found at i:2329349 original size:20 final size:20
Alignment explanation
Indices: 2329324--2329380 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
2329314 GCGATTTTCC
2329324 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
* * *
2329344 TAAATCGTAATGCGAATGCG
1 TAAATCGCAATGCGATTACG
2329364 TAAATCGCAATGCGATT
1 TAAATCGCAATGCGATT
2329381 TACATAGCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
TAAATCGCAATGCGATTACG
Found at i:2329580 original size:22 final size:22
Alignment explanation
Indices: 2329555--2329616 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
2329545 GGCGACATCC
2329555 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
2329577 GTCCCCA----CGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
** *
2329595 GTTTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
2329617 TTCACGGTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
18 15 0.48
22 16 0.52
ACGTcount: A:0.26, C:0.37, G:0.16, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:2330006 original size:20 final size:20
Alignment explanation
Indices: 2329978--2330024 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2329968 GATTCTTGCA
*
2329978 TTGCAATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
** *
2329998 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCAAATTCGCG
2330018 TTGCGAT
1 TTGCGAT
2330025 TTTCATTTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:2330030 original size:20 final size:20
Alignment explanation
Indices: 2329992--2330046 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
2329982 AATAGTCAAA
* **
2329992 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
2330012 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
2330032 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
2330047 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:2330054 original size:20 final size:20
Alignment explanation
Indices: 2330011--2330054 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2330001 CGATAGTCAT
** *
2330011 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
2330031 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
2330051 TTTC
1 TTTC
2330055 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:2331955 original size:20 final size:20
Alignment explanation
Indices: 2331930--2332093 Score: 223
Period size: 20 Copynumber: 8.5 Consensus size: 20
2331920 AGAATAGTTT
2331930 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2331950 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2331970 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
2331986 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2332004 ACTATCGCAATGTGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2332024 AATATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
2332044 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* **
2332064 ACTATCGCAGTGCGAATTTG
1 ACTATCGCAATGCGAAAATG
2332084 ACTATCGCAA
1 ACTATCGCAA
2332094 GGAAAGAATC
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
14 7 0.06
16 4 0.03
17 4 0.03
18 4 0.03
20 108 0.85
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:2332021 original size:54 final size:54
Alignment explanation
Indices: 2331933--2332131 Score: 238
Period size: 54 Copynumber: 3.6 Consensus size: 54
2331923 ATAGTTTACT
* *
2331933 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGAAAGA
* *
2331987 ATCGCAATGCGAAAATGACTATCGCAATGTGAAAATGAATATCGCAATGCGAAAATGA
1 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAA--CG-AAA-GA
* ** *
2332045 CTATCGCAATGCGAAAATGACTATCGCAGTGCGAATTTGACTATCGCAAGGAAAGA
1 --ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGAAAGA
** *
2332101 ATCGCAATGCG-AAATGAAAATCGCATTGCGA
1 ATCGCAATGCGAAAATGACTATCGCAATGCGA
2332132 TTCTCTCGTT
Statistics
Matches: 126, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
53 17 0.13
54 55 0.44
56 4 0.03
57 5 0.04
58 3 0.02
60 42 0.33
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (54 bp):
ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGAAAGA
Found at i:2332042 original size:40 final size:40
Alignment explanation
Indices: 2331930--2332131 Score: 214
Period size: 40 Copynumber: 5.4 Consensus size: 40
2331920 AGAATAGTTT
* *
2331930 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATGAATATCGCAATGCGAAAATG
*
2331970 ACTATCGCAA--CG-AGA-G-A-ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGAATATCGCAATGCGAAAATG
*
2332004 ACTATCGCAATGTGAAAATGAATATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGAATATCGCAATGCGAAAATG
* * **
2332044 ACTATCGCAATGCGAAAATGACTATCGCAGTGCGAATTTG
1 ACTATCGCAATGCGAAAATGAATATCGCAATGCGAAAATG
2332084 ACTATCGCAA-G-G-AAA-G-A-ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATGAATATCGCAATGCGAAAATG
** *
2332117 AAAATCGCATTGCGA
1 ACTATCGCAATGCGA
2332132 TTCTCTCGTT
Statistics
Matches: 136, Mismatches: 17, Indels: 22
0.78 0.10 0.13
Matches are distributed among these distances:
33 10 0.07
34 37 0.27
35 1 0.01
36 3 0.02
37 7 0.05
38 4 0.03
39 2 0.01
40 72 0.53
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (40 bp):
ACTATCGCAATGCGAAAATGAATATCGCAATGCGAAAATG
Found at i:2332168 original size:20 final size:20
Alignment explanation
Indices: 2332140--2332247 Score: 162
Period size: 20 Copynumber: 5.3 Consensus size: 20
2332130 GATTCTCTCG
* **
2332140 TTGCGATAGACAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2332160 TTACGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
2332180 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
2332200 TTGCGATAGTCATTTTTCGCA
1 TTGCGATAGTCA-TTTTCGCA
*
2332221 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
2332241 TTGCGAT
1 TTGCGAT
2332248 TTTGTTGTTG
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
20 61 0.75
21 20 0.25
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:2332229 original size:41 final size:40
Alignment explanation
Indices: 2332140--2332247 Score: 162
Period size: 41 Copynumber: 2.7 Consensus size: 40
2332130 GATTCTCTCG
* ** *
2332140 TTGCGATAGACAAATTCGCATTACGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCA
2332180 TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTTCGCA
1 TTGCGATAGTCATTTTCGCATTGCGATAGTCA-TTTTCGCA
*
2332221 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCATTGCGAT
2332248 TTTGTTGTTG
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
40 28 0.45
41 34 0.55
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.38
Consensus pattern (40 bp):
TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCA
Found at i:2332278 original size:33 final size:34
Alignment explanation
Indices: 2332221--2332317 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
2332211 ATTTTTCGCA
* *
2332221 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCGTTGCGATTTTCTCG
** * *
2332255 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCGTTGCGATTTTCTCG
2332288 TTGCGATAGTCATTTTCGCGTTGCGATTTT
1 TTGCGATAGTCATTTTCGCGTTGCGATTTT
2332318 AAGTTTCAGA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 27 0.52
