Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009065.1 Hibiscus syriacus cultivar Beakdansim tig00112488_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: 1198333
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:177460 original size:19 final size:18
Alignment explanation
Indices: 177421--177465 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
177411 ACTTTTGATA
* *
177421 TTTATTATAAAGTTTATT
1 TTTATTTTAAAGTTAATT
177439 TTTATTTTAAAGTCTAATT
1 TTTATTTTAAAGT-TAATT
177458 TTTATTTT
1 TTTATTTT
177466 TGAAATCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (18 bp):
TTTATTTTAAAGTTAATT
Found at i:179103 original size:2 final size:2
Alignment explanation
Indices: 179096--179233 Score: 125
Period size: 2 Copynumber: 74.0 Consensus size: 2
179086 TCGGGTCGGG
* * * *
179096 TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- 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
* * * * *
179136 TT TA -A TT TA -A TT TA AA TT TA T- TA -A TA T- 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
179173 TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA T- 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
179212 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
179234 ATTATTTTTA
Statistics
Matches: 108, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
1 10 0.09
2 98 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:179151 original size:37 final size:38
Alignment explanation
Indices: 179096--179220 Score: 153
Period size: 37 Copynumber: 3.2 Consensus size: 38
179086 TCGGGTCGGG
*
179096 TATATATATTTAAATTAAATATATAAATATTATATATA
1 TATATATATTTAATTTAAATATATAAATATTATATATA
* * *
179134 TATTTA-ATTTAATTTAAATTTATTAATATTATATATA
1 TATATATATTTAATTTAAATATATAAATATTATATATA
* * *
179171 TATATATATATATATATATATATATTAATATATTATATATA
1 TATATATATTTA-ATTTAAATATA-TAA-ATATTATATATA
179212 TATATATAT
1 TATATATAT
179221 ATATATATAT
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
37 33 0.45
38 9 0.12
39 8 0.11
40 2 0.03
41 21 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (38 bp):
TATATATATTTAATTTAAATATATAAATATTATATATA
Found at i:179283 original size:13 final size:12
Alignment explanation
Indices: 179249--179285 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
179239 TTTTAATATT
*
179249 TATCGGGCCGGG
1 TATCGGGGCGGG
179261 TATCGGGGCGGG
1 TATCGGGGCGGG
179273 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
179286 ATTATCAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.19, G:0.54, T:0.16
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:185828 original size:59 final size:59
Alignment explanation
Indices: 185745--185865 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 59
185735 AGTATATGGA
* ** *
185745 TAAGTGTCCTATCGAACCCTCCTAGTCGTAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCATATCGAACCCTCCTAGTCACAATGAAAAGGCAAACTCGATAATATGACTC
* *
185804 TAAGTGTCATATTGAACCCTCCTAGTCACAATGAAAAGGCAAACTCGATAGTATGACTC
1 TAAGTGTCATATCGAACCCTCCTAGTCACAATGAAAAGGCAAACTCGATAATATGACTC
185863 TAA
1 TAA
185866 CCAACCCTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (59 bp):
TAAGTGTCATATCGAACCCTCCTAGTCACAATGAAAAGGCAAACTCGATAATATGACTC
Found at i:190556 original size:20 final size:20
Alignment explanation
Indices: 190525--190575 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
190515 TTGTTTTAGT
* *
190525 ATGTTAGAAATTAATGTTGGA
1 ATGTT-GAAATTAATGATAGA
*
190546 ATGTTGAAATTGATGATAGA
1 ATGTTGAAATTAATGATAGA
190566 ATG-TGAAATT
1 ATGTTGAAATT
190576 GGGTCATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (20 bp):
ATGTTGAAATTAATGATAGA
Found at i:191918 original size:24 final size:23
Alignment explanation
Indices: 191891--192090 Score: 109
Period size: 24 Copynumber: 8.3 Consensus size: 23
191881 TCAATCATGT
191891 TTAGTGCATTCGTGCACTCTAGTA
1 TTAGTGCATTCGTGCACTCT-GTA
* *
191915 TTAGTGCATTTGTTGCACTCCTGTT
1 TTAGTGCATTCG-TGCACT-CTGTA
* *
191940 TTAGTGCCTT-GATGCACTCCAGT-
1 TTAGTGCATTCG-TGCACT-CTGTA
*
191963 TATAGTGCATTTGTGCACTCCTGTA
1 T-TAGTGCATTCGTGCACT-CTGTA
* *
191988 TAAGTGCATACGTGCACTCTTGTA
1 TTAGTGCATTCGTGCACTC-TGTA
* * * * * * *
192012 TTATTACTTTTGGGTACTCCTGCA
1 TTAGTGCATTCGTGCACT-CTGTA
* *
192036 TTAGTGCATCCGTGCACTCCTGAA
1 TTAGTGCATTCGTGCACT-CTGTA
* *
192060 TCAGTGCCATT-GAGCACTCATGTA
1 TTAGTG-CATTCGTGCACTC-TGTA
192084 TTAGTGC
1 TTAGTGC
192091 TAGTATGCAC
Statistics
Matches: 135, Mismatches: 32, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
23 4 0.03
24 106 0.79
25 23 0.17
26 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (23 bp):
TTAGTGCATTCGTGCACTCTGTA
Found at i:191956 original size:49 final size:48
Alignment explanation
Indices: 191890--192006 Score: 148
Period size: 49 Copynumber: 2.4 Consensus size: 48
191880 ATCAATCATG
*
191890 TTTAGTGCATTCGTGCACTCTAG-TATTAGTGCATTTGTTGCACTCCTGT
1 TTTAGTGCATTCGTGCACTCCAGTTA-TAGTGCATTTG-TGCACTCCTGT
*
191939 TTTAGTGCCTT-GATGCACTCCAGTTATAGTGCATTTGTGCACTCCTGT
1 TTTAGTGCATTCG-TGCACTCCAGTTATAGTGCATTTGTGCACTCCTGT
* * *
191987 ATAAGTGCATACGTGCACTC
1 TTTAGTGCATTCGTGCACTC
192007 TTGTATTATT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
48 26 0.44
49 31 0.53
50 2 0.03
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (48 bp):
TTTAGTGCATTCGTGCACTCCAGTTATAGTGCATTTGTGCACTCCTGT
Found at i:196218 original size:21 final size:21
Alignment explanation
Indices: 196193--196254 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
196183 CCATAATAAG
196193 GGGTATCGGTACCCCTTCATA
1 GGGTATCGGTACCCCTTCATA
196214 GGGTATCGGTACCCCTTCATA
1 GGGTATCGGTACCCCTTCATA
* *
196235 GGGTATCAGTACACCTTCAT
1 GGGTATCGGTACCCCTTCAT
196255 TAAATTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (21 bp):
GGGTATCGGTACCCCTTCATA
Found at i:196454 original size:37 final size:35
Alignment explanation
Indices: 196395--196464 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 35
196385 GCAGTCATAG
*
196395 GTGTATGGATACACCTGCAGGGGGTATCGGTACATCA
1 GTGTATGGATACACCT-CA-GGGGTATCGATACATCA
196432 GTGTATGGATACA-CTCATAGGGGTATCGATACA
1 GTGTATGGATACACCTC--AGGGGTATCGATACA
196465 CATTTGCCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
35 1 0.03
36 15 0.50
37 14 0.47
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (35 bp):
GTGTATGGATACACCTCAGGGGTATCGATACATCA
Found at i:213383 original size:2 final size:2
Alignment explanation
Indices: 213333--213370 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
213323 AATTAAAATC
213333 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
213371 CAAATACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:214976 original size:349 final size:346
Alignment explanation
Indices: 214318--215012 Score: 1306
Period size: 349 Copynumber: 2.0 Consensus size: 346
214308 TACTCTAACA
214318 CTAACACAGTAATAGACTAAAACACTTGCATATGTTCTAGATAAGAGAGCGAGCTAGATAATAGC
1 CTAACACAGTAATAGACTAAAACACTTGCATATGTTCTAGATAAGAGAGCGAGCTAGATAATAGC
214383 TAGTGATGACCTCATTTTAGTGTGTTCAATTATGCTAAGGTGTAGTCAGGGTACCTTAGTTTGCC
66 TAGTGATGACCTCATTTTAGTGTGTTCAATTATGCTAAGGTGTAGTCAGGGTACCTTAGTTTGCC
*
214448 CTAGTGGGCATTATTAGTATTATGGCGGGTTTAGGGCCTTCAATTATATATGTATATTTGCATCA
131 CTAGTGGGCATTATTAGTATTATGGCGGGTTTAGGGCCTTCAATTATATATGTATAGTTGCATCA
214513 GTCCAGTACAACAAATATCCTTGGAGCTTGGCTTGACGTTGTGTGAAACCGAGCTAATGCTTCAG
196 GTCCAGTACAACAAATATCCTTGGAGCTTGGCTTGACGTTGTGTGAAACCGAGCTAATGCTTCAG
214578 TTGAGTTGGGAATTGTACCGATGATATGTGACACTCGATTCCCCTTCCATGATCTACCTGATAGC
261 TTGAGTTGGGAATTGTACCGATGATATGTGACACTCGATTCCCCTTCCATGATCTACCTGATAGC
214643 TATGTGGGACCAGAGAAATGT
326 TATGTGGGACCAGAGAAATGT
214664 CTAACAACAGTAATAGACTAATAAACACTTGCATAATGTTCTAGATAAGAGAGCGAGCTAGATAA
1 CTAAC-ACAGTAATAGACT-A-AAACACTTGCAT-ATGTTCTAGATAAGAGAGCGAGCTAGATAA
214729 TAGCTAGTGATGACCTCATTTTAGTGTGTTCAATTATGCTAAGGTGTAGTCAGGGTACCTTAG-T
62 TAGCTAGTGATGACCTCATTTTAGTGTGTTCAATTATGCTAAGGTGTAGTCAGGGTACCTTAGTT
214793 TGCCCTAGTGGGGCATTATTAGTATTAT-GCGGGTTTAGGGCCTTCAATTATATATGTATAGTTG
127 TGCCCTAGT-GGGCATTATTAGTATTATGGCGGGTTTAGGGCCTTCAATTATATATGTATAGTTG
214857 CATCAGTCCAGTACAACAAATATCCTTGGAGCTTGGCTTGACGGTTGTGTGAAACCGAGCTAATG
191 CATCAGTCCAGTACAACAAATATCCTTGGAGCTTGGCTTGAC-GTTGTGTGAAACCGAGCTAATG
214922 CTTCAGTTGAG-TGGGAATTGTACCGATGATATGTGACACTCGATTCCCCTTCCATGATCTACCT
255 CTTCAGTTGAGTTGGGAATTGTACCGATGATATGTGACACTCGATTCCCCTTCCATGATCTACCT
214986 GATAGCTATGTGGGACCAGAGAAATGT
320 GATAGCTATGTGGGACCAGAGAAATGT
215013 ACTTATGCTA
Statistics
Matches: 342, Mismatches: 1, Indels: 9
0.97 0.00 0.03
Matches are distributed among these distances:
346 5 0.01
347 13 0.04
348 1 0.00
349 179 0.52
350 144 0.42
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (346 bp):
CTAACACAGTAATAGACTAAAACACTTGCATATGTTCTAGATAAGAGAGCGAGCTAGATAATAGC
TAGTGATGACCTCATTTTAGTGTGTTCAATTATGCTAAGGTGTAGTCAGGGTACCTTAGTTTGCC
CTAGTGGGCATTATTAGTATTATGGCGGGTTTAGGGCCTTCAATTATATATGTATAGTTGCATCA
GTCCAGTACAACAAATATCCTTGGAGCTTGGCTTGACGTTGTGTGAAACCGAGCTAATGCTTCAG
TTGAGTTGGGAATTGTACCGATGATATGTGACACTCGATTCCCCTTCCATGATCTACCTGATAGC
TATGTGGGACCAGAGAAATGT
Found at i:215125 original size:32 final size:32
Alignment explanation
Indices: 215089--215207 Score: 150
Period size: 32 Copynumber: 3.7 Consensus size: 32
215079 CTAGTCAAGG
*
215089 TTGCATTCAAATAATGCACAACATAGTCAGTA
1 TTGCATTCATATAATGCACAACATAGTCAGTA
* *
215121 TTGCATTCATATAATGCACAGCAGAGTCAGTA
1 TTGCATTCATATAATGCACAACATAGTCAGTA
* *
215153 TTGCATTCATATAATGCACAGCAGT-GTCAGTG
1 TTGCATTCATATAATGCACAACA-TAGTCAGTA
* * *
215185 TTGCATTTAGATAATGTACAACA
1 TTGCATTCATATAATGCACAACA
215208 ATTATAATCA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
32 77 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (32 bp):
TTGCATTCATATAATGCACAACATAGTCAGTA
Found at i:220597 original size:26 final size:27
Alignment explanation
Indices: 220568--220637 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
220558 TGAGGCAAGT
*
220568 AACAAG-CTTACGAGCACAAGTCGAGC
