Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 2 of 82
Found at i:119227 original size:17 final size:18
Alignment explanation
Indices: 119202--119246 Score: 67
Period size: 16 Copynumber: 2.6 Consensus size: 18
119192 AAATATTTAT
119202 AATATTATAATTAAAATAA
1 AATA-TATAATTAAAATAA
119221 AA-ATAT-ATTAAAATAA
1 AATATATAATTAAAATAA
119237 AATATATAAT
1 AATATATAAT
119247 ATAAGAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 12 0.50
17 7 0.29
18 3 0.12
19 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATATATAATTAAAATAA
Found at i:119240 original size:15 final size:15
Alignment explanation
Indices: 119211--119359 Score: 65
Period size: 15 Copynumber: 9.8 Consensus size: 15
119201 TAATATTATA
119211 ATTAAAATAAAAATAT
1 ATTAAAAT-AAAATAT
119227 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
*
119242 A-TAATATAAGAAT-T
1 ATTAAAATAA-AATAT
* * *
119256 A-GAAATTAAAATAA
1 ATTAAAATAAAATAT
** * *
119270 AACAAAATAAAAGAA
1 ATTAAAATAAAATAT
**
119285 ATTAAAAT-TTATAT
1 ATTAAAATAAAATAT
* * * *
119299 AATATAAGTAAAAGAA
1 ATTA-AAATAAAATAT
119315 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
*
119330 ATAATATAAA-AAATTAT
1 AT--TA-AAATAAAATAT
119347 ATTAAAAATAAAA
1 ATT-AAAATAAAA
119360 NNNNNNNNNN
Statistics
Matches: 97, Mismatches: 26, Indels: 20
0.68 0.18 0.14
Matches are distributed among these distances:
13 3 0.03
14 20 0.21
15 44 0.45
16 17 0.18
17 10 0.10
18 3 0.03
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (15 bp):
ATTAAAATAAAATAT
Found at i:119247 original size:22 final size:22
Alignment explanation
Indices: 119203--119249 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
119193 AATATTTATA
*
119203 ATATTATAATTAAAATAAAAAT
1 ATATTATAAATAAAATAAAAAT
*
119225 ATATTA-AAATAAAATATATAAT
1 ATATTATAAATAAAATA-AAAAT
119247 ATA
1 ATA
119250 AGAATTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATTATAAATAAAATAAAAAT
Found at i:119645 original size:23 final size:23
Alignment explanation
Indices: 119580--119645 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
119570 ATAAATAAAA
*
119580 ATTATAATATTATAATTTTTTACAT
1 ATTA-AATATTATAA-TATTTACAT
* * ** *
119605 TTTAATTATTATTTTATTTATAT
1 ATTAAATATTATAATATTTACAT
119628 ATTAAATATTATAATATT
1 ATTAAATATTATAATATT
119646 ATTTTTTTTA
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
23 21 0.68
24 7 0.23
25 3 0.10
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
ATTAAATATTATAATATTTACAT
Found at i:125867 original size:24 final size:25
Alignment explanation
Indices: 125834--125882 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
125824 CTCTAATTTT
125834 TTTTCAAAGTTATATTTCACAACAC
1 TTTTCAAAGTTATATTTCACAACAC
*
125859 TTTT-AAAGTTATATTTTACAACAC
1 TTTTCAAAGTTATATTTCACAACAC
125883 GTTATCAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (25 bp):
TTTTCAAAGTTATATTTCACAACAC
Found at i:129744 original size:19 final size:20
Alignment explanation
Indices: 129720--129770 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
129710 ATATATATCA
*
129720 ATATCCATTGTATTTTAT-G
1 ATATCCAATGTATTTTATGG
*
129739 ATATCCAATAT-TTTTATGG
1 ATATCCAATGTATTTTATGG
129758 ATATCCAATGTAT
1 ATATCCAATGTAT
129771 ATATTTACGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.22
19 20 0.74
20 1 0.04
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (20 bp):
ATATCCAATGTATTTTATGG
Found at i:134347 original size:2 final size:2
Alignment explanation