34 25 0.48
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCGTTGCGATTTTCTCG
Found at i:2332839 original size:18 final size:19
Alignment explanation
Indices: 2332800--2332841 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
2332790 CTCACCTGTC
2332800 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
2332821 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
2332839 ATC
1 ATC
2332842 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:2332889 original size:21 final size:20
Alignment explanation
Indices: 2332794--2332896 Score: 55
Period size: 21 Copynumber: 5.0 Consensus size: 20
2332784 GCCCGACTCA
*
2332794 CCTGTCATCGTTCAAGAGGC
1 CCTGTTATCGTTCAAGAGGC
***
2332814 CTCCCCTATCGTTCAAGAGGCC
1 C-CTGTTATCGTTCAAGAGG-C
* * ** *
2332836 CCTATCATCCCTCAAGAGTC
1 CCTGTTATCGTTCAAGAGGC
*
2332856 CCT-TTCCACCGTTCAAGAGGC
1 CCTGTT--ATCGTTCAAGAGGC
*
2332877 CACTGTTATCGTTGAAGAGG
1 C-CTGTTATCGTTCAAGAGG
2332897 TCTCTCCTAA
Statistics
Matches: 59, Mismatches: 18, Indels: 11
0.67 0.20 0.12
Matches are distributed among these distances:
19 1 0.02
20 5 0.08
21 47 0.80
22 4 0.07
23 2 0.03
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.25
Consensus pattern (20 bp):
CCTGTTATCGTTCAAGAGGC
Found at i:2334280 original size:14 final size:14
Alignment explanation
Indices: 2334261--2334296 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2334251 ATTGTTTAAT
2334261 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2334275 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2334289 TGATTTGT
1 TGATTTGT
2334297 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2334486 original size:34 final size:34
Alignment explanation
Indices: 2334398--2334493 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 34
2334388 AAAACAGACT
* ** *
2334398 ATCGCAACGCGAAAATGACTATCGCAACGGGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
2334432 ATCGCAATGCG-AAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
* *
2334465 ATCGTAATGCGAAAATGAAAATCCCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
2334494 CGAAATTAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.52
34 26 0.48
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.15
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:2334528 original size:20 final size:19
Alignment explanation
Indices: 2334503--2334683 Score: 112
Period size: 20 Copynumber: 9.8 Consensus size: 19
2334493 GCGAAATTAG
2334503 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
2334522 TTTTCGCATTGCGA--TTCA
1 -TTTCGCGTTGCGATTTTCA
*
2334540 ---CTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* *
2334556 TTTCACATTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* *
2334575 TTTCACATTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
2334594 TTTCGCATTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
* **
2334610 --TCTCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
**
2334627 TTTTCGCGTTGCGATAGTCA
1 -TTTCGCGTTGCGATTTTCA
* **
2334647 TTTCCGTGTTGCGATAGTCA
1 TTT-CGCGTTGCGATTTTCA
*
2334667 TATTCACGTTGCGATTT
1 T-TTCGCGTTGCGATTT
2334684 CCTCGTTGCG
Statistics
Matches: 133, Mismatches: 15, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 17 0.13
16 6 0.05
17 3 0.02
18 4 0.03
19 48 0.36
20 53 0.40
21 2 0.02
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:2334568 original size:19 final size:19
Alignment explanation
Indices: 2334544--2334608 Score: 121
Period size: 19 Copynumber: 3.4 Consensus size: 19
2334534 GATTCACTCG
2334544 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCACA
2334563 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCACA
*
2334582 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCACA
2334601 TTGCGATT
1 TTGCGATT
2334609 CTCTCGTTGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCACA
Found at i:2334692 original size:34 final size:34
Alignment explanation
Indices: 2334601--2334700 Score: 96
Period size: 40 Copynumber: 2.8 Consensus size: 34
2334591 TCATTTCGCA
* *
2334601 TTGCGA-TTCTCTCGTTGCGATAGTCATTTTCGCG
1 TTGCGATTTC-CTCGTTGCGATAGTCATATTCACG
2334635 TTGCGATAGTCATTTCCGT-GTTGCGATAGTCATATTCACG
1 TTGC----G--ATTTCC-TCGTTGCGATAGTCATATTCACG
2334675 TTGCGATTTCCTCGTTGCGATAGTCA
1 TTGCGATTTCCTCGTTGCGATAGTCA
2334701 AATGAATGTC
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
33 1 0.02
34 23 0.42
36 1 0.02
38 1 0.02
40 25 0.45
41 4 0.07
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (34 bp):
TTGCGATTTCCTCGTTGCGATAGTCATATTCACG
Found at i:2337148 original size:24 final size:24
Alignment explanation
Indices: 2337114--2337167 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2337104 CTGAAAAATC
2337114 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2337138 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2337162 ATCAAA
1 ATCAAA
2337168 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2337181 original size:24 final size:24
Alignment explanation
Indices: 2337114--2337181 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2337104 CTGAAAAATC
* * *
2337114 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
2337138 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2337162 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2337182 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:2338045 original size:20 final size:20
Alignment explanation
Indices: 2338029--2338111 Score: 112
Period size: 20 Copynumber: 4.1 Consensus size: 20
2338019 CAGAATCTCG
2338029 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
2338049 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
* ** *
2338069 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTACGTAA-TCGCA
*
2338090 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCA
2338110 TT
1 TT
2338112 ACGAATTAGG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 38 0.72
21 15 0.28
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:2338139 original size:21 final size:21
Alignment explanation
Indices: 2338113--2338157 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2338103 ATTCGCATTA
*
2338113 CGAATTAGGAAAATCTCAACG
1 CGAATTAGGAAAATCGCAACG
* * *
2338134 CGAATTTGGGAAATCGCAATG
1 CGAATTAGGAAAATCGCAACG
2338155 CGA
1 CGA
2338158 TAGTCAGAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACG
Found at i:2338614 original size:2 final size:2
Alignment explanation
Indices: 2338607--2338633 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2338597 TATGTTTAAC
2338607 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
2338634 ATTTATTTAA
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:2338909 original size:2 final size:2
Alignment explanation
Indices: 2338902--2338988 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
2338892 TTTGATGAGT
2338902 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
2338944 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
2338986 TA T
1 TA T
2338989 TTATTTTGTT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2339521 original size:23 final size:23