1 AACAAGTCTAACGAGCACAAGTCGAGC
*
220594 AACAAGTTCTAACGAGCACGAGTCGAGC
1 AACAAG-TCTAACGAGCACAAGTCGAGC
* *
220622 AA-AATTTTAACGAGCA
1 AACAAGTCTAACGAGCA
220638 TCGAGTCAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 16 0.42
27 2 0.05
28 20 0.53
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (27 bp):
AACAAGTCTAACGAGCACAAGTCGAGC
Found at i:220610 original size:28 final size:26
Alignment explanation
Indices: 220577--220637 Score: 86
Period size: 28 Copynumber: 2.3 Consensus size: 26
220567 TAACAAGCTT
220577 ACGAGCACAAGTCGAGCAACAAGTTCTA
1 ACGAGCACAAGTCGAGCAA-AA-TTCTA
* *
220605 ACGAGCACGAGTCGAGCAAAATTTTA
1 ACGAGCACAAGTCGAGCAAAATTCTA
220631 ACGAGCA
1 ACGAGCA
220638 TCGAGTCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 11 0.35
27 2 0.06
28 18 0.58
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.15
Consensus pattern (26 bp):
ACGAGCACAAGTCGAGCAAAATTCTA
Found at i:221825 original size:21 final size:20
Alignment explanation
Indices: 221799--221842 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
221789 GGGACTCATT
221799 CTTTCAATAA-ATCATTATGTA
1 CTTTCAATAAGA--ATTATGTA
*
221820 CTTTCATTAAGAATTATGTA
1 CTTTCAATAAGAATTATGTA
221840 CTT
1 CTT
221843 ACCGATTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 11 0.52
21 9 0.43
22 1 0.05
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (20 bp):
CTTTCAATAAGAATTATGTA
Found at i:224909 original size:57 final size:56
Alignment explanation
Indices: 224822--224934 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 56
224812 CTCTCTAGCA
224822 TAGCTTTTTCTTTGCGTGTTTGAGATACACTATCATCACCATCAACCATTCAACTT
1 TAGCTTTTTCTTTGCGTGTTTGAGATACACTATCATCACCATCAACCATTCAACTT
224878 TAGCTTTTTCTTTGGCGTGTTTGAGATACACTATCATCACCATCAACCATTCAACTT
1 TAGCTTTTTCTTT-GCGTGTTTGAGATACACTATCATCACCATCAACCATTCAACTT
224935 CAACACCATC
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 13 0.23
57 43 0.77
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.39
Consensus pattern (56 bp):
TAGCTTTTTCTTTGCGTGTTTGAGATACACTATCATCACCATCAACCATTCAACTT
Found at i:231151 original size:64 final size:64
Alignment explanation
Indices: 231074--231218 Score: 177
Period size: 64 Copynumber: 2.3 Consensus size: 64
231064 CACTACATTG
** * *
231074 ATGCATCGATGCAC-CCTTGAATAAATTGAATTTTGAATGCATTTTGTGTACCGATGCATAAGGC
1 ATGCATCGATGCACTCCTT-AATAAATTGAACATCGAATGCATTTAGTGTACCGATGCATAAGGC
* ** * *
231138 ATGCATCGGTGCACTCCTTAATATTTTGAACATCGAATGCATTTAGTGTACCGATGCA-CAGATC
1 ATGCATCGATGCACTCCTTAATAAATTGAACATCGAATGCATTTAGTGTACCGATGCATAAG-GC
231202 ATGCATCGATGCACTCC
1 ATGCATCGATGCACTCC
231219 AGGCTTGTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
63 2 0.03
64 63 0.91
65 4 0.06
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (64 bp):
ATGCATCGATGCACTCCTTAATAAATTGAACATCGAATGCATTTAGTGTACCGATGCATAAGGC
Found at i:233226 original size:21 final size:21
Alignment explanation
Indices: 233202--233241 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
233192 AAGACTTTAT
*
233202 TTTCAAAATATAAAAATGATA
1 TTTCAAAATAGAAAAATGATA
*
233223 TTTCAAAATGGAAAAATGA
1 TTTCAAAATAGAAAAATGA
233242 GAATAGTCTT
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:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (21 bp):
TTTCAAAATAGAAAAATGATA
Found at i:237096 original size:23 final size:23
Alignment explanation
Indices: 237066--237144 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 23
237056 ACACTAGTTA
*
237066 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCATACCTTGAAT
* * *
237089 GTGCATCGAT--TTACCATGAAG
1 GTGCATCGATGCATACCTTGAAT
* * *
237110 GTACACCGATGCATGCCTTGAAT
1 GTGCATCGATGCATACCTTGAAT
237133 GTGCATCG-TGCA
1 GTGCATCGATGCA
237145 CTCTGCTGTG
Statistics
Matches: 42, Mismatches: 12, Indels: 5
0.71 0.20 0.08
Matches are distributed among these distances:
21 15 0.36
22 4 0.10
23 23 0.55
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (23 bp):
GTGCATCGATGCATACCTTGAAT
Found at i:239501 original size:64 final size:64
Alignment explanation
Indices: 239424--239568 Score: 186
Period size: 64 Copynumber: 2.3 Consensus size: 64
239414 CACTACATTG
** *
239424 ATGCATCGATGCAC-CCTTGAATAAATTGAATTTCGAATGCATTTTGTGTACCGATGCACAAGGC
1 ATGCATCGATGCACTCCTT-AATAAATTGAACATCGAATGCATTTAGTGTACCGATGCACAAGGC
* ** *
239488 ATGCATCGGTGCACTCCTTAATATTTTGAACATCGAATGCATTTAGTGTACCGATGCAC-AGACC
1 ATGCATCGATGCACTCCTTAATAAATTGAACATCGAATGCATTTAGTGTACCGATGCACAAG-GC
*
239552 CTGCATCGATGCACTCC
1 ATGCATCGATGCACTCC
239569 AGGCTTGTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
63 2 0.03
64 64 0.91
65 4 0.06
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (64 bp):
ATGCATCGATGCACTCCTTAATAAATTGAACATCGAATGCATTTAGTGTACCGATGCACAAGGC
Found at i:239628 original size:19 final size:19
Alignment explanation
Indices: 239604--239670 Score: 125
Period size: 19 Copynumber: 3.5 Consensus size: 19
239594 TTTTATGCAT
239604 CGATGCACTCCTAGTGTAC
1 CGATGCACTCCTAGTGTAC
239623 CGATGCACTCCTAGTGTAC
1 CGATGCACTCCTAGTGTAC
239642 CGATGCACTCCTAGTGTAC
1 CGATGCACTCCTAGTGTAC
*
239661 TGATGCACTC
1 CGATGCACTC
239671 AATCTTCCAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (19 bp):
CGATGCACTCCTAGTGTAC
Found at i:242965 original size:46 final size:46
Alignment explanation
Indices: 242906--243002 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 46
242896 GAGTCGAGGG
* * * * *
242906 TTCTATGCGGTCCTTCGGGATAATTCTACGTGGTCCTTGGGGACAT
1 TTCTACGCAGTCCTTCGGGACAATACTACGTGGTCCTTCGGGACAT
*
242952 TTCTACGCAGTCCTTCGGGACAATACTATGTGGTCCTTCGGGACAT
1 TTCTACGCAGTCCTTCGGGACAATACTACGTGGTCCTTCGGGACAT
242998 TTCTA
1 TTCTA
243003 TGTGGAGCTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.34
Consensus pattern (46 bp):
TTCTACGCAGTCCTTCGGGACAATACTACGTGGTCCTTCGGGACAT
Found at i:243005 original size:23 final size:23
Alignment explanation
Indices: 242906--243007 Score: 114
Period size: 23 Copynumber: 4.4 Consensus size: 23
242896 GAGTCGAGGG
* *
242906 TTCTATGCGGTCCTTCGGGATAA
1 TTCTATGTGGTCCTTCGGGACAA
* * *
242929 TTCTACGTGGTCCTTGGGGACAT
1 TTCTATGTGGTCCTTCGGGACAA
* **
242952 TTCTACGCAGTCCTTCGGGACAA
1 TTCTATGTGGTCCTTCGGGACAA
* *
242975 TACTATGTGGTCCTTCGGGACAT
1 TTCTATGTGGTCCTTCGGGACAA
242998 TTCTATGTGG
1 TTCTATGTGG
243008 AGCTTCGGTG
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGGACAA
Found at i:243013 original size:23 final size:23
Alignment explanation
Indices: 242963--243015 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
242953 TCTACGCAGT
*
242963 CCTTCGGGACAATACTATGTGGT
1 CCTTCGGGACAATACTATGTGGA
* *
242986 CCTTCGGGACATTTCTATGTGGA
1 CCTTCGGGACAATACTATGTGGA
*
243009 GCTTCGG
1 CCTTCGG
243016 TGCAATTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (23 bp):
CCTTCGGGACAATACTATGTGGA
Found at i:249050 original size:106 final size:99
Alignment explanation
Indices: 248905--249255 Score: 434
Period size: 99 Copynumber: 3.5 Consensus size: 99
248895 AAATTGTTTA
* * * * *
248905 TTGACAACTAGTCGTCCCTTCGATGTGAAGTTGAACTTGTGTTGTCGCGAGTCCAATATCCTTCG
1 TTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCG
248970 CTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTTG
66 CTGTGAAGTTGAAATTGGCTCTGAAA-TGGG-AA--A---G
* *
249011 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCG
1 TTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCG
*
249076 CTGTGAAGTTGAAATTGGCTCTGCAATTGGG-AAG
66 CTGTGAAGTTGAAATTGGCTCTG-AAATGGGAAAG
* ** * * * * *
249110 TTAACAGTCAGTCGCCCCTTCGCTGTGAAATTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCG
1 TTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCG
* *
249175 TTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAG
66 CTGTGAAGTTGAAATTGGCTCTGAAATGGGAAAG
** *
249209 TTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCT
1 TTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
249256 TGTGTGGATG
Statistics
Matches: 221, Mismatches: 22, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
98 5 0.02
99 124 0.56
102 1 0.00
104 1 0.00
106 88 0.40
107 2 0.01
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.33
Consensus pattern (99 bp):
TTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCG
CTGTGAAGTTGAAATTGGCTCTGAAATGGGAAAG
Found at i:250377 original size:16 final size:15
Alignment explanation
Indices: 250353--250418 Score: 69
Period size: 16 Copynumber: 4.2 Consensus size: 15
250343 ACCCACCTTA
250353 TTTTCTTTTCTTTTTC
1 TTTT-TTTTCTTTTTC
*
250369 TTTTGTTTTTTTTTTC
1 TTTT-TTTTCTTTTTC
*
250385 TCTTTTTTCTTTTTTC
1 TTTTTTTTC-TTTTTC
* *
250401 CTTTTCTTCTTTTTC
1 TTTTTTTTCTTTTTC
250416 TTT
1 TTT
250419 CAATTTAGGG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.29
16 29 0.71
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.82
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:250378 original size:22 final size:21
Alignment explanation
Indices: 250353--250418 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
250343 ACCCACCTTA
250353 TTTTCTTTTCTTTTTCTT-TTGT
1 TTTTCTTTTCTTTTT-TTCTT-T
*
250375 TTTTTTTTTCTCTTTTTTCTTT
1 TTTTCTTTTCT-TTTTTTCTTT
*
250397 TTTCCTTTTCTTCTTTTTCTTT
1 TTTTCTTTTCTT-TTTTTCTTT
250419 CAATTTAGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.03
22 31 0.82
23 6 0.16
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.82
Consensus pattern (21 bp):
TTTTCTTTTCTTTTTTTCTTT
Found at i:250390 original size:9 final size:8
Alignment explanation
Indices: 250363--250414 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
250353 TTTTCTTTTC
250363 TTTTTCTT
1 TTTTTCTT
250371 TTGTTT-TT
1 TT-TTTCTT
250379 TTTTTCTCT
1 TTTTTCT-T
250388 TTTTTCTT
1 TTTTTCTT
*
250396 TTTTCCTT
1 TTTTTCTT
*
250404 TTCTTCTT
1 TTTTTCTT
250412 TTT
1 TTT
250415 CTTTCAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 3 0.08
8 23 0.62
9 11 0.30
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:250405 original size:25 final size:24