Alignment explanation
Indices: 2339495--2339542 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
2339485 GTGAGACACT
* *
2339495 AAACATTTTTTTATTATTCGACC
1 AAACATTTTATTATTATTCAACC
2339518 AAACATTTTATTATTATTCAACC
1 AAACATTTTATTATTATTCAACC
2339541 AA
1 AA
2339543 TTAATAGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.44
Consensus pattern (23 bp):
AAACATTTTATTATTATTCAACC
Found at i:2342576 original size:27 final size:27
Alignment explanation
Indices: 2342541--2342592 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2342531 TGTGAATTCC
*
2342541 TCCTCCTAGATCCGTCATCCCTGTAAT
1 TCCTCCTAGATCCATCATCCCTGTAAT
*
2342568 TCCTTCTAGATCCATCATCCCTGTA
1 TCCTCCTAGATCCATCATCCCTGTA
2342593 TGAGTTAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.37, G:0.10, T:0.35
Consensus pattern (27 bp):
TCCTCCTAGATCCATCATCCCTGTAAT
Found at i:2350069 original size:23 final size:23
Alignment explanation
Indices: 2350006--2350060 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
2349996 AAATTTCAAG
*
2350006 AGCTCGATTAAAACTCGAAACTA
1 AGCTCGATTAAAACTCAAAACTA
*
2350029 AGCTCTATTAAAACTCAAAACTA
1 AGCTCGATTAAAACTCAAAACTA
2350052 AGCTCGATT
1 AGCTCGATT
2350061 CAAGTTCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (23 bp):
AGCTCGATTAAAACTCAAAACTA
Found at i:2351502 original size:27 final size:27
Alignment explanation
Indices: 2351464--2351562 Score: 137
Period size: 27 Copynumber: 3.6 Consensus size: 27
2351454 GTGTATAACT
*
2351464 TAAACCCTAAATCCTAACTC-TAATACA
1 TAAACCCTAAATCCTAACACATAA-ACA
*
2351491 TAAACCCTAAATCCTAACACATAAACC
1 TAAACCCTAAATCCTAACACATAAACA
*
2351518 TAAACCTTAAATCCTAACACATAAACTA
1 TAAACCCTAAATCCTAACACATAAAC-A
*
2351546 TAAACCCTAAACCCTAA
1 TAAACCCTAAATCCTAA
2351563 ACCCTAAATC
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 46 0.72
28 18 0.28
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.22
Consensus pattern (27 bp):
TAAACCCTAAATCCTAACACATAAACA
Found at i:2351556 original size:14 final size:14
Alignment explanation
Indices: 2351491--2351579 Score: 58
Period size: 14 Copynumber: 6.4 Consensus size: 14
2351481 CTCTAATACA
* *
2351491 TAAACCCTAAATCC
1 TAAACCATAAACCC
2351505 T-AACACATAAA-CC
1 TAAAC-CATAAACCC
* *
2351518 TAAACCTTAAATCC
1 TAAACCATAAACCC
**
2351532 T-AACACATAAACTA
1 TAAAC-CATAAACCC
*
2351546 TAAACCCTAAACCC
1 TAAACCATAAACCC
* *
2351560 TAAACCCTAAATCC
1 TAAACCATAAACCC
2351574 TAAACC
1 TAAACC
2351580 TTATCACATA
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
13 14 0.23
14 43 0.72
15 3 0.05
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:2351577 original size:21 final size:21
Alignment explanation
Indices: 2351491--2351579 Score: 74
Period size: 21 Copynumber: 4.3 Consensus size: 21
2351481 CTCTAATACA
* ** *
2351491 TAAACCCTAAATCCTAACACA
1 TAAACCCTAAACCCTAAATCC
*
2351512 TAAA-CCTAAACCTTAAATCC
1 TAAACCCTAAACCCTAAATCC
* ** *
2351532 T-AACACATAAACTATAAACCC
1 TAAAC-CCTAAACCCTAAATCC
2351553 TAAACCCTAAACCCTAAATCC
1 TAAACCCTAAACCCTAAATCC
2351574 TAAACC
1 TAAACC
2351580 TTATCACATA
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
19 2 0.04
20 12 0.23
21 35 0.67
22 3 0.06
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAATCC
Found at i:2351858 original size:14 final size:14
Alignment explanation
Indices: 2351841--2351881 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2351831 TTTATTCATC
2351841 AATAATGTATTTTT
1 AATAATGTATTTTT
2351855 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
2351866 AATAATGTAATTTT
1 AATAATGTATTTTT
2351880 AA
1 AA
2351882 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:2352316 original size:96 final size:96
Alignment explanation
Indices: 2352212--2352406 Score: 320
Period size: 96 Copynumber: 2.0 Consensus size: 96
2352202 TGTATCATCG
* *
2352212 TATAATTGGAGGATTAAATATATTGAATTAATTTAAAATATGACCAATTTGATAGATTGTGTAAG
1 TATAATTGGAGAATTAAATATATTGAATTAATTTAAAATATGACCAACTTGATAGATT-TGTAAG
* * *
2352277 TAATAAGGACT-AGTGTAAATTATATCAATTT
65 TAATAAAGACTAAATGTAAATTATACCAATTT
2352308 TATAATTGGAGAATTAAATATATTGAATTAATTTAAAATATGACCAACTTGATAGATTTGTAAGT
1 TATAATTGGAGAATTAAATATATTGAATTAATTTAAAATATGACCAACTTGATAGATTTGTAAGT
*
2352373 AATAAAGACTAAATGTAAATTATACCGATTT
66 AATAAAGACTAAATGTAAATTATACCAATTT
2352404 TAT
1 TAT
2352407 TCTCGGCACT
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
95 16 0.17
96 76 0.83
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (96 bp):
TATAATTGGAGAATTAAATATATTGAATTAATTTAAAATATGACCAACTTGATAGATTTGTAAGT
AATAAAGACTAAATGTAAATTATACCAATTT
Found at i:2356412 original size:24 final size:24
Alignment explanation
Indices: 2356367--2356413 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2356357 TACATTATTA
*
2356367 ACTTTTAAAAGTTTTCTAAAAATT
1 ACTTTTAAAAATTTTCTAAAAATT
*
2356391 ACTTTTAAAAATATTTTTAAAAA
1 ACTTTTAAAAAT-TTTCTAAAAA
2356414 GTATGATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (24 bp):
ACTTTTAAAAATTTTCTAAAAATT
Found at i:2359959 original size:36 final size:35
Alignment explanation
Indices: 2359888--2360084 Score: 279
Period size: 36 Copynumber: 5.5 Consensus size: 35
2359878 ATGAACACTC
* * * *
2359888 GAATCGAAAGTGCGATACATCCTTCCGTTCAACTT
1 GAATCGGAAGTGCGATGCTTCCTTCCGTTCGACTT
2359923 GAATCGGAAGTGCTGATGCTTCCTTCCGTTCGACTT
1 GAATCGGAAGTGC-GATGCTTCCTTCCGTTCGACTT
*
2359959 GAATCGGAAGTGCCGATGCTTCCCTCCGTTCGACTT
1 GAATCGGAAGTG-CGATGCTTCCTTCCGTTCGACTT
* *
2359995 GAATCGGGAGTGCCGACGCTTTCC-TCCGTTCGACTT
1 GAATCGGAAGTG-CGATGC-TTCCTTCCGTTCGACTT
2360031 GAATCGGAAGTGTCGATGCTTCCTTCCGTTCGACTT
1 GAATCGGAAGTG-CGATGCTTCCTTCCGTTCGACTT
2360067 GAATCGGAAGTGCGATGC
1 GAATCGGAAGTGCGATGC
2360085 ATTCTTTCGT
Statistics
Matches: 148, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
35 22 0.15
36 121 0.82
37 5 0.03
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.29
Consensus pattern (35 bp):
GAATCGGAAGTGCGATGCTTCCTTCCGTTCGACTT
Found at i:2370190 original size:41 final size:40
Alignment explanation
Indices: 2370145--2370273 Score: 129
Period size: 41 Copynumber: 3.1 Consensus size: 40
2370135 TTATTTTTAT
2370145 ATATTATTAAAATATATTATTTAATTATTAAAAATATAAAA
1 ATATTATTAAAATATATTATTTAATTATT-AAAATATAAAA
** *
2370186 ATATTA-TAAAATATATTAATTTAACAATTTAAATATAATAA
1 ATATTATTAAAATATATT-ATTTAATTATTAAAATATAA-AA
* *
2370227 ATA--ATTATAAATATATTATTATAATTATTTTAAAATATTAAT
1 ATATTATTA-AAATATATTATT-TAATTA--TTAAAATATAAAA
2370269 ATATT
1 ATATT
2370274 CATGTCGAGT
Statistics
Matches: 71, Mismatches: 8, Indels: 15
0.76 0.09 0.16
Matches are distributed among these distances:
39 1 0.01
40 24 0.34
41 33 0.46
42 4 0.06
43 9 0.13
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (40 bp):
ATATTATTAAAATATATTATTTAATTATTAAAATATAAAA
Found at i:2371224 original size:7 final size:7
Alignment explanation
Indices: 2371209--2371280 Score: 94
Period size: 7 Copynumber: 10.6 Consensus size: 7
2371199 TTGCAATGAG
2371209 CCCTAAA
1 CCCTAAA
*
2371216 CCTTAAA
1 CCCTAAA
2371223 CCCTAAA
1 CCCTAAA
2371230 CCCTAAA
1 CCCTAAA
2371237 -CCTAAA
1 CCCTAAA
*
2371243 CCTTAAA
1 CCCTAAA
2371250 CCCTAAA
1 CCCTAAA
2371257 CCCTAAA
1 CCCTAAA
**
2371264 TACTAAA
1 CCCTAAA
2371271 -CCTAAA
1 CCCTAAA
2371277 CCCT
1 CCCT
2371281 TAATCTAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
6 11 0.20
7 45 0.80
ACGTcount: A:0.43, C:0.38, G:0.00, T:0.19
Consensus pattern (7 bp):
CCCTAAA
Found at i:2371240 original size:27 final size:28
Alignment explanation
Indices: 2371213--2371280 Score: 113
Period size: 27 Copynumber: 2.5 Consensus size: 28
2371203 AATGAGCCCT
2371213 AAACCTTAAACCCTAAACCCTAAA-CCT
1 AAACCTTAAACCCTAAACCCTAAATCCT
*
2371240 AAACCTTAAACCCTAAACCCTAAATACT
1 AAACCTTAAACCCTAAACCCTAAATCCT
2371268 AAACC-TAAACCCT
1 AAACCTTAAACCCT
2371281 TAATCTAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 32 0.82
28 7 0.18
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (28 bp):
AAACCTTAAACCCTAAACCCTAAATCCT
Found at i:2371257 original size:34 final size:35
Alignment explanation
Indices: 2371212--2371283 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 35
2371202 CAATGAGCCC
* *
2371212 TAAACCTTAAACCCTAAACCCTAAACCTAAA-CCT
1 TAAACCCTAAACCCTAAACACTAAACCTAAACCCT
*
2371246 TAAACCCTAAACCCTAAATACTAAACCTAAACCCT
1 TAAACCCTAAACCCTAAACACTAAACCTAAACCCT
2371281 TAA
1 TAA
2371284 TCTAATTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 28 0.82
35 6 0.18
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (35 bp):
TAAACCCTAAACCCTAAACACTAAACCTAAACCCT
Found at i:2371280 original size:20 final size:20
Alignment explanation
Indices: 2371209--2371278 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
2371199 TTGCAATGAG
2371209 CCCTAAACCTTAAACCCTAAA
1 CCCTAAACC-TAAACCCTAAA
*
2371230 CCCTAAACCTAAACCTTAAA
1 CCCTAAACCTAAACCCTAAA
**
2371250 CCCTAAACCCTAAATACTAAA
1 CCCTAAA-CCTAAACCCTAAA
2371271 -CCTAAACC
1 CCCTAAACC
2371279 CTTAATCTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.05
20 23 0.52
21 19 0.43
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (20 bp):
CCCTAAACCTAAACCCTAAA
Found at i:2372145 original size:27 final size:27
Alignment explanation
Indices: 2372107--2372171 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
2372097 TGCAAAATAG
*
2372107 TTGCAAAAGAAATAAAATCTTATGGGA
1 TTGCAAAAGAAATAAAATCTTAAGGGA
2372134 TTGCAAAAGAAATAAAATCTTAAGGGA
1 TTGCAAAAGAAATAAAATCTTAAGGGA
2372161 TTGCAAAAGAA
1 TTGCAAAAGAA
2372172 CATAGTTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.51, C:0.08, G:0.18, T:0.23
Consensus pattern (27 bp):
TTGCAAAAGAAATAAAATCTTAAGGGA
Found at i:2374759 original size:18 final size:18
Alignment explanation
Indices: 2374736--2374778 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2374726 TGACCGGTCA
2374736 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
2374754 CGACCCTACCCGTTGACC
1 CGACCCGACCCGTTGACC
2374772 CGACCCG
1 CGACCCG
2374779 TTGCCCGGTG
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:0.16, C:0.51, G:0.21, T:0.12
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:2374914 original size:29 final size:29
Alignment explanation
Indices: 2374785--2374916 Score: 219
Period size: 29 Copynumber: 4.6 Consensus size: 29
2374775 CCCGTTGCCC
*
2374785 GGTGCTATTCTAGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
* *
2374814 AGTGCTATTCTGATAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
2374843 GGTGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
2374872 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
2374901 GGTGCTATTATGGTAA
1 GGTGCTATTCTGGTAA
2374917 TTATTTTTAA
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 96 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:2374946 original size:58 final size:58
Alignment explanation
Indices: 2374815--2374939 Score: 142
Period size: 58 Copynumber: 2.2 Consensus size: 58
2374805 TTCGGTTTTA
* * * *****
2374815 GTGCTATTCTGATAAATAATTCGGTTTTGGTGCTATTCTGGTAAATAATTCGGTTTTG
1 GTGCTATTTTGGTAAATAATTCGGTTTTGGTGCTATTATGGTAAATAATTCGAAAAGG
* * **
2374873 GTGCTATTTTGGTAAATAATTCGGTTTTGGTGCTATTATGGTAATTATTTTTAAAAGG
1 GTGCTATTTTGGTAAATAATTCGGTTTTGGTGCTATTATGGTAAATAATTCGAAAAGG
2374931 GTGCTATTT
1 GTGCTATTT
2374940 GTGTAAAATG
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.23, C:0.08, G:0.22, T:0.46
Consensus pattern (58 bp):
GTGCTATTTTGGTAAATAATTCGGTTTTGGTGCTATTATGGTAAATAATTCGAAAAGG
Found at i:2381109 original size:125 final size:125
Alignment explanation
Indices: 2380887--2381128 Score: 342
Period size: 125 Copynumber: 1.9 Consensus size: 125
2380877 TAATGCCGCA
* *
2380887 ACATTATCTTATTCAGGTACAAGCCTTCAAAATGCCCCAACACCTCAAATTATAAGGCTCATTTT
1 ACATTATCTCATACAGGTACAAGCCTTCAAAATGCCCCAACACCTCAAATTATAAGGCTCATTTT
* * ** *
2380952 CAATGCCTTCTTGGTCTGAATCTTATCATCTCAACATGATGTGTGTTCAGTCGTTCCCCG
66 CAATGACTCCTTGGTCCAAATCTTATCATCTCAACATGATGTGGGTTCAGTCGTTCCCCG
* * * * *
2381012 ACATTATCTCATACTGGTACGAGCCTTCAAAATGCCCCATCACCTCAATTTTTAAGGCTCATTCT
1 ACATTATCTCATACAGGTACAAGCCTTCAAAATGCCCCAACACCTCAAATTATAAGGCTCATT-T
* *
2381077 TC-ATGACTCCTTGGTCCAAATCTTGTCATCTCAACATGATGTGGGTTTAGTC
65 TCAATGACTCCTTGGTCCAAATCTTATCATCTCAACATGATGTGGGTTCAGTC
2381129 ATGCCCTGAT
Statistics
Matches: 102, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
125 99 0.97
126 3 0.03
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (125 bp):
ACATTATCTCATACAGGTACAAGCCTTCAAAATGCCCCAACACCTCAAATTATAAGGCTCATTTT
CAATGACTCCTTGGTCCAAATCTTATCATCTCAACATGATGTGGGTTCAGTCGTTCCCCG
Found at i:2384641 original size:72 final size:72
Alignment explanation
Indices: 2384524--2384674 Score: 257
Period size: 72 Copynumber: 2.1 Consensus size: 72
2384514 CCCCTAACAG
*
2384524 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCTGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
*
2384589 TTCATCT
66 TTCATAT
* *
2384596 GTTCTTGATCATTTGCTATCATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
2384661 TTCATAT
66 TTCATAT
*
2384668 TTTCTTG
1 GTTCTTG
2384675 TGTAATAGGG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.37
Consensus pattern (72 bp):
GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
TTCATAT
Found at i:2385825 original size:47 final size:47
Alignment explanation
Indices: 2385770--2385908 Score: 176
Period size: 45 Copynumber: 3.0 Consensus size: 47
2385760 TGTCATTCAC
* * *
2385770 AAAA-AATCCTAACCGCATGATATCTAATTCGTATGCTTGTTCGAGA
1 AAAATAATCCTAACCGCATGATTTCTAGTTCGCATGCTTGTTCGAGA
* * * *
2385816 AAAATAATCCTAGCCGCATGATTTCTAGTTCGCATACATGATC-A-A
1 AAAATAATCCTAACCGCATGATTTCTAGTTCGCATGCTTGTTCGAGA
* *
2385861 AAAATAAACCTAACCACATGATTTCTAGTTCGCATGCTTGTTCGAGA
1 AAAATAATCCTAACCGCATGATTTCTAGTTCGCATGCTTGTTCGAGA
2385908 A
1 A
2385909 GAAAAGAAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
45 38 0.49
46 6 0.08
47 33 0.43
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (47 bp):
AAAATAATCCTAACCGCATGATTTCTAGTTCGCATGCTTGTTCGAGA
Found at i:2388804 original size:12 final size:12
Alignment explanation
Indices: 2388787--2388826 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2388777 ATTTATCATT
2388787 TTAAAAAAACAC
1 TTAAAAAAACAC
2388799 TTAAAAACACACAC