Alignment explanation
Indices: 250353--250414 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
250343 ACCCACCTTA
*
250353 TTTTCTT-TTCTTTTTCTTTTGTTT
1 TTTTCTTCTT-TTTTTCTTTTGTTC
*
250377 TTTTTTTCTCTTTTTTCTTTT-TTCC
1 TTTTCTTCT-TTTTTTCTTTTGTT-C
250402 TTTTCTTCTTTTT
1 TTTTCTTCTTTTT
250415 CTTTCAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
24 12 0.38
25 19 0.59
26 1 0.03
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (24 bp):
TTTTCTTCTTTTTTTCTTTTGTTC
Found at i:250505 original size:62 final size:64
Alignment explanation
Indices: 250394--250514 Score: 158
Period size: 62 Copynumber: 1.9 Consensus size: 64
250384 CTCTTTTTTC
* * * *
250394 TTTTTTCCTTTTCTTCTTTTTCTTTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAATGAT
1 TTTTTTCCTTTTCTTCTTTTTCTTTCAATTTAGGACGCCATCTCAGGTTTTCACCCTAAATGAT
* *
250458 TTTTTTCC-TTT-TTCTTTGTT-TTTCAATTTAGGACGTCATCTCAGGTTTTCATCCTAA
1 TTTTTTCCTTTTCTTCTTT-TTCTTTCAATTTAGGACGCCATCTCAGGTTTTCACCCTAA
250515 GCGAAGTACT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
62 37 0.74
63 5 0.10
64 8 0.16
ACGTcount: A:0.14, C:0.21, G:0.12, T:0.53
Consensus pattern (64 bp):
TTTTTTCCTTTTCTTCTTTTTCTTTCAATTTAGGACGCCATCTCAGGTTTTCACCCTAAATGAT
Found at i:267967 original size:41 final size:41
Alignment explanation
Indices: 267889--268099 Score: 237
Period size: 41 Copynumber: 5.2 Consensus size: 41
267879 AACACAAACA
*
267889 CCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAAAAATG
1 CCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATG
* * * * *
267930 CCATTAAAGTACAAGTCTATAACGGTGTTTCTGT-AAAATG
1 CCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATG
* *
267970 CCA-TTAAGTACAAGTGTATAGCGGCGTTTGTATAAAAATG
1 CCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATG
* * * *
268010 CCACTAAAGTACGAGTCTCTAGTGGCGTTTGTATAAAAATA
1 CCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATG
* * * * * *
268051 CCACTAAAGTACGAGTCTTTAGCGGTGTTTTTATAGAAACG
1 CCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATG
*
268092 CTACTAAA
1 CCACTAAA
268100 ATACTACTAT
Statistics
Matches: 142, Mismatches: 26, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
39 24 0.17
40 18 0.13
41 100 0.70
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (41 bp):
CCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATG
Found at i:268047 original size:80 final size:80
Alignment explanation
Indices: 267895--268047 Score: 234
Period size: 80 Copynumber: 1.9 Consensus size: 80
267885 AACACCACTA
* *
267895 AAGTACAAGTGTATAGCGGCGTTTGTATAAAAATGCCATTAAAGTACAAGTCTATAACGGTGTTT
1 AAGTACAAGTGTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTATAACGGCGTTT
*
267960 CTGTAAAATGCCATT
66 CTATAAAATGCCATT
* * **
267975 AAGTACAAGTGTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTCTAGTGGCGTTT
1 AAGTACAAGTGTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTATAACGGCGTTT
*
268040 GTATAAAA
66 CTATAAAA
268048 ATACCACTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.30
Consensus pattern (80 bp):
AAGTACAAGTGTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTATAACGGCGTTT
CTATAAAATGCCATT
Found at i:269996 original size:2 final size:2
Alignment explanation
Indices: 269989--270024 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
269979 AATCCTCTTT
269989 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
270025 CAACAACAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:272304 original size:2 final size:2
Alignment explanation
Indices: 272297--272325 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
272287 CTTGGCCTCT
272297 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 T
272326 CCTTTGTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:280488 original size:20 final size:20
Alignment explanation
Indices: 280459--280497 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
280449 AGAGCTCATA
*
280459 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
280479 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
280498 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:286814 original size:20 final size:20
Alignment explanation
Indices: 286789--286826 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
286779 CCACATGCAA
*
286789 CTATATGCTCCTAAATGAAT
1 CTATATGATCCTAAATGAAT
*
286809 CTATATGATCCTATATGA
1 CTATATGATCCTAAATGA
286827 GCTCTTAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (20 bp):
CTATATGATCCTAAATGAAT
Found at i:291307 original size:60 final size:60
Alignment explanation
Indices: 291218--291336 Score: 238
Period size: 60 Copynumber: 2.0 Consensus size: 60
291208 CCTTATCTGC
291218 CTGACAAAGTTTACTAAGGGTGCCCTATGCTATCTCTAGTTAAGGGACTCGACAGATTAT
1 CTGACAAAGTTTACTAAGGGTGCCCTATGCTATCTCTAGTTAAGGGACTCGACAGATTAT
291278 CTGACAAAGTTTACTAAGGGTGCCCTATGCTATCTCTAGTTAAGGGACTCGACAGATTA
1 CTGACAAAGTTTACTAAGGGTGCCCTATGCTATCTCTAGTTAAGGGACTCGACAGATTA
291337 AAGATACCTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (60 bp):
CTGACAAAGTTTACTAAGGGTGCCCTATGCTATCTCTAGTTAAGGGACTCGACAGATTAT
Found at i:297194 original size:34 final size:34
Alignment explanation
Indices: 297130--297229 Score: 121
Period size: 34 Copynumber: 3.0 Consensus size: 34
297120 TTTTATAACC
* * * *
297130 ATCGATTT-TTGATTTATTGATCGATGAATTCAA
1 ATCGATTTAATGATATATTAATCGATAAATTCAA
*
297163 ATCGATTTAATGATATATTAATCGATAAATTCAG
1 ATCGATTTAATGATATATTAATCGATAAATTCAA
* * *
297197 ATCGATTTAATGATCTATTAATCTACAAATTCA
1 ATCGATTTAATGATATATTAATCGATAAATTCA
297230 TATCAGTTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 8 0.14
34 50 0.86
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (34 bp):
ATCGATTTAATGATATATTAATCGATAAATTCAA
Found at i:297662 original size:12 final size:12
Alignment explanation
Indices: 297645--297671 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
297635 AAGTTACGCC
297645 ATTTGTGTGTAT
1 ATTTGTGTGTAT
297657 ATTTGTGTGTAT
1 ATTTGTGTGTAT
297669 ATT
1 ATT
297672 AGAGCAAAGC
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:0.19, C:0.00, G:0.22, T:0.59
Consensus pattern (12 bp):
ATTTGTGTGTAT
Found at i:300224 original size:60 final size:60
Alignment explanation
Indices: 300141--300267 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
300131 ATAGTTGAGT
* * * *
300141 GACCATTTTGTAACTCTTAATAGTCGAGGGACTCAACAAAGCAACACACTATAGTCAGGG
1 GACCATTCTATAACTCTTAATAGTCGAGGGACTCAACAAAACAACACACTATAGTCAAGG
* ** *
300201 GACCATTCTATAACT-TTCAATAGTCGAGGGACTCAACAAAACAATAGTCTATTGTCAAGG
1 GACCATTCTATAACTCTT-AATAGTCGAGGGACTCAACAAAACAACACACTATAGTCAAGG
300261 GACCATT
1 GACCATT
300268 TATGTACTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 2 0.03
60 56 0.97
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.25
Consensus pattern (60 bp):
GACCATTCTATAACTCTTAATAGTCGAGGGACTCAACAAAACAACACACTATAGTCAAGG
Found at i:303293 original size:21 final size:21
Alignment explanation
Indices: 303264--303316 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
303254 ATTCTGACTA
303264 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
303285 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
303306 TCGCAATGCGA
1 TCGCATTGCGA
303317 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:303331 original size:20 final size:20
Alignment explanation
Indices: 303306--303521 Score: 148
Period size: 20 Copynumber: 10.7 Consensus size: 20
303296 TTTTCCTAAT
303306 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
303326 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
303346 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
303367 TCGCAATGCGATTACGT-AT
1 TCGCAATGCGAATACGTAAA
* * * * *
303386 TCGCATTGCGATTTTCCTAAT
1 TCGCAATGCGA-ATACGTAAA
* * *
303407 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGA-ATACGTAAA
** * * * *
303427 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGA-ATACGTAAA
* *
303448 TCACAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
* *
303468 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
303489 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
303509 TCGCAATGCGAAT
1 TCGCAATGCGAAT
303522 CTGACTATCG
Statistics
Matches: 160, Mismatches: 31, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
19 11 0.07
20 87 0.54
21 62 0.39
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:303337 original size:41 final size:42
Alignment explanation
Indices: 303292--303379 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 42
303282 AATTCGCGTT
** * *
303292 GCGATTTTCCTAATTCGCAATGCGAA-TACGTAAATCGCAAC
1 GCGATTTAACTAAATCGCAATGCGAATTACGAAAATCGCAAC
* * *
303333 GCGA-TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAAT
1 GCGATTTAACTAAATCGCAATGCGAATTACGAAAATCGCAAC
303374 GCGATT
1 GCGATT
303380 ACGTATTCGC
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
40 17 0.45
41 20 0.53
42 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (42 bp):
GCGATTTAACTAAATCGCAATGCGAATTACGAAAATCGCAAC
Found at i:303380 original size:41 final size:41
Alignment explanation
Indices: 303306--303521 Score: 179
Period size: 41 Copynumber: 5.3 Consensus size: 41
303296 TTTTCCTAAT
* * *
303306 TCGCAATGCGAA-TACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAATGCGATTACGTAAA
* *
303346 TCGCAATGCGAATTAGGAAAATCGCAATGCGATTACGT-AT
1 TCGCAATGCGAATTACGAAAATCGCAATGCGATTACGTAAA
* * * ** * * *
303386 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT-AT
1 TCGCAATGCGAATTACGAAAATCGCAATGCGA-TTACGTAAA
** * * * * * *
303427 TCGCGTTGCGATTTTC-ATAATTCACAATGCGAATACATAAA
1 TCGCAATGCGAATTACGA-AAATCGCAATGCGATTACGTAAA
* *
303468 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAATGCGATTACGTAAA
303509 TCGCAATGCGAAT
1 TCGCAATGCGAAT
303522 CTGACTATCG
Statistics
Matches: 143, Mismatches: 28, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
40 41 0.29
41 101 0.71
42 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCGCAATGCGATTACGTAAA
Found at i:303532 original size:61 final size:60
Alignment explanation
Indices: 303306--303539 Score: 172
Period size: 61 Copynumber: 3.8 Consensus size: 60
303296 TTTTCCTAAT
* *
303306 TCGCAATGCGAATACGTAAATCGCAACGCGAT-TAAGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGATCT-ACT-AATCGCAATGCGAATTAGGAAAA
* * * * * * * * * *
303367 TCGCAATGCGATTACGT-ATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACG-TAT
1 TCGCAATGCGAATACGTAAATCGCAATGCGA-TCTACTAA-TCGCAATGCGAATTAGGAAAA
** * * * * * *
303427 TCGCGTTGCGATTTTCATAATTCACAATGCGA-ATACATAAATCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGA-ATACGTAAATCGCAATGCGATCTAC-T-AATCGCAATGCGAATTAGGAAAA
303489 TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGACT-ATCGCAATGCGA
1 TCGCAATGCGAATACGTAAATCGCAATGCG-ATCT-ACTAATCGCAATGCGA
303540 TTTACATAGC
Statistics
Matches: 130, Mismatches: 32, Indels: 22
0.71 0.17 0.12
Matches are distributed among these distances:
60 24 0.18
61 77 0.59
62 25 0.19
63 2 0.02
64 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (60 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGATCTACTAATCGCAATGCGAATTAGGAAAA
Found at i:304099 original size:14 final size:14
Alignment explanation
Indices: 304080--304140 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
304070 GGAAATGACT
*
304080 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
304094 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
*
304113 ATCGCAACGAGATA
1 ATCGCAACGAGAAA
*
304127 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
304141 CCAAAATCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:304117 original size:33 final size:33
Alignment explanation
Indices: 304059--304151 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
304049 CGAGAATGAA
**
304059 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
*
304093 AATCGCAACGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
**
304126 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
304152 TTGCGATTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 43 0.80
34 11 0.20
ACGTcount: A:0.43, C:0.25, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:304212 original size:33 final size:33
Alignment explanation
Indices: 304152--304214 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
304142 CAAAATCGCA
* **
304152 TTGCGATTCTCTCGTTGCGATTTTCATTTCGTG
1 TTGCGATTCTCTCGTTGAGATAGTCATTTCGTG
304185 TTGCGATTCTCTCGTTGAGATAGTCATTTC
1 TTGCGATTCTCTCGTTGAGATAGTCATTTC
304215 CGCATTGCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTCTCTCGTTGAGATAGTCATTTCGTG
Found at i:306163 original size:94 final size:93
Alignment explanation
Indices: 305940--306217 Score: 410
Period size: 94 Copynumber: 3.1 Consensus size: 93
305930 TAGATTGCTT
* *
305940 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
306001 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
*
306030 AGT--A--TATTCGGTTGCTTCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
306091 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
306120 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
306185 ATTTGTGTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
306213 AGTAA
1 AGTAA
306218 TGCAATCCAT
Statistics
Matches: 170, Mismatches: 9, Indels: 15
0.88 0.05 0.08
Matches are distributed among these distances:
86 26 0.15
88 4 0.02
89 22 0.13
90 33 0.19
92 1 0.01
93 6 0.04
94 78 0.46
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:306333 original size:20 final size:20
Alignment explanation
Indices: 306308--306369 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
306298 TTTTGGTTGA
306308 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
306328 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
306347 AATGAAAATCACAACGAGAG
1 AATGAAAATCGCAACGAGAG
306367 AAT
1 AAT
306370 CGCAACGCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 17 0.45
20 21 0.55
ACGTcount: A:0.52, C:0.16, G:0.21, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:306349 original size:39 final size:35
Alignment explanation
Indices: 306306--306429 Score: 139
Period size: 33 Copynumber: 3.5 Consensus size: 35
306296 TCTTTTGGTT
306306 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAG-A-G--AATCGCAACGC
*
306345 GAAATGAAAATCACAAC--GAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAGAATCGCAACGC
*
306378 GAAATGAAAATCGCAACGACA-A-AATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAGAATCGCAACGC
**
306411 GAAACCAAAAATCGCAACG
1 GAAA-TGAAAATCGCAACG
306430 TGAAACTATA
Statistics
Matches: 77, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
33 42 0.55
34 13 0.17
35 2 0.03
36 1 0.01
37 3 0.04
39 16 0.21
ACGTcount: A:0.49, C:0.22, G:0.20, T:0.09
Consensus pattern (35 bp):
GAAATGAAAATCGCAACGAGAGAGAATCGCAACGC
Found at i:306352 original size:19 final size:19
Alignment explanation
Indices: 306306--306395 Score: 109
Period size: 19 Copynumber: 4.9 Consensus size: 19
306296 TCTTTTGGTT
*
306306 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
306325 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
*
306345 GAAATGAAAATCACAA--C
1 GAAATGAAAATCGCAACGC
*
306362 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
306378 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
306396 ACAAAATCGC
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
14 9 0.15
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 27 0.45
20 18 0.30
ACGTcount: A:0.49, C:0.19, G:0.22, T:0.10
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:306421 original size:20 final size:20
Alignment explanation
Indices: 306398--306435 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
306388 TCGCAACGAC
306398 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
*
306418 AAAATCGCAACGTGAAAC
1 AAAATCGCAACGCGAAAC
306436 TATAATCGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.08
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:306482 original size:19 final size:19
Alignment explanation
Indices: 306458--306542 Score: 72
Period size: 19 Copynumber: 4.6 Consensus size: 19
306448 GCGATTTTGT
306458 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
306477 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
306491 CATTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
** *
306510 CGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCA--TTTCG
306531 CGTTGCGATTTT
1 CGTTGCGATTTT
306543 AAGTTACAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
14 9 0.18
16 3 0.06
17 3 0.06
19 21 0.42
21 14 0.28
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:306483 original size:33 final size:33
Alignment explanation
Indices: 306441--306518 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
306431 GAAACTATAA
* * *
306441 TCGCGTTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTCTCTCATTGCGATTTTCATT
306474 TCGCGTTGCGATTCTCTCATTGCGATTTTCATT
1 TCGCGTTGCGATTCTCTCATTGCGATTTTCATT
306507 TCGCGTTGCGAT
1 TCGCGTTGCGAT
306519 AGTCATTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.10, C:0.22, G:0.23, T:0.45
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCATTGCGATTTTCATT
Found at i:307020 original size:42 final size:43
Alignment explanation
Indices: 306974--307062 Score: 101
Period size: 43 Copynumber: 2.1 Consensus size: 43
306964 CTATTGTTGT
* * *
306974 AGAGGCCTCTATCATTCCTCG-AGA-GTCCCCTTCCACCGTTCA
1 AGAGGCCACTATCA-TCCTCGAAGAGGTCCCCTCCCACCATTCA
* * *
307016 AGAGGCCACTGTCATCGTTGAAGAGGTCCCCTCCCACCATTCA
1 AGAGGCCACTATCATCCTCGAAGAGGTCCCCTCCCACCATTCA
307059 AGAG
1 AGAG
307063 CCCGATTCAC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
41 4 0.10
42 15 0.38
43 20 0.51
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.22
Consensus pattern (43 bp):
AGAGGCCACTATCATCCTCGAAGAGGTCCCCTCCCACCATTCA
Found at i:308432 original size:14 final size:14
Alignment explanation
Indices: 308413--308448 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
308403 TTATTTTAAT
308413 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
308427 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
308441 TGATTTGT
1 TGATTTGT
308449 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:308614 original size:19 final size:19
Alignment explanation
Indices: 308555--308617 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 19
308545 AAAAATGACT
*
308555 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
308574 ATCGTAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
308588 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
308607 ATCGCAACGCG
1 ATCGCAACGCG
308618 CAAACTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 9 0.26
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 20 0.57
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:308627 original size:19 final size:18
Alignment explanation
Indices: 308587--308631 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
308577 GTAACGAGAG
308587 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAAT-AA
308606 AATCGCAACGCGCAAACTAA
1 AATCGCAACGCG-AAA-TAA
*
308626 ATTCGC
1 AATCGC
308632 GTTTCGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 12 0.52
20 10 0.43
21 1 0.04
ACGTcount: A:0.42, C:0.27, G:0.18, T:0.13
Consensus pattern (18 bp):
AATCGCAACGCGAAATAA
Found at i:308658 original size:19 final size:19
Alignment explanation
Indices: 308627--308711 Score: 56
Period size: 19 Copynumber: 4.7 Consensus size: 19
308617 GCAAACTAAA
308627 TTCGCGTTT-CGATTTTCAT
1 TTCGC-TTTGCGATTTTCAT
*
308646 TTCGCTTTGCGA--TTC-C
1 TTCGCTTTGCGATTTTCAT
*
308662 CTCG--TTGCGATTTTCAT
1 TTCGCTTTGCGATTTTCAT
* **
308679 TTCGCATTGCGATAGTCAT
1 TTCGCTTTGCGATTTTCAT
*
308698 TTCCGCGTTGCGAT
1 TT-CGCTTTGCGAT
308712 AGACATTAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
14 6 0.12
16 6 0.12
17 6 0.12
18 3 0.06
19 21 0.40