1 TTAAAAA-A-ACAC
*
2388813 TTAAAAACACAC
1 TTAAAAAAACAC
2388825 TT
1 TT
2388827 CTCCCCCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 13 0.52
13 1 0.04
14 11 0.44
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (12 bp):
TTAAAAAAACAC
Found at i:2388814 original size:14 final size:14
Alignment explanation
Indices: 2388787--2388824 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
2388777 ATTTATCATT
2388787 TTAAAAA-A-ACAC
1 TTAAAAACACACAC
2388799 TTAAAAACACACAC
1 TTAAAAACACACAC
2388813 TTAAAAACACAC
1 TTAAAAACACAC
2388825 TTCTCCCCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 7 0.29
13 1 0.04
14 16 0.67
ACGTcount: A:0.61, C:0.24, G:0.00, T:0.16
Consensus pattern (14 bp):
TTAAAAACACACAC
Found at i:2391077 original size:21 final size:20
Alignment explanation
Indices: 2391051--2391089 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2391041 AGAACCCCAG
2391051 GGGGGGTATCGATTCCCCTGT
1 GGGGGG-ATCGATTCCCCTGT
*
2391072 GGGGGGATCGGTTCCCCT
1 GGGGGGATCGATTCCCCT
2391090 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.08, C:0.26, G:0.41, T:0.26
Consensus pattern (20 bp):
GGGGGGATCGATTCCCCTGT
Found at i:2391120 original size:20 final size:21
Alignment explanation
Indices: 2391071--2391132 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
2391061 GATTCCCCTG
*
2391071 TGGGGGGATCGGTTCCCCTTCAA
1 TGGGGGAATCGGTT-CCC-TCAA
*
2391094 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGAATCGGTTCCCTCAA
*
2391114 TGGGGGAATCGATTCCCTC
1 TGGGGGAATCGGTTCCCTC
2391133 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 3 0.09
23 12 0.34
ACGTcount: A:0.16, C:0.26, G:0.34, T:0.24
Consensus pattern (21 bp):
TGGGGGAATCGGTTCCCTCAA
Found at i:2398513 original size:16 final size:16
Alignment explanation
Indices: 2398492--2398527 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2398482 CTCCAATTAT
* *
2398492 TCTGCTTCGGGTCTGC
1 TCTGCTTCAGGTCTAC
2398508 TCTGCTTCAGGTCTAC
1 TCTGCTTCAGGTCTAC
2398524 TCTG
1 TCTG
2398528 ACTTAGCCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.31, G:0.25, T:0.39
Consensus pattern (16 bp):
TCTGCTTCAGGTCTAC
Found at i:2399518 original size:3 final size:3
Alignment explanation
Indices: 2399510--2399541 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2399500 CTACAAAAAA
*
2399510 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2399542 ATATGACTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2399542 original size:12 final size:12
Alignment explanation
Indices: 2399510--2399545 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2399500 CTACAAAAAA
*
2399510 TATTATTATTAT
1 TATTATTAATAT
2399522 TATTATTAATAT
1 TATTATTAATAT
2399534 TATTATTAATAT
1 TATTATTAATAT
2399546 GACTTATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATTAATAT
Found at i:2400023 original size:29 final size:30
Alignment explanation
Indices: 2399960--2400121 Score: 202
Period size: 30 Copynumber: 5.4 Consensus size: 30
2399950 ATAATTATTG
* * *
2399960 TTTAGTCCCTTAAGTTTCTATTTTTTCTAT
1 TTTAGTCCTTTAAGTTTATGTTTTTTCTAT
* * *
2399990 TTTAGTCTTTTAAATTTTTGTTTTTTCTA-
1 TTTAGTCCTTTAAGTTTATGTTTTTTCTAT
*
2400019 TTTAGTCCTTTAAGTTTCTGTTTTTGT-TAT
1 TTTAGTCCTTTAAGTTTATGTTTTT-TCTAT
* *
2400049 TTTAGCCCTTTAAGTTTATGTTTTTGCTAT
1 TTTAGTCCTTTAAGTTTATGTTTTTTCTAT
* *
2400079 TTTAGCCCTTTAAGTTTATGTTTTTGCTAT
1 TTTAGTCCTTTAAGTTTATGTTTTTTCTAT
2400109 TTTAGTCCTTTAA
1 TTTAGTCCTTTAA
2400122 ATCAAATATG
Statistics
Matches: 117, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.21
30 93 0.79
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.60
Consensus pattern (30 bp):
TTTAGTCCTTTAAGTTTATGTTTTTTCTAT
Found at i:2400032 original size:59 final size:60
Alignment explanation
Indices: 2399960--2400123 Score: 215
Period size: 59 Copynumber: 2.8 Consensus size: 60
2399950 ATAATTATTG
* * * * *
2399960 TTTAGTCCCTTAAGTTTCTATTTTTTCTATTTTAGTCTTTTAAATTTTTGTTTTTTCTA-
1 TTTAGTCCTTTAAGTTTCTGTTTTTTCTATTTTAGTCCTTTAAATTTATGTTTTTGCTAT
* *
2400019 TTTAGTCCTTTAAGTTTCTGTTTTTGT-TATTTTAGCCCTTTAAGTTTATGTTTTTGCTAT
1 TTTAGTCCTTTAAGTTTCTGTTTTT-TCTATTTTAGTCCTTTAAATTTATGTTTTTGCTAT
* * *
2400079 TTTAGCCCTTTAAGTTTATGTTTTTGCTATTTTAGTCCTTTAAAT
1 TTTAGTCCTTTAAGTTTCTGTTTTTTCTATTTTAGTCCTTTAAAT
2400124 CAAATATGAT
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
59 50 0.56
60 40 0.44
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.60
Consensus pattern (60 bp):
TTTAGTCCTTTAAGTTTCTGTTTTTTCTATTTTAGTCCTTTAAATTTATGTTTTTGCTAT
Found at i:2402530 original size:27 final size:29
Alignment explanation
Indices: 2402479--2402544 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 29
2402469 GATCAATATT
*
2402479 TTTTGCATCTGCATTTGCATCTTT-A-CA
1 TTTTGCATATGCATTTGCATCTTTAAGCA
*
2402506 TTTTGCATATGCATTT-CATTTTTTAAGCA
1 TTTTGCATATGCATTTGCA-TCTTTAAGCA
2402535 TTTTCGCATA
1 TTTT-GCATA
2402545 CATCATTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 2 0.06
27 19 0.58
28 1 0.03
29 6 0.18
30 5 0.15
ACGTcount: A:0.21, C:0.18, G:0.11, T:0.50
Consensus pattern (29 bp):
TTTTGCATATGCATTTGCATCTTTAAGCA
Found at i:2403801 original size:12 final size:12
Alignment explanation
Indices: 2403783--2403887 Score: 50
Period size: 15 Copynumber: 7.7 Consensus size: 12
2403773 ACAAAGAGAG
2403783 AAGAAAAAAAAGA
1 AAGAAAAAAAA-A
2403796 AA-AAAAAAAGCAA
1 AAGAAAAAAA--AA
2403809 GGAACGAAAAAAAGAA
1 --AA-GAAAAAAA-AA
*
2403825 AAGAAAAATGAAGCA
1 AAGAAAAA--AA-AA
2403840 AAGAAAAAAAAA
1 AAGAAAAAAAAA
*
2403852 GAGCAAAGAAAAAACA
1 AAG--AA-AAAAAA-A
*
2403868 AAGAAAAAAACA
1 AAGAAAAAAAAA
2403880 AAGAAAAA
1 AAGAAAAA
2403888 GGAAAAAAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 25
0.70 0.06 0.24
Matches are distributed among these distances:
12 19 0.26
13 16 0.22
14 7 0.09
15 20 0.27
16 5 0.07
17 7 0.09
ACGTcount: A:0.78, C:0.06, G:0.15, T:0.01
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:2403819 original size:28 final size:28
Alignment explanation
Indices: 2403787--2403887 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 28
2403777 AGAGAGAAGA
* *
2403787 AAAAAAAGAAAA-AAAAAAGCAAGGAACG
1 AAAAAAAGAAAAGAAAAAAG-AAGCAAAG
*
2403815 AAAAAAAGAAAAGAAAAATGAAGCAAAG
1 AAAAAAAGAAAAGAAAAAAGAAGCAAAG
* *
2403843 AAAAAAA-AAGAGCAAAGAAA-AAACAAAG
1 AAAAAAAGAAAAG-AAA-AAAGAAGCAAAG
*
2403871 AAAAAAA-CAAAGAAAAA
1 AAAAAAAGAAAAGAAAAA
2403888 GGAAAAAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
26 2 0.03
27 7 0.11
28 45 0.73
29 8 0.13
ACGTcount: A:0.78, C:0.06, G:0.15, T:0.01
Consensus pattern (28 bp):
AAAAAAAGAAAAGAAAAAAGAAGCAAAG
Found at i:2403839 original size:32 final size:28
Alignment explanation
Indices: 2403786--2403896 Score: 95
Period size: 30 Copynumber: 3.8 Consensus size: 28
2403776 AAGAGAGAAG
*
2403786 AAAAAAAAG-AAA-AAAAAAAGCAAGGA
1 AAAAAAAAGAAAAGAAAAAAAGCAAAGA
2403812 ACGAAAAAAAGAAAAGAAAAATGAAGCAAAGA
1 A--AAAAAAAGAAAAGAAAAA--AAGCAAAGA
2403844 AAAAAAAAGAGCAAAG-AAAAAA-CAAAGAA
1 AAAAAAAAGA--AAAGAAAAAAAGCAAAG-A
2403873 AAAAACAAAGAAAAAGGAAAAAAA
1 AAAAA-AAAG-AAAA-GAAAAAAA
2403897 AGTACATGCA
Statistics
Matches: 71, Mismatches: 1, Indels: 21
0.76 0.01 0.23
Matches are distributed among these distances:
26 1 0.01
28 13 0.18
29 14 0.20
30 19 0.27
31 11 0.15
32 13 0.18
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.01
Consensus pattern (28 bp):
AAAAAAAAGAAAAGAAAAAAAGCAAAGA
Found at i:2403856 original size:17 final size:17
Alignment explanation
Indices: 2403791--2403871 Score: 73
Period size: 17 Copynumber: 4.9 Consensus size: 17
2403781 AGAAGAAAAA
2403791 AAAGAAAAAAAAA-AGC
1 AAAGAAAAAAAAAGAGC
*
2403807 AAGGAACGAAAAAAAGA--
1 AAAGAA--AAAAAAAGAGC
**
2403824 AAAG-AAAAATGA-AGC
1 AAAGAAAAAAAAAGAGC
2403839 AAAGAAAAAAAAAGAGC
1 AAAGAAAAAAAAAGAGC
2403856 AAAGAAAAAACAAAGA
1 AAAGAAAAAA-AAAGA
2403872 AAAAAACAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
13 1 0.02
14 5 0.10
15 4 0.08
16 12 0.24
17 16 0.31
18 12 0.24
19 1 0.02
ACGTcount: A:0.75, C:0.06, G:0.17, T:0.01
Consensus pattern (17 bp):
AAAGAAAAAAAAAGAGC
Found at i:2403898 original size:28 final size:28
Alignment explanation
Indices: 2403781--2403895 Score: 85
Period size: 28 Copynumber: 3.9 Consensus size: 28
2403771 AAACAAAGAG
2403781 AGAAGAAAAAAA-AGAAAA-AAAAAAGCAA
1 AGAA-AAAAAAAGAGAAAAGAAAAAA-CAA
* *
2403809 GGAACGAAAAAA-AGAAAAGAAAAATGAAGCAA
1 AGAA-AAAAAAAGAGAAAAG-AAAA--AA-CAA
*
2403841 AGAAAAAAAAAGAGCAAAGAAAAAACAA
1 AGAAAAAAAAAGAGAAAAGAAAAAACAA
2403869 AGAAAAAAACAA-AGAAAAAGGAAAAAA
1 AGAAAAAAA-AAGAG-AAAA-GAAAAAA
2403896 AAGTACATGC
Statistics
Matches: 72, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
28 29 0.40
29 7 0.10
30 11 0.15
31 10 0.14
32 15 0.21
ACGTcount: A:0.77, C:0.05, G:0.17, T:0.01
Consensus pattern (28 bp):
AGAAAAAAAAAGAGAAAAGAAAAAACAA
Found at i:2405065 original size:37 final size:37
Alignment explanation
Indices: 2405023--2405126 Score: 122
Period size: 36 Copynumber: 2.8 Consensus size: 37
2405013 TCTGTCGCTT
**
2405023 TTGAGACTATTTTCTTTAAAAACAAATTTTGTCTCGC
1 TTGAGACTATTTTCTTTAAAAACAAATTTCATCTCGC
* *
2405060 TTGAGAC-AATTTCTCTAAAAACAAATTTCATCTCGC
1 TTGAGACTATTTTCTTTAAAAACAAATTTCATCTCGC
2405096 TTGAGA-TATTTTTTTCTTTAAAACACAAATT
1 TTGAGACTA---TTTTCTTTAAAA-ACAAATT
2405127 CTGAAGTTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
36 32 0.57
37 7 0.12
39 10 0.18
40 7 0.12
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (37 bp):
TTGAGACTATTTTCTTTAAAAACAAATTTCATCTCGC
Found at i:2405250 original size:30 final size:29
Alignment explanation
Indices: 2405216--2405284 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
2405206 AAACTTCTCG
2405216 TGAAACACCAAAA-TTTGAGAT-TGTTTCCCT
1 TGAAACA--AAAACTTTGAG-TCTGTTTCCCT
*
2405246 TGAAACAAAAATCTTTGAGTCTTTTTCCCT
1 TGAAACAAAAA-CTTTGAGTCTGTTTCCCT
2405276 TGAAACAAA
1 TGAAACAAA
2405285 GTTTTGTCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
28 4 0.11
29 1 0.03
30 30 0.86
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (29 bp):
TGAAACAAAAACTTTGAGTCTGTTTCCCT
Found at i:2405301 original size:97 final size:97
Alignment explanation
Indices: 2405159--2405348 Score: 258
Period size: 97 Copynumber: 2.0 Consensus size: 97
2405149 AAAATTTATG
*
2405159 ATCTTTGAGTATGTTTTCTCTTGAAACAAATTTTATCTCTCTTGAGAAAACTTCTCGTGAAACAC
1 ATCTTTGAGTATGTTTTCCCTTGAAACAAATTTTATCTCTCTTGAGAAAACTTCTCGTGAAACAC
2405224 CAAAATTTGAGAT-TGTTTCCCTTGAAACAAAA
66 CAAAATTTGAGATCT-TTTCCCTTGAAACAAAA
* * * ** *
2405256 ATCTTTGAGTCT-TTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 ATCTTTGAGTATGTTTTCCCTTGAAACAAA-TTTTATCTCTCTTGAGAAAACTTCTCGTGAAACA
* **
2405320 CCCATCTTTGAGATCTTTTCCCTTGAAAC
65 CCAAAATTTGAGATCTTTTCCCTTGAAAC
2405349 CAATTTTGTC
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
96 16 0.20
97 64 0.79
98 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.39
Consensus pattern (97 bp):
ATCTTTGAGTATGTTTTCCCTTGAAACAAATTTTATCTCTCTTGAGAAAACTTCTCGTGAAACAC
CAAAATTTGAGATCTTTTCCCTTGAAACAAAA
Found at i:2405315 original size:67 final size:66
Alignment explanation
Indices: 2405238--2405417 Score: 213
Period size: 67 Copynumber: 2.7 Consensus size: 66
2405228 ATTTGAGATT
* *
2405238 GTTTCCCTTGAAACAAAAATCTTTGAGTCTTTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGA
1 GTTTCTCTTGAAACAAACATCTTTGAGTCTTTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGA
2405303 CA
65 CA
** *
2405305 GTTTCTCTTGAAACACCCATCTTTGAGATC-TTTTCCCTTGAAACCAATTTTGTCTCTCTTGAGA
1 GTTTCTCTTGAAACAAACATCTTTGAG-TCTTTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA
2405369 CA
65 CA
** * * * *
2405371 ACTTATCTTAAAAC-ATCATCTTTGAGT-TTGTTTCCCTTAAAACAAAT
1 GTTTCTCTTGAAACAAACATCTTTGAGTCTT-TTTCCCTTGAAACAAAT
2405418 CCCTAAAGAT
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 2 0.02
65 25 0.26
66 29 0.30
67 39 0.40
68 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.39
Consensus pattern (66 bp):
GTTTCTCTTGAAACAAACATCTTTGAGTCTTTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAC
A
Found at i:2405655 original size:131 final size:131
Alignment explanation
Indices: 2405416--2405797 Score: 392
Period size: 131 Copynumber: 2.9 Consensus size: 131
2405406 CTTAAAACAA
* * * *
2405416 ATCCCTAAAGATGGCATGCCATCTTCATCACGTAGAAACCGTGTCATCCCCCGACCAGACCTCCT
1 ATCCCTAAAGATGGCTTGCCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCCT
* * * * ** * *
2405481 CATCACGTAGGAGTCGTGTCAGCCTTATATAAACAACCGTCCTCATCACGTAGGAGCCATGTTAT
66 CATCACGTAGGAGCCGTGTCA-CCCTAGATAACCAACTATCCTCATCACGTAAGAACCATGTTAT
2405546 -C
130 CC
* *
2405547 ATCCCTAAAGATGGCTTGTCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAAACCTCCT
1 ATCCCTAAAGATGGCTTGCCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCCT
* ** * *
2405612 CATCACGTAAGAGCCGTGTCATCCCTAGATAACCAACTATCCTCATCGTGTAAGAATCGTGTTAT
66 CATCACGTAGGAGCCGTGTCA-CCCTAGATAACCAACTATCCTCATCACGTAAGAACCATGTTAT
2405677 CACC
130 --CC
* * * * * * * * * *
2405681 ATTCCTAAATATAG-TCTACCGTCCTCATCGCGTAGGAACTGTGTCATCCACTGACTAGATCTCC
1 ATCCCTAAAGATGGCT-TGCCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCC
* * *
2405745 TCATCACGTAGGAGCCGCGTCACCCTTAGATGACCAGA-TATCTTCATCACGTA
65 TCATCACGTAGGAGCCGTGTCACCC-TAGATAACCA-ACTATCCTCATCACGTA
2405798 TGAGTCGTGT
Statistics
Matches: 207, Mismatches: 38, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
131 110 0.53
133 4 0.02
134 92 0.44
135 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (131 bp):
ATCCCTAAAGATGGCTTGCCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCCT
CATCACGTAGGAGCCGTGTCACCCTAGATAACCAACTATCCTCATCACGTAAGAACCATGTTATC
C
Found at i:2406580 original size:27 final size:28
Alignment explanation
Indices: 2406550--2406608 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
2406540 ACATAAAGCC
*
2406550 AAAA-GAGAGAGAGATTCG-GGTTGAAAA
1 AAAAGGAGAGA-ACATTCGAGGTTGAAAA
*
2406577 AAAAGGAGAGAACATTCGATGTTGAAAA
1 AAAAGGAGAGAACATTCGAGGTTGAAAA
2406605 AAAA
1 AAAA
2406609 AGAAGACAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 10 0.36
28 18 0.64
ACGTcount: A:0.53, C:0.05, G:0.27, T:0.15
Consensus pattern (28 bp):
AAAAGGAGAGAACATTCGAGGTTGAAAA
Found at i:2411797 original size:2 final size:2