20 10 0.19
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCTTTGCGATTTTCAT
Found at i:308710 original size:20 final size:20
Alignment explanation
Indices: 308664--308757 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
308654 GCGATTCCCT
**
308664 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
308683 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
308703 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
308722 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
308744 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
308758 AATGAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:311295 original size:24 final size:24
Alignment explanation
Indices: 311244--311295 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
311234 ATCTGAGTAT
** *
311244 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
311268 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
311292 TGAC
1 TGAC
311296 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:312164 original size:20 final size:20
Alignment explanation
Indices: 312141--312441 Score: 319
Period size: 20 Copynumber: 14.9 Consensus size: 20
312131 AGAATCTCGT
312141 TGCGATTTAC-TAAATCGCAA
1 TGCGA-TTACGTAAATCGCAA
312161 TGCGATTACGTAAATCG-AA
1 TGCGATTACGTAAATCGCAA
* * *
312180 GTGCGAATTAGGAAAATCGAAA
1 -TGCG-ATTACGTAAATCGCAA
312202 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
312222 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
312242 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
* * *
312262 TGCGAATTAGGAAAATCGAAA
1 TGCG-ATTACGTAAATCGCAA
* *
312283 TGCGATTACTTAATTCGCAA
1 TGCGATTACGTAAATCGCAA
* *
312303 TGCGAATTAGGAAAATCGCAA
1 TGCG-ATTACGTAAATCGCAA
*
312324 TGCGATTACGTAATTCGCAA
1 TGCGATTACGTAAATCGCAA
* * *
312344 TGCGAATTAGGAAAATCACAA
1 TGCG-ATTACGTAAATCGCAA
312365 TGCGATTACGTAAATCGC-A
1 TGCGATTACGTAAATCGCAA
* * *
312384 TGCGATT--TTAATTCGTAA
1 TGCGATTACGTAAATCGCAA
312402 TGCGATTTACGT-AATCGCAA
1 TGCGA-TTACGTAAATCGCAA
312422 TTGCGATTTACGT-AATCGCA
1 -TGCGA-TTACGTAAATCGCA
312442 TTACGATTTC
Statistics
Matches: 236, Mismatches: 33, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
17 6 0.03
18 6 0.03
19 16 0.07
20 122 0.52
21 84 0.36
22 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (20 bp):
TGCGATTACGTAAATCGCAA
Found at i:312176 original size:81 final size:80
Alignment explanation
Indices: 312141--312415 Score: 348
Period size: 81 Copynumber: 3.4 Consensus size: 80
312131 AGAATCTCGT
312141 TGCGATTTAC-TAAATCGCAATGCGATTACGTAAATCGAAGTGCGAATTAGGAAAATCGAAATGC
1 TGCGA-TTACGTAAATCGCAATGCGATTACGTAAATCGAAGTGCGAATTAGGAAAATCGAAATGC
312205 GATTACGTAAATCGCAA
65 GATTACG-AAATCGCAA
312222 TGCGATTACGTAAATCGCAATGCGATTACGTAAATCGCAA-TGCGAATTAGGAAAATCGAAATGC
1 TGCGATTACGTAAATCGCAATGCGATTACGTAAATCG-AAGTGCGAATTAGGAAAATCGAAATGC
* *
312286 GATTACTTAATTCGCAA
65 GATTAC-GAAATCGCAA
* * *
312303 TGCGAATTAGGAAAATCGCAATGCGATTACGTAATTCGCAA-TGCGAATTAGGAAAATC-ACAAT
1 TGCG-ATTACGTAAATCGCAATGCGATTACGTAAATCG-AAGTGCGAATTAGGAAAATCGA-AAT
312366 GCGATTACGTAAATCGC-A
63 GCGATTACG-AAATCGCAA
* * *
312384 TGCGATT--TTAATTCGTAATGCGATTTACGTAA
1 TGCGATTACGTAAATCGCAATGCGA-TTACGTAA
312416 TCGCAATTGC
Statistics
Matches: 176, Mismatches: 11, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
78 12 0.07
79 8 0.05
80 7 0.04
81 80 0.45
82 69 0.39
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (80 bp):
TGCGATTACGTAAATCGCAATGCGATTACGTAAATCGAAGTGCGAATTAGGAAAATCGAAATGCG
ATTACGAAATCGCAA
Found at i:312204 original size:41 final size:41
Alignment explanation
Indices: 312152--312388 Score: 356
Period size: 41 Copynumber: 5.8 Consensus size: 41
312142 GCGATTTACT
*
312152 AAATCGCAATGCGATTACGTAAATCG-AAGTGCGAATTAGGA
1 AAATCGAAATGCGATTACGTAAATCGCAA-TGCGAATTAGGA
* *
312193 AAATCGAAATGCGATTACGTAAATCGCAATGCG-ATTACGT
1 AAATCGAAATGCGATTACGTAAATCGCAATGCGAATTAGGA
*
312233 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
1 AAATCGAAATGCGATTACGTAAATCGCAATGCGAATTAGGA
* *
312274 AAATCGAAATGCGATTACTTAATTCGCAATGCGAATTAGGA
1 AAATCGAAATGCGATTACGTAAATCGCAATGCGAATTAGGA
* *
312315 AAATCGCAATGCGATTACGTAATTCGCAATGCGAATTAGGA
1 AAATCGAAATGCGATTACGTAAATCGCAATGCGAATTAGGA
312356 AAATC-ACAATGCGATTACGTAAATCGC-ATGCGA
1 AAATCGA-AATGCGATTACGTAAATCGCAATGCGA
312389 TTTTAATTCG
Statistics
Matches: 180, Mismatches: 13, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
40 43 0.24
41 135 0.75
42 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (41 bp):
AAATCGAAATGCGATTACGTAAATCGCAATGCGAATTAGGA
Found at i:312206 original size:61 final size:59
Alignment explanation
Indices: 312141--312429 Score: 298
Period size: 61 Copynumber: 4.8 Consensus size: 59
312131 AGAATCTCGT
* *
312141 TGCGATTTACTAAATCGCAATGCGATTACGTAAATCG-AAGTGCGAATTAGGAAAATCGAAA
1 TGCGA-TTACTAAATCGCAATGCGATTACGTAAATCGCAA-TGCG-ATTACGAAAATCGCAA
*
312202 TGCGATTACGTAAATCGCAATGCGATTACGTAAATCGCAATGCGATTACGTAAATCGCAA
1 TGCGATTAC-TAAATCGCAATGCGATTACGTAAATCGCAATGCGATTACGAAAATCGCAA
** * * * *
312262 TGCGAATTAGGAAAATCGAAATGCGATTACTTAATTCGCAATGCGAATTAGGAAAATCGCAA
1 TGCG-ATTA-CTAAATCGCAATGCGATTACGTAAATCGCAATGCG-ATTACGAAAATCGCAA
* * * * *
312324 TGCGATTACGTAATTCGCAATGCGAATTAGGAAAATCACAATGCGATTACGTAAATCGC-A
1 TGCGATTAC-TAAATCGCAATGCG-ATTACGTAAATCGCAATGCGATTACGAAAATCGCAA
* * *
312384 TGCGATT-TTAATTCGTAATGCGATTTACGT-AATCGCAATTGCGATT
1 TGCGATTACTAAATCGCAATGCGA-TTACGTAAATCGCAA-TGCGATT
312430 TACGTAATCG
Statistics
Matches: 193, Mismatches: 26, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
57 8 0.04
58 24 0.12
60 29 0.15
61 97 0.50
62 35 0.18
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (59 bp):
TGCGATTACTAAATCGCAATGCGATTACGTAAATCGCAATGCGATTACGAAAATCGCAA
Found at i:312450 original size:20 final size:20
Alignment explanation
Indices: 312140--312514 Score: 162
Period size: 20 Copynumber: 18.3 Consensus size: 20
312130 CAGAATCTCG
312140 TTGCGATTTAC-TAAATCGCA
1 TTGCGATTTACGT-AATCGCA
* *
312160 ATGCGA-TTACGTAAATCGAA
1 TTGCGATTTACGT-AATCGCA
* * * * *
312180 GTGCGAATTAGGAAAATCGAA
1 TTGCGATTTACG-TAATCGCA
*
312201 ATGCGA-TTACGTAAATCGCA
1 TTGCGATTTACGT-AATCGCA
*
312221 ATGCGA-TTACGTAAATCGCA
1 TTGCGATTTACGT-AATCGCA
*
312241 ATGCGA-TTACGTAAATCGCA
1 TTGCGATTTACGT-AATCGCA
* * * * *
312261 ATGCGAATTAGGAAAATCGAA
1 TTGCGATTTACG-TAATCGCA
* *
312282 ATGCGA-TTACTTAATTCGCA
1 TTGCGATTTACGTAA-TCGCA
* * * *
312302 ATGCGAATTAGGAAAATCGCA
1 TTGCGATTTACG-TAATCGCA
*
312323 ATGCGA-TTACGTAATTCGCA
1 TTGCGATTTACGTAA-TCGCA
* * * * *
312343 ATGCGAATTAGGAAAATCACA
1 TTGCGATTTACG-TAATCGCA
*
312364 ATGCGA-TTACGTAAATCGCA
1 TTGCGATTTACGT-AATCGCA
*
312384 -TGCGATTT---TAATTCGTA
1 TTGCGATTTACGTAA-TCGCA
*
312401 ATGCGATTTACGTAATCGCAA
1 TTGCGATTTACGTAATCGC-A
312422 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
* *
312442 TTACGATTTCCATTTTCCTAATTCGCA
1 TTGCGATTT--A----CGTAA-TCGCA
* *
312469 TTGCGATTTACTTAATCGCG
1 TTGCGATTTACGTAATCGCA
*
312489 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCA
312509 TTGCGA
1 TTGCGA
312515 ATTAGGAAAA
Statistics
Matches: 290, Mismatches: 38, Indels: 54
0.76 0.10 0.14
Matches are distributed among these distances:
16 2 0.01
17 5 0.02
18 8 0.03
19 13 0.04
20 153 0.53
21 86 0.30
22 5 0.02
25 1 0.00
26 4 0.01
27 13 0.04
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:312535 original size:21 final size:21
Alignment explanation
Indices: 312511--312577 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
312501 TATTCGCATT
* *
312511 GCGAATTAGGAAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
312532 GCGAATTTGGGAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
*
312553 GCGAATTTGGGAAATCGCAAT
1 GCGAATTTGGGAAATCGCAAC
312574 GCGA
1 GCGA
312578 TAATCAGAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (21 bp):
GCGAATTTGGGAAATCGCAAC
Found at i:314762 original size:4 final size:4
Alignment explanation
Indices: 314753--314779 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
314743 TAGATTTGTA
314753 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
314780 TAAGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:326061 original size:133 final size:133
Alignment explanation
Indices: 325823--326089 Score: 518
Period size: 133 Copynumber: 2.0 Consensus size: 133
325813 ATTTTGTTTA
325823 GGAGAGTAAAAGATAAGATAATGAACACAAGAATTTATAGTGTTCAACTTCTCAATTAAGTCTAC
1 GGAGAGTAAAAGATAAGATAATGAACACAAGAATTTATAGTGTTCAACTTCTCAATTAAGTCTAC
325888 CTCCACTACCTTAGCTCCACACTAAGGATTTTCTAATAAATTCACTATTTTGTTCTTTCTTTTTA
66 CTCCACTACCTTAGCTCCACACTAAGGATTTTCTAATAAATTCACTATTTTGTTCTTTCTTTTTA
325953 AAG
131 AAG
325956 GGAGAGTAAAAGATAAGAT-ATGAACACAAGAATTTATAGTGTTTCAACTTCTCAATTAAGTCTA
1 GGAGAGTAAAAGATAAGATAATGAACACAAGAATTTATAGTG-TTCAACTTCTCAATTAAGTCTA
326020 CCTCCACTACCTTAGCTCCACACTAAGGATTTTCTAATAAATTCACTATTTTGTTCTTTCTTTTT
65 CCTCCACTACCTTAGCTCCACACTAAGGATTTTCTAATAAATTCACTATTTTGTTCTTTCTTTTT
326085 AAAG
130 AAAG
326089 G
1 G
326090 ATCAAGAGAT
Statistics
Matches: 133, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
132 22 0.17
133 111 0.83
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (133 bp):
GGAGAGTAAAAGATAAGATAATGAACACAAGAATTTATAGTGTTCAACTTCTCAATTAAGTCTAC
CTCCACTACCTTAGCTCCACACTAAGGATTTTCTAATAAATTCACTATTTTGTTCTTTCTTTTTA
AAG
Found at i:331473 original size:20 final size:20
Alignment explanation
Indices: 331445--331482 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
331435 GGCCGTTTCT
* *
331445 AGCCGTTGGGGATGATTTGG
1 AGCCATTGGGGATAATTTGG
331465 AGCCATTGGGGATAATTT
1 AGCCATTGGGGATAATTT
331483 TTTTGCAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (20 bp):
AGCCATTGGGGATAATTTGG
Found at i:335457 original size:21 final size:21
Alignment explanation
Indices: 335433--335487 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
335423 ACCCTACGGT
*
335433 GGTGGTATCTGAACTGGCTGC
1 GGTGGCATCTGAACTGGCTGC
* *
335454 GGTGGCGTCTGAATTGGCTGC
1 GGTGGCATCTGAACTGGCTGC
*
335475 GGTGCCATCTGAA
1 GGTGGCATCTGAA
335488 GTAGTTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.15, C:0.20, G:0.38, T:0.27
Consensus pattern (21 bp):
GGTGGCATCTGAACTGGCTGC
Found at i:335513 original size:21 final size:21
Alignment explanation
Indices: 335472--335513 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
335462 CTGAATTGGC
* * *
335472 TGCGGTGCCATCTGAAGTAGT
1 TGCGATGCCATCTAAAATAGT
335493 TGCGATGCCATCTAAAATAGT
1 TGCGATGCCATCTAAAATAGT
335514 GGTTTACCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (21 bp):
TGCGATGCCATCTAAAATAGT
Found at i:337776 original size:16 final size:16
Alignment explanation
Indices: 337755--337786 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
337745 ATATTATCCG
*
337755 ATCCGAATTTTCGGAT
1 ATCCGAAATTTCGGAT
337771 ATCCGAAATTTCGGAT
1 ATCCGAAATTTCGGAT
337787 CGGATATCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (16 bp):
ATCCGAAATTTCGGAT
Found at i:347780 original size:21 final size:21
Alignment explanation
Indices: 347762--347880 Score: 80
Period size: 21 Copynumber: 5.7 Consensus size: 21
347752 ATAAAGCAAG
347762 GGAAGCAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
** *
347783 GGAAGCAGCTAGAGCAGTAGC
1 GGAAGCAGAGAGAGCAGCAGC
* * *
347804 GGAAGCAGAGAAAGAAGCAGT
1 GGAAGCAGAGAGAGCAGCAGC
* * *
347825 GGCAGCACAGATAG-AGGCAGC
1 GGAAGCAGAGAGAGCA-GCAGC
* * *
347846 -GACAGCACAGAGAGAAGCAGT
1 GGA-AGCAGAGAGAGCAGCAGC
* *
347867 GGCAGCACAGAGAG
1 GGAAGCAGAGAGAG
347881 AAGTAATATA
Statistics
Matches: 77, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.03
21 73 0.95
22 2 0.03
ACGTcount: A:0.39, C:0.18, G:0.39, T:0.04
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:347881 original size:21 final size:21
Alignment explanation
Indices: 347807--347883 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
347797 CAGTAGCGGA
* *
347807 AGCAGAGAAAGAAGCAGTGGC
1 AGCACAGAGAGAAGCAGTGGC
* * * *
347828 AGCACAGATAGAGGCAGCGAC
1 AGCACAGAGAGAAGCAGTGGC
347849 AGCACAGAGAGAAGCAGTGGC
1 AGCACAGAGAGAAGCAGTGGC
347870 AGCACAGAGAGAAG
1 AGCACAGAGAGAAG
347884 TAATATATCA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.42, C:0.18, G:0.36, T:0.04
Consensus pattern (21 bp):
AGCACAGAGAGAAGCAGTGGC
Found at i:348283 original size:43 final size:42
Alignment explanation
Indices: 348222--348460 Score: 198
Period size: 43 Copynumber: 5.5 Consensus size: 42
348212 CATACATTTA
* *
348222 GCGGCGTTT-TTGATAAAAACGCCGCTAAATCTCAATACATATT
1 GCGGCGTTTGTTG--AAAAACGCCGCTAAATATCAATACCTATT
* * * * *
348265 GCGGCGTTTGTAGGAAAAACGTCAG-TAAAAATCAACATCTATT
1 GCGGCGTTTGT-TGAAAAACG-CCGCTAAATATCAATACCTATT
*
348308 GCGGCGTTTG-TGAAGAAAACGCCGCTAAACATCAACT-CCTATT
1 GCGGCGTTTGTTG-A-AAAACGCCGCTAAATATCAA-TACCTATT
** * * *
348351 GCGGCGTTTGTTTGCCAAATGCCGTTAAATATCAACACCTATT
1 GCGGCGTTTG-TTGAAAAACGCCGCTAAATATCAATACCTATT
* ** *
348394 GCGGCGTTTTTCTGCCAAACGCCGCTAAATATCAATACCTTTT
1 GCGGCGTTTGT-TGAAAAACGCCGCTAAATATCAATACCTATT
*
348437 GCGGCATTTGTTGAACAAACGCCG
1 GCGGCGTTTGTTGAA-AAACGCCG
348461 TTATATGTTG
Statistics
Matches: 157, Mismatches: 27, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
41 1 0.01
42 6 0.04
43 144 0.92
44 3 0.02
45 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (42 bp):
GCGGCGTTTGTTGAAAAACGCCGCTAAATATCAATACCTATT
Found at i:348448 original size:86 final size:86
Alignment explanation
Indices: 348238--348490 Score: 214
Period size: 86 Copynumber: 2.9 Consensus size: 86
348228 TTTTTGATAA
* * * * *
348238 AAACGCCGCTAAATC-TCAA-TACATATTGCGGCGTTTGTAGGAA-AAACGTCAG-TAAAAATCA
1 AAACGCCGCTAAA-CATCAACT-CCTATTGCGGCATTTGT-TGAACAAACG-CCGTTAAATATCA
* *** *
348299 ACATCTATTGCGGCGTTTGTGAAG-A
62 ACACCTATTGCGGCGTTT-TTCTGCC
* * *
348324 AAACGCCGCTAAACATCAACTCCTATTGCGGCGTTTGTTTG-CCAAATGCCGTTAAATATCAACA
1 AAACGCCGCTAAACATCAACTCCTATTGCGGCATTTG-TTGAACAAACGCCGTTAAATATCAACA
348388 CCTATTGCGGCGTTTTTCTGCC
65 CCTATTGCGGCGTTTTTCTGCC
* * * * ***
348410 AAACGCCGCTAAATATCAA-TACCTTTTGCGGCATTTGTTGAACAAACGCCGTTATATGTTGTCA
1 AAACGCCGCTAAACATCAACT-CCTATTGCGGCATTTGTTGAACAAACGCCGTTAAATATCAACA
348474 CCTATTGCGGCGTTTTT
65 CCTATTGCGGCGTTTTT
348491 TGTTGAAAAA
Statistics
Matches: 138, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
85 9 0.07
86 127 0.92
87 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (86 bp):
AAACGCCGCTAAACATCAACTCCTATTGCGGCATTTGTTGAACAAACGCCGTTAAATATCAACAC
CTATTGCGGCGTTTTTCTGCC
Found at i:354022 original size:23 final size:22
Alignment explanation
Indices: 353991--354054 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
353981 TAGGAGGAAT
*
353991 CGATACCCCCTTGAAGGGAAAC
1 CGATTCCCCCTTGAAGGGAAAC
* * *
354013 TGATTTCCCCTTTGAAGGGGAAC
1 CGA-TTCCCCCTTGAAGGGAAAC
354036 CGATTCCCCCTTG-AGGGAA
1 CGATTCCCCCTTGAAGGGAA
354055 TCGATCCCCC
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
21 5 0.15
22 11 0.32
23 18 0.53
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (22 bp):
CGATTCCCCCTTGAAGGGAAAC
Found at i:356436 original size:23 final size:23
Alignment explanation
Indices: 356410--356465 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
356400 ACCGGTCATA
*
356410 ACCCGACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGACCCATTG
* *
356433 ACCCGACCCGACTCGACCTATTG
1 ACCCGACCCGACCCGACCCATTG
356456 ACCCGACCCG
1 ACCCGACCCG
356466 TTGACTGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.50, G:0.20, T:0.11
Consensus pattern (23 bp):
ACCCGACCCGACCCGACCCATTG
Found at i:356437 original size:13 final size:13
Alignment explanation
Indices: 356419--356470 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
356409 AACCCGACCC
356419 GACCCGACCCGTT
1 GACCCGACCCGTT
356432 GACCCGACCC---
1 GACCCGACCCGTT
* **
356442 GACTCGACCTATT
1 GACCCGACCCGTT
356455 GACCCGACCCGTT
1 GACCCGACCCGTT
356468 GAC
1 GAC
356471 TGTTGACCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
10 8 0.26
13 23 0.74
ACGTcount: A:0.19, C:0.44, G:0.21, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:357769 original size:18 final size:18
Alignment explanation
Indices: 357743--357778 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
357733 TCGAAAGGAC
*
357743 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
357761 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
357779 CGGATGACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:358963 original size:24 final size:24
Alignment explanation
Indices: 358936--359001 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
358926 ACCTGAATCA
* *
358936 TGTTCTGATTTCTGATCTGGATTC
1 TGTTCTGATTTCTGATATGAATTC
*
358960 TGTTCTGATATCTGATATGAATTC
1 TGTTCTGATTTCTGATATGAATTC
* *
358984 TGTTTTGATTTTTGATAT
1 TGTTCTGATTTCTGATAT
359002 CTCCGTTTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTCTGATTTCTGATATGAATTC
Found at i:360561 original size:24 final size:24
Alignment explanation
Indices: 360534--360599 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
360524 GTAAACGGAG
* * *
360534 ATATCAAAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATCC
*
360558 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATCC
*
360582 AGATCAGAAATCAGAACA
1 ATATCAGAAATCAGAACA
360600 TGATTCAGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.53, C:0.18, G:0.11, T:0.18
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATCC
Found at i:360642 original size:24 final size:24
Alignment explanation
Indices: 360541--360644 Score: 81
Period size: 24 Copynumber: 4.3 Consensus size: 24
360531 GAGATATCAA
*
360541 AAATCAAAACAGAATTCATA-TCAG
1 AAATCAGAACAGAATTCA-AGTCAG
* *
360565 ATATCAGAACAGAA-TCCAGATCAG
1 AAATCAGAACAGAATTCAAG-TCAG
* *
360589 AAATCAGAACATG-ATTCAGGTAATG
1 AAATCAGAACA-GAATTCAAGTCA-G
* *
360614 -TATCATAACAGAATTCAAGTCAG
1 AAATCAGAACAGAATTCAAGTCAG
360637 AAATCAGA
1 AAATCAGA
360645 TAAAATATTT
Statistics
Matches: 60, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
22 1 0.02
23 4 0.07
24 50 0.83
25 5 0.08
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.21
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAAGTCAG
Found at i:361778 original size:18 final size:18
Alignment explanation
Indices: 361757--361792 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
361747 CTGTCATCCG
*
361757 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
361775 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
361793 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:363135 original size:13 final size:13
Alignment explanation
Indices: 363117--363161 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
363107 CAACGATCAA
363117 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
363130 CGGGTCAACAGGT
1 CGGGTCAACGGGT
*
363143 CGGGTAAACGGGT
1 CGGGTCAACGGGT
363156 CGGGTC
1 CGGGTC
363162 GGGTCGGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.18, C:0.22, G:0.44, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:364201 original size:40 final size:41
Alignment explanation
Indices: 364146--364267 Score: 205
Period size: 40 Copynumber: 3.0 Consensus size: 41
364136 TGTAGGTTTA
364146 TAATACAC-TTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
364186 TAATATA-TTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
364226 TAATACACTTT-AGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTTCGGTGTATATGGTGGGCACGACCTTATGTG
364266 TA
1 TA
364268 GCACTACAGT
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
40 74 0.96
41 3 0.04
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (41 bp):
TAATACACTTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:364467 original size:45 final size:45
Alignment explanation
Indices: 364372--364657 Score: 430
Period size: 45 Copynumber: 6.4 Consensus size: 45
364362 GTAAGTACGC
* * * **
364372 AAATAAGCTTACGAGCTTATGAAAT-AATGACAAGTATATTGGTA
1 AAATAAGCTTATGAGCTTATGGAATAAAAGGTAAGTATATTGGTA