Alignment explanation
Indices: 2411790--2411849 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
2411780 ATAATAATTA
2411790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2411832 AT AT AT A- AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
2411850 ACTGTAATTA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2412172 original size:27 final size:27
Alignment explanation
Indices: 2412134--2412186 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
2412124 ATGCTTCAAT
2412134 TCGATTGGAGTGTGCAGTTCCAGTACA
1 TCGATTGGAGTGTGCAGTTCCAGTACA
2412161 TCGATTGGAGTGTGCAGTTCCAGTAC
1 TCGATTGGAGTGTGCAGTTCCAGTAC
2412187 GTCGCTCGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (27 bp):
TCGATTGGAGTGTGCAGTTCCAGTACA
Found at i:2413120 original size:226 final size:226
Alignment explanation
Indices: 2412834--2413526 Score: 1064
Period size: 226 Copynumber: 3.1 Consensus size: 226
2412824 TGGAAACTTA
* *
2412834 GACGATAACATAACC-AGTTAATTACGGGAAATATTATCAAGCATAATAACATATTAGGTAGCGC
1 GACGATAACATAACCGA-TTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGC
* * * * * *
2412898 TTATATAATGTAATATGTAACGTCTTTTTAAAGATGATGGGGCTTTAAAAACCCGACGATAATAA
65 TTATATAACGTAATATGTAACGTATTTTTAAAGCTGATGGGGCTTTAGAAATCCGACGATAACAA
2412963 AATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAC
130 AATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAC
2413028 CAATGTTTAAGCTGATAGAGCCTTAGAAATCC
195 CAATGTTTAAGCTGATAGAGCCTTAGAAATCC
2413060 GACGATAACATAACCGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
1 GACGATAACATAACCGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
* * *
2413125 TATATAACGTAATATGCAATGCTTTTTTTAAAGCTGATGGGGCTTTAGAAATCCGACGATAACAA
66 TATATAACGTAATATGTAACG-TATTTTTAAAGCTGATGGGGCTTTAGAAATCCGACGATAACAA
*
2413190 AATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGACTAAAATGTTAC
130 AATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAC
*
2413255 CAATGTTTAAGCTGATAGAGCCTTAGAAATCT
195 CAATGTTTAAGCTGATAGAGCCTTAGAAATCC
**
2413287 GACGATAACATAACCGATTAATTACTATAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
1 GACGATAACATAACCGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
* * * * * * ** *
2413352 TATGTAACGTAATAGGTAGCGAATTATTAAAGCTGATGGGGCCTTAGAAATTTGACAATAACAAA
66 TATATAACGTAATATGTAACGTATTTTTAAAGCTGATGGGGCTTTAGAAATCCGACGATAACAAA
** * **
2413417 ATAGGTTAATTACTTAATTTGTTACCAGTATTATCAACATATTAGGTAACACCTAAAATGTTAAA
131 ATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACC
** * *
2413482 AAAATTTAAGCTGATGGAGCCTTAGGAATCC
196 AATGTTTAAGCTGATAGAGCCTTAGAAATCC
2413513 GACGATAACATAAC
1 GACGATAACATAAC
2413527 TAGTTAATTA
Statistics
Matches: 428, Mismatches: 37, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
226 215 0.50
227 213 0.50
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (226 bp):
GACGATAACATAACCGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
TATATAACGTAATATGTAACGTATTTTTAAAGCTGATGGGGCTTTAGAAATCCGACGATAACAAA
ATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACC
AATGTTTAAGCTGATAGAGCCTTAGAAATCC
Found at i:2413203 original size:119 final size:115
Alignment explanation
Indices: 2412717--2413433 Score: 463
Period size: 108 Copynumber: 6.3 Consensus size: 115
2412707 AAAAAATATA
* * *
2412717 GACGATAACATAACCTG-TTAATTACTAGAAACATTATCAAGCATAATAACATATTAGGTAGCGC
1 GACGATAACA-AAACAGATTAATTACT-TAAACATTATCAAGCATAATAACATATTAGGTAGCGC
** * * * * * **
2412781 TTATATAACGTAATAG-GTTGCGGTTTTAAAGCTGATGGGGCTTTGGAAACTTA
64 TTATATAACGTAATAGCAATGC-TTTTTAAAGCTGATAGAGCCTTAGAAA-TCC
* ** *
2412834 GACGATAACATAACCAG-TTAATTACGGGAAATATTATCAAGCATAATAACATATTAGGTAGCGC
1 GACGATAACA-AAACAGATTAATTAC-TTAAACATTATCAAGCATAATAACATATTAGGTAGCGC
* * * * * * * * *
2412898 TTATATAATGTAATATGTAACGTCTTTTTAAAGATGATGGGGCTTTAAAAACCC
64 TTATATAACGTAATA-GCAATG-CTTTTTAAAGCTGATAGAGCCTTAGAAATCC
* * * *** * * * *
2412952 GACGATAATAAAATAGGTTAATTACTTAATTTGTTAT-TAGTATTATCAACATATTAGGTAACGC
1 GACGATAACAAAACAGATTAATTACTTAA-ACATTATCAAGCATAAT-AACATATTAGGTAGCGC
* * *
2413016 CTA-A-AATGT--TACCAATG---TTT-AAGCTGATAGAGCCTTAGAAATCC
64 TTATATAACGTAATAGCAATGCTTTTTAAAGCTGATAGAGCCTTAGAAATCC
* * *
2413060 GACGATAACATAACCGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
1 GACGATAACAAAACAGATTAATTACT-TAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
* * *
2413125 TATATAACGTAATATGCAATGCTTTTTTTAAAGCTGATGGGGCTTTAGAAATCC
65 TATATAACGTAATA-GCAATGC--TTTTTAAAGCTGATAGAGCCTTAGAAATCC
* * *** * * * *
2413179 GACGATAACAAAATAGGTTAATTACTTAATTTGTTAT-TAGTATTATCAACATATTAGGTAACGA
1 GACGATAACAAAACAGATTAATTACTTAA-ACATTATCAAGCATAAT-AACATATTAGGTAGCG-
* * *
2413243 C-TA-A-AATGT--TACCAATG---TTT-AAGCTGATAGAGCCTTAGAAATCT
63 CTTATATAACGTAATAGCAATGCTTTTTAAAGCTGATAGAGCCTTAGAAATCC
* *
2413287 GACGATAACATAACCGATTAATTACTATAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
1 GACGATAACAAAACAGATTAATTACT-TAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
* ** * * * **
2413352 TATGTAACGTAATAGGTA-GCGAATTATTAAAGCTGATGGGGCCTTAGAAATTT
65 TATATAACGTAATAGCAATGC---TTTTTAAAGCTGATAGAGCCTTAGAAATCC
* * *
2413405 GACAATAACAAAATAGGTTAATTACTTAA
1 GACGATAACAAAACAGATTAATTACTTAA
2413434 TTTGTTACCA
Statistics
Matches: 466, Mismatches: 97, Indels: 74
0.73 0.15 0.12
Matches are distributed among these distances:
107 1 0.00
108 124 0.27
109 24 0.05
110 8 0.02
111 1 0.00
112 5 0.01
113 8 0.02
114 7 0.02
115 2 0.00
116 5 0.01
117 96 0.21
118 95 0.20
119 88 0.19
120 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (115 bp):
GACGATAACAAAACAGATTAATTACTTAAACATTATCAAGCATAATAACATATTAGGTAGCGCTT
ATATAACGTAATAGCAATGCTTTTTAAAGCTGATAGAGCCTTAGAAATCC
Found at i:2413308 original size:108 final size:109
Alignment explanation
Indices: 2413150--2413569 Score: 361
Period size: 108 Copynumber: 3.8 Consensus size: 109
2413140 GCAATGCTTT
* * *
2413150 TTTTAAAGCTGATGGGGCTTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTA
1 TTTT-AAGCTGATGGAGCCTTAGAAATCCGACGATAACAAAATAGATTAATTACTTAATTTGTTA
* *
2413215 T-TAGTATTATCAACATATTAGGTAACGA-CTAAAATGTTACCAA
65 TCAAGTATTATCAACATATTAGGTAACGACCTAAAATGTTACAAA
* * * ** ***
2413258 TGTTTAAGCTGATAGAGCCTTAGAAATCTGACGATAACATAACCGATTAATTACTATAA-ACATT
1 T-TTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACAAAATAGATTAATTACT-TAATTTGTT
* * * ** * *
2413322 ATCAAGCATAAT-AACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCGAA
64 ATCAAGTATTATCAACATATTAGGTAACG---ACCTAA---AAT-GTTA-CAAA
* ** * *
2413375 TTATTAAAGCTGATGGGGCCTTAGAAATTTGACAATAACAAAATAGGTTAATTACTTAATTTGTT
1 TT-TT-AAGCTGATGGAGCCTTAGAAATCCGACGATAACAAAATAGATTAATTACTTAATTTGTT
* *
2413440 A-CCAGTATTATCAACATATTAGGTAAC-ACCTAAAATGTTAAAAAA
64 ATCAAGTATTATCAACATATTAGGTAACGACCTAAAATGTT-ACAAA
* * * *
2413485 ATTTAAGCTGATGGAGCCTTAGGAATCCGACGATAACATAACTAG-TTAATTACTTGATTTGTTA
1 TTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACA-AAATAGATTAATTACTTAATTTGTTA
2413549 TCAAGCT-TTATCAACATATTA
65 TCAAG-TATTATCAACATATTA
2413570 CCATGTACAT
Statistics
Matches: 245, Mismatches: 47, Indels: 39
0.74 0.14 0.12
Matches are distributed among these distances:
108 109 0.44
109 36 0.15
110 6 0.02
111 5 0.02
112 3 0.01
114 4 0.02
115 3 0.01
116 4 0.02
117 16 0.07
118 59 0.24
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (109 bp):
TTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACAAAATAGATTAATTACTTAATTTGTTAT
CAAGTATTATCAACATATTAGGTAACGACCTAAAATGTTACAAA
Found at i:2417079 original size:449 final size:449
Alignment explanation
Indices: 2415945--2417141 Score: 1798
Period size: 451 Copynumber: 2.7 Consensus size: 449
2415935 ATTTATCAGT
* * *
2415945 TTTTTATCAAATTTTAACCTTTTATATTGTCATGTATCGAAACATGTGTCATAGGTATCGATACT
1 TTTTTATCAATTTTTAACCTGTTATATTGTCATGTATCGATACATGTGTCATAGGTATCGATACT
* * *
2416010 TCGTACGTGCATCTAGTTTGGGAAGCATACTGGACAAAACATTATTGATACATATACCAAAAGTA
66 TCATACGTGCATCTAGTTTGGGAAGCATACTGGACAAAA-AGTATCGATACATATACCAAAAGTA
* * * *
2416075 TTGATACTTTATGTAAACATATTTTTTCATTAAACCGATATATTTTTATAAATTACATTGTAAAT
130 TCGATACTTTATGTAAACGTATTTTATCATTAAA-CGATATATTTTTATAACTTACATTGTAAAT
* *
2416140 TTACCTATTACTTTAAAGTAATTGGTTTTGAATTTTTAAGAATTTG-TACTTTTCATACGTGTAT
194 TTACCTATTACTTTAAAGTAATCGGTTTTGAATTTTTAAGAA-TCGATACTTTTCATACGTGTAT
* *
2416204 CGATACTTTATAGGCGCAATTATAGAAACTGATTTTGTCAAAAAGATGAACCTGTTATATTATTT
258 CGATACTTTATAGGCGCAATTATAGAAACCGATTTTGTCAAAAAGATGAACCTGCTATATTATTT
** *
2416269 ATATTTAATCGATACCATTACCCTTACCTAAGTATCGATACTTTTGTGTACGGTATTGATACTTT
323 ATATTTAATCGATACCATTACCCTTACCTAAGTATCGATACTTTTGTGTACGGTATCAATAATTT
* * *
2416334 CGAGACGTTTCGTTTTTTTTCAAAACAGGTAGCTATTTACCGGTTTTGTCATATTGAAATCG
388 CGAGACATTTCGATTTTTTTCAAAACAGATAGCTATTTACCGGTTTTGTCATATTGAAATCG
* *
2416396 GTTTTATCAATTTTTAACATGTTATATTGTCATGTATCGATACATGTGTCATAGGTATCGATACT
1 TTTTTATCAATTTTTAACCTGTTATATTGTCATGTATCGATACATGTGTCATAGGTATCGATACT
* **
2416461 TCATACGTTCATCTAGTTTGGGAAGCATACTGGACAAAAAAGTATCGATACATATACTTAAAGTA
66 TCATACGTGCATCTAGTTTGGGAAGCATACTGGAC-AAAAAGTATCGATACATATACCAAAAGTA
* * *
2416526 TCGACACTTTATGTAAACGTATTTTATCATTAAATCGATATATTTTTACATCTTACATTGTAAAT
130 TCGATACTTTATGTAAACGTATTTTATCATTAAA-CGATATATTTTTATAACTTACATTGTAAAT
* *
2416591 TTACCTATTACTTTAAAGTAATCGATTTTGATTTTTTAAGAATCGATACTTTTCATACGTGTATC
194 TTACCTATTACTTTAAAGTAATCGGTTTTGAATTTTTAAGAATCGATACTTTTCATACGTGTATC
* * * *
2416656 GATACTTTATAAGG-GTAATTATGGAAACCGGTTTTGTCAAAAAGATGAACCTGCTATGTTATTT
259 GATACTTTAT-AGGCGCAATTATAGAAACCGATTTTGTCAAAAAGATGAACCTGCTATATTATTT
*
2416720 ATATTTAATCGATACCATTACCCTTA-CTAAAGTATCGATATTTTTGTGTACGGTATCAATAATT
323 ATATTTAATCGATACCATTACCCTTACCT-AAGTATCGATACTTTTGTGTACGGTATCAATAATT
*
2416784 TCGAGACATTTC-ATTTTTTT-AAAACTGATAGCTATTTACCGGTTTTGTCATATTGAAATCG
387 TCGAGACATTTCGATTTTTTTCAAAACAGATAGCTATTTACCGGTTTTGTCATATTGAAATCG
* *
2416845 ATTTTTATTAATTTTTAACCTGTTATATTATCATGTATCGATACATGTGTCATAGGTATCGATAC
1 -TTTTTATCAATTTTTAACCTGTTATATTGTCATGTATCGATACATGTGTCATAGGTATCGATAC
* *
2416910 TTTC-TACGTGCATCTAGTTTGGGAAGCATACTAGACAAAAAGGATCGATACATATACCAAAAGT
65 -TTCATACGTGCATCTAGTTTGGGAAGCATACTGGACAAAAAGTATCGATACATATACCAAAAGT
* * *
2416974 ATCGATACTTTATGTAAACGTATTTTGTCATTAAACAAATATATTTTTATAGCTTACATTGTAAA
129 ATCGATACTTTATGTAAACGTATTTTATCATTAAAC-GATATATTTTTATAACTTACATTGTAAA
** *
2417039 TTTACCTATTACTTTAAAGTAATCGGTTTCAAAGTTTTAAGAATCGATACTTTTCATACGTGTAT
193 TTTACCTATTACTTTAAAGTAATCGGTTTTGAATTTTTAAGAATCGATACTTTTCATACGTGTAT
* *
2417104 CGATACTTTATCGG-GACAATTAT-GAAAACTGATTTTGT
258 CGATACTTTATAGGCG-CAATTATAG-AAACCGATTTTGT
2417142 AAATTTTTTA
Statistics
Matches: 677, Mismatches: 60, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
448 5 0.01
449 210 0.31
450 101 0.15
451 354 0.52
452 7 0.01
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (449 bp):
TTTTTATCAATTTTTAACCTGTTATATTGTCATGTATCGATACATGTGTCATAGGTATCGATACT
TCATACGTGCATCTAGTTTGGGAAGCATACTGGACAAAAAGTATCGATACATATACCAAAAGTAT
CGATACTTTATGTAAACGTATTTTATCATTAAACGATATATTTTTATAACTTACATTGTAAATTT
ACCTATTACTTTAAAGTAATCGGTTTTGAATTTTTAAGAATCGATACTTTTCATACGTGTATCGA
TACTTTATAGGCGCAATTATAGAAACCGATTTTGTCAAAAAGATGAACCTGCTATATTATTTATA
TTTAATCGATACCATTACCCTTACCTAAGTATCGATACTTTTGTGTACGGTATCAATAATTTCGA
GACATTTCGATTTTTTTCAAAACAGATAGCTATTTACCGGTTTTGTCATATTGAAATCG
Found at i:2417490 original size:18 final size:18
Alignment explanation
Indices: 2417440--2417486 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
2417430 GCTGAAAATG
* *
2417440 AAATTGAAATTCAAACTC
1 AAATTTAAATTTAAACTC
2417458 AAATTTAAATTTAAACTC
1 AAATTTAAATTTAAACTC
*
2417476 CAA-TTAAATTT
1 AAATTTAAATTT
2417487 TAAATGAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (18 bp):
AAATTTAAATTTAAACTC
Found at i:2436748 original size:22 final size:21
Alignment explanation
Indices: 2436722--2436802 Score: 76
Period size: 22 Copynumber: 3.8 Consensus size: 21
2436712 ATAGGGCAGA
2436722 GGGAATCGATACCCCCATTAAG
1 GGGAATCGATACCCCC-TTAAG
* * *
2436744 GGGAACCGATTCCCCCTCTGAAT
1 GGGAATCGATACCCCCT-T-AAG
*
2436767 GGGAA-CTGATTCCCCCTT-AG
1 GGGAATC-GATACCCCCTTAAG
2436787 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
2436803 AAGGGTTCTG
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
20 14 0.28
21 2 0.04
22 17 0.34
23 17 0.34
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (21 bp):
GGGAATCGATACCCCCTTAAG
Found at i:2441850 original size:13 final size:13
Alignment explanation
Indices: 2441832--2441856 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2441822 TTCTAAACAA
2441832 AATTTACCTTAAC
1 AATTTACCTTAAC
2441845 AATTTACCTTAA
1 AATTTACCTTAA
2441857 TAATATACGT
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:0.20, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTTACCTTAAC
Found at i:2443185 original size:32 final size:33
Alignment explanation
Indices: 2443149--2443240 Score: 88
Period size: 32 Copynumber: 2.9 Consensus size: 33
2443139 ACAATTACAA
2443149 TATTTTCTCATAATAACAAATTATGAAAAAT-T
1 TATTTTCTCATAATAACAAATTATGAAAAATAT
**
2443181 TATTTAGTCATAATAAC-AATTCAT-AACAAATAT
1 TATTTTCTCATAATAACAAATT-ATGAA-AAATAT
*
2443214 TAATTTCTC--AATATA-AAATTATGAAAA
1 TATTTTCTCATAATA-ACAAATTATGAAAA
2443241 TAATATTCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
31 14 0.29
32 28 0.57
33 7 0.14
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (33 bp):
TATTTTCTCATAATAACAAATTATGAAAAATAT
Found at i:2445730 original size:26 final size:26
Alignment explanation
Indices: 2445694--2445749 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
2445684 CTTGGTGTAG
*
2445694 TCGTGATCAACTCTTCGATTAGAGAT
1 TCGTGATCAACTCTTCAATTAGAGAT
2445720 TCGTGATCAACTCTTCAATTAGAGAT
1 TCGTGATCAACTCTTCAATTAGAGAT
2445746 TCGT
1 TCGT
2445750 TCGTGGTTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (26 bp):
TCGTGATCAACTCTTCAATTAGAGAT
Found at i:2447046 original size:24 final size:24
Alignment explanation
Indices: 2447019--2447064 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
2447009 GTGATAAGGC
2447019 GATAAGCATGGTCGAGGGTGAGGT
1 GATAAGCATGGTCGAGGGTGAGGT
2447043 GATAAGCATGGTCGAGGGTGAG
1 GATAAGCATGGTCGAGGGTGAG
2447065 AGTTTCGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.09, G:0.46, T:0.20
Consensus pattern (24 bp):
GATAAGCATGGTCGAGGGTGAGGT
Done.