364416 AAATAAGCTTATGAGCTTATGGAATAAAAGGTAAGTATATTGGTA
1 AAATAAGCTTATGAGCTTATGGAATAAAAGGTAAGTATATTGGTA
* *
364461 AAATAAGCTTATGAGCTTATGGAATAAAATGTAAGTATATTAGTA
1 AAATAAGCTTATGAGCTTATGGAATAAAAGGTAAGTATATTGGTA
* * *
364506 AAATAAGTTTATGAGCTAATGAAATAAAAGGTAAGTATATTGGTA
1 AAATAAGCTTATGAGCTTATGGAATAAAAGGTAAGTATATTGGTA
364551 AAATAAGCTTATGAGCTTATGGAATAAAAGGTAAGTATATTGGTA
1 AAATAAGCTTATGAGCTTATGGAATAAAAGGTAAGTATATTGGTA
* * * *
364596 AAACAAGCTTATGAGCTTATGGAATTAATGGTAAGTATATTGATA
1 AAATAAGCTTATGAGCTTATGGAATAAAAGGTAAGTATATTGGTA
*
364641 AAATAAGCTTACGAGCT
1 AAATAAGCTTATGAGCT
364658 CATAGGATAA
Statistics
Matches: 220, Mismatches: 21, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
44 23 0.10
45 197 0.90
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAAAAGGTAAGTATATTGGTA
Found at i:365750 original size:16 final size:16
Alignment explanation
Indices: 365711--365758 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
365701 TCAAACTAAA
* *
365711 ATAAAATTT-TATTTA
1 ATAAAATTTATATATG
*
365726 ATAATATTTATATATG
1 ATAAAATTTATATATG
*
365742 ATAAAATTTAAATATG
1 ATAAAATTTATATATG
365758 A
1 A
365759 CCTTTCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 8 0.30
16 19 0.70
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (16 bp):
ATAAAATTTATATATG
Found at i:371118 original size:30 final size:30
Alignment explanation
Indices: 371079--371303 Score: 102
Period size: 30 Copynumber: 7.5 Consensus size: 30
371069 TTAAAGCATG
* * * *
371079 AACTCAAAGGATTAAAATAGCATAAACAGA
1 AACTTAAAGGACTAAAATAGAAAAAACAGA
* * *
371109 AATTTAAAGGACTAAAATGGAAAAAATAGA
1 AACTTAAAGGACTAAAATAGAAAAAACAGA
*
371139 AACTTAAAGGACT-AAATA-ACAAAAATAGA
1 AACTTAAAGGACTAAAATAGA-AAAAACAGA
* *** * ** *
371168 AAATTAAATTCCTAAAACA-ATAATTATAGA
1 AACTTAAAGGACTAAAATAGA-AAAAACAGA
* *
371198 AACTTAAAGGACCAACAA-AGAAAAAATAGA
1 AACTTAAAGGACTAA-AATAGAAAAAACAGA
* * ** *
371228 GACTTAAGGGGA-TAAAATATCAAAAATAGA
1 AACTTAA-AGGACTAAAATAGAAAAAACAGA
* * * *
371258 AATTTAAAAGG-CTAAAATAGGAAAAATATA
1 AACTT-AAAGGACTAAAATAGAAAAAACAGA
* *
371288 AAGTTAAATGACTAAA
1 AACTTAAAGGACTAAA
371304 TTGGTATTAA
Statistics
Matches: 149, Mismatches: 37, Indels: 18
0.73 0.18 0.09
Matches are distributed among these distances:
28 1 0.01
29 28 0.19
30 112 0.75
31 8 0.05
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.20
Consensus pattern (30 bp):
AACTTAAAGGACTAAAATAGAAAAAACAGA
Found at i:372550 original size:3 final size:3
Alignment explanation
Indices: 372538--372566 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
372528 TGCAAACATT
372538 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
372567 TTTTTTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:372859 original size:64 final size:65
Alignment explanation
Indices: 372728--372850 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 65
372718 TCATACGTGC
* * * *
372728 TGAAGACTTCTGGTCGTCTAAGGGTTGACACGACTCCTACGTGATGAGGAGATCTGGTCATGGGA
1 TGAAGACTTCTGGTCATCTAAGGGTTGACACGACTCATACATAATGAGGAGATCTGGTCATGGGA
* * **
372793 TGAAGAGTTCTGGTTATC-AAGGGTTGACACGGTTCATACATAATGAGGAGATCTGGTC
1 TGAAGACTTCTGGTCATCTAAGGGTTGACACGACTCATACATAATGAGGAGATCTGGTC
372851 GAGTGATGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
64 35 0.70
65 15 0.30
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (65 bp):
TGAAGACTTCTGGTCATCTAAGGGTTGACACGACTCATACATAATGAGGAGATCTGGTCATGGGA
Found at i:373021 original size:126 final size:126
Alignment explanation
Indices: 372815--373526 Score: 1014
Period size: 126 Copynumber: 5.7 Consensus size: 126
372805 GTTATCAAGG
* * * * *
372815 GTTGACACGGTTCATACATAATGAGGAGATCTGGTC-GAGTGATGATATTGCTCACCTG-TCATG
1 GTTGACACAGCTCCTACATAATGAGGAGATCTGGTCAG-GTGATGACATTGCTCATCTGTTCATG
* *
372878 AGTCTTGGCCATCTAAGGGTGATAACACAATTCCTACGTGATGAGGACGATTGGTTATCTGA
65 AGTCTTGGCCATCTAAGGGTGATAACACAGTTCCTACGTGATGAGGACGGTTGGTTATCTGA
* * *
372940 GTTAACACAACTCCTACATAATGAGGAGGTCTGGTCAGGTGATGACATTGCTCATCTGTTCATGA
1 GTTGACACAGCTCCTACATAATGAGGAGATCTGGTCAGGTGATGACATTGCTCATCTGTTCATGA
* ** * **
373005 GTCTTGGCCATCTAAGGTTGATAACATGGTTCCTACGTGATGAGGATGACTGGTTATCTGA
66 GTCTTGGCCATCTAAGGGTGATAACACAGTTCCTACGTGATGAGGACGGTTGGTTATCTGA
* * * * * *
373066 GTTGACATAGCTCCTACATAATGAGGAGATATGTTTAGGTGATGACATTACTCATCTATTCATGA
1 GTTGACACAGCTCCTACATAATGAGGAGATCTGGTCAGGTGATGACATTGCTCATCTGTTCATGA
* ** ** * * *
373131 GCCTTAACCATCTAAGGGTGATAACATGGTTCATAAGTGATGAGGACGGCTGGTTATCTGA
66 GTCTTGGCCATCTAAGGGTGATAACACAGTTCCTACGTGATGAGGACGGTTGGTTATCTGA
*
373192 GTTGACACAGCTCCTACATAATGAGGAGATCTGGTCAGGTGATGACATTGCTCATTTGTTCATGA
1 GTTGACACAGCTCCTACATAATGAGGAGATCTGGTCAGGTGATGACATTGCTCATCTGTTCATGA
* *
373257 GTCTTGGCCATCTAAGGGTAATAACACAGTTCCTATGTGATGAGGACGGTTGGTTATCTGA
66 GTCTTGGCCATCTAAGGGTGATAACACAGTTCCTACGTGATGAGGACGGTTGGTTATCTGA
* * *
373318 GTTGACGCAACTCCTACATAATGAGGAGATCTGGTCAGGTGATGACATTGCTCATGTGTTCATGA
1 GTTGACACAGCTCCTACATAATGAGGAGATCTGGTCAGGTGATGACATTGCTCATCTGTTCATGA
* **
373383 GTCTTGGCCATCTAAGGGTGATAACACAGTTCCTACATGATGAGGGTGGTTGGTTATCTGA
66 GTCTTGGCCATCTAAGGGTGATAACACAGTTCCTACGTGATGAGGACGGTTGGTTATCTGA
* * * *
373444 TTTGACACAGCTCCTACATAATGAGGAGATTTGATCAGGTGATGACACTGCTCATCTGTTCATGA
1 GTTGACACAGCTCCTACATAATGAGGAGATCTGGTCAGGTGATGACATTGCTCATCTGTTCATGA
373509 GTCTTGGCCATCTAAGGG
66 GTCTTGGCCATCTAAGGG
373527 ATTTTGGTTT
Statistics
Matches: 523, Mismatches: 62, Indels: 3
0.89 0.11 0.01
Matches are distributed among these distances:
125 48 0.09
126 475 0.91
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (126 bp):
GTTGACACAGCTCCTACATAATGAGGAGATCTGGTCAGGTGATGACATTGCTCATCTGTTCATGA
GTCTTGGCCATCTAAGGGTGATAACACAGTTCCTACGTGATGAGGACGGTTGGTTATCTGA
Found at i:373834 original size:32 final size:32
Alignment explanation
Indices: 373785--373873 Score: 119
Period size: 32 Copynumber: 2.8 Consensus size: 32
373775 TTCGCATCAG
*
373785 GATGTTGAATC-CACAAAGATGCCCCAATATTT
1 GATGTTGAATCTC-CAAAGATGCCCCAACATTT
373817 GATGTCT-AATCTCCAAAGATGCCCCAACATTT
1 GATGT-TGAATCTCCAAAGATGCCCCAACATTT
* *
373849 GTTGTTGAATCTTCAAAGATGCCCC
1 GATGTTGAATCTCCAAAGATGCCCC
373874 CATTGTTCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
31 1 0.02
32 48 0.94
33 2 0.04
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCCAACATTT
Found at i:374042 original size:24 final size:22
Alignment explanation
Indices: 374015--374073 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 22
374005 TTTCAAGATC
*
374015 TGAAAATATTAATTAGAAGAGTTT
1 TGAAAATATTAATCA-AAGA-TTT
*
374039 TGAAAAATGTTTAATCAAAGATTT
1 TG-AAAAT-ATTAATCAAAGATTT
374063 TGAAAATATTA
1 TGAAAATATTA
374074 CCCCTTTCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 3 0.10
23 5 0.17
24 7 0.23
25 9 0.30
26 6 0.20
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (22 bp):
TGAAAATATTAATCAAAGATTT
Found at i:377946 original size:27 final size:27
Alignment explanation
Indices: 377916--377985 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
377906 GCTTAAAATG
*
377916 AAATGCAGATGCAAAATGAAAATATGC
1 AAATGCAGATGCAAAATGAAAAGATGC
* * *
377943 AAATACAGATGAAAAATGCAAAGATGC
1 AAATGCAGATGCAAAATGAAAAGATGC
*
377970 AAATGTAGATGCAAAA
1 AAATGCAGATGCAAAA
377986 ATGTTGATCC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.54, C:0.10, G:0.19, T:0.17
Consensus pattern (27 bp):
AAATGCAGATGCAAAATGAAAAGATGC
Found at i:378533 original size:32 final size:32
Alignment explanation
Indices: 378497--378558 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
378487 ATGAAAAATG
*
378497 ACACAAA-TAAAAGAAAAGAAATAAGTTAGTGT
1 ACACAAACAAAAAG-AAAGAAATAAGTTAGTGT
* *
378529 ACACAAACAAAAAGAAAGAGATCAGTTAGT
1 ACACAAACAAAAAGAAAGAAATAAGTTAGT
378559 ACAGGTAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 21 0.81
33 5 0.19
ACGTcount: A:0.58, C:0.10, G:0.16, T:0.16
Consensus pattern (32 bp):
ACACAAACAAAAAGAAAGAAATAAGTTAGTGT
Found at i:378906 original size:37 final size:37
Alignment explanation
Indices: 378853--378923 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
378843 CACACATTTT
*
378853 GTCCTACTAGGGTTCAAACTCCTAAAAATAGGATAGA
1 GTCCTACTAGGATTCAAACTCCTAAAAATAGGATAGA
*
378890 GTCCTACTAGGATTCAAACTCCTAAAGATAGGAT
1 GTCCTACTAGGATTCAAACTCCTAAAAATAGGAT
378924 CCACAAGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (37 bp):
GTCCTACTAGGATTCAAACTCCTAAAAATAGGATAGA
Found at i:379577 original size:21 final size:20
Alignment explanation
Indices: 379542--379650 Score: 62
Period size: 21 Copynumber: 5.2 Consensus size: 20
379532 TTCATCTATC
*
379542 ATTATTATTTATATATTTTTT
1 ATTACTATTT-TATATTTTTT
*
379563 ATTACTATTATTATATGTTATAT
1 ATTACTATT-TTATAT-TT-TTT
* *
379586 ATTTATTATTTTATATATTTT
1 A-TTACTATTTTATATTTTTT
*
379607 ATT-TTATCTTCTAT-TTTTTT
1 ATTACTAT-TT-TATATTTTTT
*
379627 ATCTTCTATTTT-TATTTTTGT
1 AT-TACTATTTTATATTTTT-T
379648 ATT
1 ATT
379651 GTTATTGTTA
Statistics
Matches: 71, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
19 5 0.07
20 18 0.25
21 25 0.35
22 7 0.10
23 9 0.13
24 7 0.10
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.69
Consensus pattern (20 bp):
ATTACTATTTTATATTTTTT
Found at i:379584 original size:30 final size:30
Alignment explanation
Indices: 379537--379595 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
379527 TCTTTTTCAT
*
379537 CTATCATTATTATTTATATATTTTTTATTA
1 CTATCATTATTATTTATATATTTATTATTA
*
379567 CTATTATTA-TATGTTATATATTTATTATT
1 CTATCATTATTAT-TTATATATTTATTATT
379596 TTATATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (30 bp):
CTATCATTATTATTTATATATTTATTATTA
Found at i:379586 original size:9 final size:9
Alignment explanation
Indices: 379549--379608 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
379539 ATCATTATTA
379549 TTTATATAT
1 TTTATATAT
*
379558 TTTTTATTACT
1 TTTATA-TA-T
*
379569 ATTATTATAT
1 TTTA-TATAT
*
379579 GTTATATA-
1 TTTATATAT
379587 TTTAT-TAT
1 TTTATATAT
379595 TTTATATAT
1 TTTATATAT
379604 TTTAT
1 TTTAT
379609 TTTATCTTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
7 2 0.05
8 9 0.22
9 17 0.41
10 6 0.15
11 5 0.12
12 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTATATAT
Found at i:379628 original size:15 final size:15
Alignment explanation
Indices: 379608--379639 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
379598 ATATATTTTA
379608 TTTTATCTTCTATTT
1 TTTTATCTTCTATTT
379623 TTTTATCTTCTATTT
1 TTTTATCTTCTATTT
379638 TT
1 TT
379640 ATTTTTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTATCTTCTATTT
Found at i:379628 original size:20 final size:19
Alignment explanation
Indices: 379603--379656 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
379593 ATTTTATATA
379603 TTTTATTTTATCTTCTATTT
1 TTTTATTTTAT-TTCTATTT
*
379623 TTTTATCTTCTATTTTTATTT
1 TTTTAT-TT-TATTTCTATTT
*
379644 TTGTATTGTTATT
1 TTTTATT-TTATT
379657 GTTATTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 11 0.38
21 15 0.52
22 3 0.10
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTTATTTTATTTCTATTT
Found at i:383004 original size:29 final size:28
Alignment explanation
Indices: 382955--383010 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
382945 ATCAAGAATA
*
382955 AAAAAGAAAAGAAGCAAAAAAAGAAAAT
1 AAAAAGAAAACAAGCAAAAAAAGAAAAT
*
382983 AAAAAGAGAAACAAG-AACAAAAGGAAAA
1 AAAAAGA-AAACAAGCAA-AAAAAGAAAA
383011 AAGAGCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (28 bp):
AAAAAGAAAACAAGCAAAAAAAGAAAAT
Found at i:385589 original size:106 final size:106
Alignment explanation
Indices: 385436--385860 Score: 726
Period size: 106 Copynumber: 4.0 Consensus size: 106
385426 TGTGCCACTT
*
385436 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGA-TGGTTGTCAACAAACAATTTCCCAGT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGAC-GATTGGTTGTCAACAAACAATTTCCCAAT
385500 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
65 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* *
385542 GATACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGATTGGTTGTCAACAAACAATTTCCCAATT
*
385607 TCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
66 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* *
385648 GAGACAACACAAGTTCAACTTCACAACGAAGAGATGATTGGTTGTCAACAAACAATTTCCCAATT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGATTGGTTGTCAACAAACAATTTCCCAATT
385713 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
66 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* * * *
385754 GAGACAACACAAGTTCAACTTCACAATGAATGGACGGTTGGCTGTCAACAAACAATTTCCCAATT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGATTGGTTGTCAACAAACAATTTCCCAATT
* *
385819 TCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTC
66 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
385860 G
1 G
385861 GAACAATACA
Statistics
Matches: 302, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
105 2 0.01
106 300 0.99
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
GAGACAACACAAGTTCAACTTCACAACGAAGGGACGATTGGTTGTCAACAAACAATTTCCCAATT
TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
Found at i:386650 original size:37 final size:37
Alignment explanation
Indices: 386588--386694 Score: 151
Period size: 37 Copynumber: 2.9 Consensus size: 37
386578 CACCTTTTCG
*
386588 TCCTACTAGGATTCAAACTCATAAAAATAGGATAGAA
1 TCCTACTAGGATTCAAACTCCTAAAAATAGGATAGAA
** * * *
386625 TTTTATTAGTATTCAAACTCCTAAAAATAGGATAGAG
1 TCCTACTAGGATTCAAACTCCTAAAAATAGGATAGAA
*
386662 TCCTACTAGGATTCAAACTCCTAAAGATAGGAT
1 TCCTACTAGGATTCAAACTCCTAAAAATAGGAT
386695 CCACAAGCAT
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (37 bp):
TCCTACTAGGATTCAAACTCCTAAAAATAGGATAGAA
Found at i:387356 original size:19 final size:20
Alignment explanation
Indices: 387343--387384 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
387333 TTTATTACTA
387343 TTATTATATGTTATATATAT
1 TTATTATATGTTATATATAT
387363 TTATTAT-T-TTATATAT-T
1 TTATTATATGTTATATATAT
387380 TTATT
1 TTATT
387385 TTATCTTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.27
18 8 0.36
19 1 0.05
20 7 0.32
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTATTATATGTTATATATAT
Found at i:387357 original size:32 final size:32
Alignment explanation
Indices: 387308--387370 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
387298 CTTTTTTCAT
387308 CTATCATTATTATTTATATATATATT-TTATTA
1 CTATCATTATTATTTATATATAT-TTATTATTA
*
387340 CTATTATTA-TATGTTATATATATTTATTATT
1 CTATCATTATTAT-TTATATATATTTATTATT
387371 TTATATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (32 bp):
CTATCATTATTATTTATATATATTTATTATTA
Found at i:387359 original size:9 final size:9
Alignment explanation
Indices: 387326--387383 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
387316 ATTATTTATA
387326 TATATATTT
1 TATATATTT
*
387335 TAT-TACTAT
1 TATATA-TTT
*
387344 TATTATATGT
1 TA-TATATTT
387354 TATATATATT
1 TATATAT-TT
387364 TAT-TATTT
1 TATATATTT
387372 TATATATTT
1 TATATATTT
387381 TAT
1 TAT
387384 TTTATCTTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
8 7 0.17
9 23 0.56
10 9 0.22
11 2 0.05
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (9 bp):
TATATATTT
Found at i:387403 original size:15 final size:15
Alignment explanation
Indices: 387383--387414 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
387373 ATATATTTTA
387383 TTTTATCTTCTATTT
1 TTTTATCTTCTATTT
387398 TTTTATCTTCTATTT
1 TTTTATCTTCTATTT
387413 TT
1 TT
387415 ATTTTTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTATCTTCTATTT
Found at i:387403 original size:20 final size:19
Alignment explanation
Indices: 387378--387431 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
387368 ATTTTATATA
387378 TTTTATTTTATCTTCTATTT
1 TTTTATTTTAT-TTCTATTT
*
387398 TTTTATCTTCTATTTTTATTT
1 TTTTAT-TT-TATTTCTATTT
*
387419 TTGTATTGTTATT
1 TTTTATT-TTATT
387432 GTTATTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 11 0.38
21 15 0.52
22 3 0.10
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTTATTTTATTTCTATTT
Found at i:389458 original size:30 final size:30
Alignment explanation
Indices: 389416--389615 Score: 152
Period size: 30 Copynumber: 6.7 Consensus size: 30
389406 AACAACATAT
* *
389416 ACAGAAATTTAAAGGACTAAAATGGCAAAA
1 ACAGAAACTTAAAGGACTAAAATAGCAAAA
* *
389446 ACAAAAACTTAAAGGACT-AAATAGAAAAA
1 ACAGAAACTTAAAGGACTAAAATAGCAAAA
* ** * * **
389475 ATAGAAACTTAAAGTCCTAAAACAGTAATT
1 ACAGAAACTTAAAGGACTAAAATAGCAAAA
* * *
389505 ATAGAAACTTAAAGGACCAACATAGCAAAA
1 ACAGAAACTTAAAGGACTAAAATAGCAAAA
* * * * * *
389535 TCATAGACTTAAGGGGCTAAAATATCAAAA
1 ACAGAAACTTAAAGGACTAAAATAGCAAAA
* *
389565 ACAGGAATTTAAAAGG-CTAAAATAGCAAAA
1 ACAGAAACTT-AAAGGACTAAAATAGCAAAA
* * *
389595 ATATAAAGTTAAAGGACTAAA
1 ACAGAAACTTAAAGGACTAAA
389616 TTGGTATTAA
Statistics
Matches: 127, Mismatches: 40, Indels: 6
0.73 0.23 0.03
Matches are distributed among these distances:
29 28 0.22
30 95 0.75
31 4 0.03
ACGTcount: A:0.56, C:0.12, G:0.14, T:0.19
Consensus pattern (30 bp):
ACAGAAACTTAAAGGACTAAAATAGCAAAA
Found at i:396624 original size:20 final size:20
Alignment explanation
Indices: 396591--396639 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
396581 TTGTTGCGGA
* *
396591 TGCGGTTGCGGTGTCACGGT
1 TGCGGATGCAGTGTCACGGT
396611 TGCGGATGCAGTGTCACGGT
1 TGCGGATGCAGTGTCACGGT
396631 TGCGGATGC
1 TGCGGATGC
396640 TGCGGACCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.10, C:0.20, G:0.43, T:0.27
Consensus pattern (20 bp):
TGCGGATGCAGTGTCACGGT
Found at i:397002 original size:23 final size:23
Alignment explanation
Indices: 396959--397004 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
396949 ATGTTCATTT
*
396959 TACATAACTTAGAAAGAAAAAAA
1 TACATAACTTACAAAGAAAAAAA
* *
396982 TACATAAC-TACAAATATAAAAA
1 TACATAACTTACAAAGAAAAAAA
397004 T
1 T
397005 TCTTTATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.63, C:0.11, G:0.04, T:0.22
Consensus pattern (23 bp):
TACATAACTTACAAAGAAAAAAA
Found at i:397156 original size:3 final size:3
Alignment explanation
Indices: 397148--397206 Score: 75
Period size: 3 Copynumber: 19.3 Consensus size: 3
397138 GGTCAAAAAA
* *
397148 TAT TAT TAT T-T TAAT TAT TAT TAT TAT TAT TAT TAT TGT TGT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
397193 TAT TAT TAGT TAT T
1 TAT TAT TA-T TAT T
397207 TTAAAAATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 2 0.04
3 44 0.86
4 5 0.10
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:401933 original size:20 final size:20
Alignment explanation
Indices: 401891--401946 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
401881 AAAAATATTT
* * *
401891 TATGAATAATAT-TATACTG
1 TATGAATAGTATCGATACTA
401910 TATGAATAGTATCGATACTA
1 TATGAATAGTATCGATACTA
401930 TATGAATAGTATCGATA
1 TATGAATAGTATCGATA
401947 ATGTGTGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 11 0.33
20 22 0.67
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TATGAATAGTATCGATACTA
Found at i:404726 original size:20 final size:20
Alignment explanation
Indices: 404687--404756 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 20
404677 CAAATTTTTT
*
404687 TATGAATAATATTG-TACTG
1 TATGAATAGTATTGATACTG
*
404706 TATGAATAGTACTGATACTG
1 TATGAATAGTATTGATACTG
*
404726 TAT-AATTGTATTAGATACTG
1 TATGAATAGTATT-GATACTG
* *
404746 TGTGAACAGTA
1 TATGAATAGTA
404757 ATGAATAATA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 19 0.46
20 17 0.41
21 5 0.12
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.39
Consensus pattern (20 bp):
TATGAATAGTATTGATACTG
Found at i:407936 original size:12 final size:12
Alignment explanation
Indices: 407919--407944 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
407909 AGTTTCTTTC
407919 TCTAATACTAAT
1 TCTAATACTAAT
407931 TCTAATACTAAT
1 TCTAATACTAAT
407943 TC
1 TC
407945 CTTGGAATTA
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:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (12 bp):
TCTAATACTAAT
Done.