Indices: 134340--134370 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
134330 TTACAAAGAC
134340 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
134371 AGAGAGAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:138515 original size:14 final size:14
Alignment explanation
Indices: 138496--138525 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
138486 TATGAATTAT
138496 TTACATATACATAA
1 TTACATATACATAA
138510 TTACATATACATAA
1 TTACATATACATAA
138524 TT
1 TT
138526 TATATATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
TTACATATACATAA
Found at i:140815 original size:2 final size:2
Alignment explanation
Indices: 140808--140833 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
140798 ATGATGGGTG
140808 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
140834 AGTGTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:144997 original size:3 final size:3
Alignment explanation
Indices: 144946--144982 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
144936 GATAAAAGAC
*
144946 ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
144983 GAGGAAGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:151226 original size:23 final size:23
Alignment explanation
Indices: 151196--151240 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
151186 TAGAATAACA
*
151196 ATTCCTAATTCTATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
151219 ATTCCTAATTATATTAGGATAA
1 ATTCCTAATTATATTAGGATAA
151241 AGTTATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (23 bp):
ATTCCTAATTATATTAGGATAAG
Found at i:155601 original size:27 final size:27
Alignment explanation
Indices: 155562--155657 Score: 95
Period size: 27 Copynumber: 3.5 Consensus size: 27
155552 CCTGGAGTTA
* *
155562 ATGAATACTTTTAACCTACTAAGAATGG
1 ATGAATACTTTTAAAC-ACCAAGAATGG
**
155590 -TGAATACTTTTAAACACCAAGTGTGG
1 ATGAATACTTTTAAACACCAAGAATGG
* * *
155616 ATGAATACTTTTAAACAACAAAGAGTAG
1 ATGAATACTTTTAAAC-ACCAAGAATGG
*
155644 ATTAATACTTTTAA
1 ATGAATACTTTTAA
155658 CCATAAAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 8 0.14
27 29 0.50
28 21 0.36
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (27 bp):
ATGAATACTTTTAAACACCAAGAATGG
Found at i:159433 original size:41 final size:41
Alignment explanation
Indices: 159384--159490 Score: 205
Period size: 41 Copynumber: 2.6 Consensus size: 41
159374 GTATTAAGGT
159384 TAGGGTTAGGGTAGTAATTTTTAAATTATTCGGATAGTTAA
1 TAGGGTTAGGGTAGTAATTTTTAAATTATTCGGATAGTTAA
159425 TAGGGTTAGGGTAGTAATTTTTAAATTATTCGGATAGTTAA
1 TAGGGTTAGGGTAGTAATTTTTAAATTATTCGGATAGTTAA
159466 TAGGGTTAGGGTAGTTAATTTTTAA
1 TAGGGTTAGGGTAG-TAATTTTTAA
159491 TAGGGTTAGG
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 55 0.85
42 10 0.15
ACGTcount: A:0.31, C:0.02, G:0.25, T:0.42
Consensus pattern (41 bp):
TAGGGTTAGGGTAGTAATTTTTAAATTATTCGGATAGTTAA
Found at i:163223 original size:39 final size:41
Alignment explanation
Indices: 163148--163233 Score: 113
Period size: 39 Copynumber: 2.1 Consensus size: 41
163138 TTGGCCATTG
* * *
163148 TTCACCTTAGTGGGGTTTTCTAATCTTGTCAAGATTG-GTT
1 TTCACCTTAATGGGGTTTTCTAACCTTGCCAAGATTGAGTT
*
163188 TTCACCTTAATGGGG-TTTCTAACCTTGCCATGATTGATGTT
1 TTCACCTTAATGGGGTTTTCTAACCTTGCCAAGATTGA-GTT
163229 TTCAC
1 TTCAC
163234 AACACCCTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
39 18 0.45
40 14 0.35
41 8 0.20
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.43
Consensus pattern (41 bp):
TTCACCTTAATGGGGTTTTCTAACCTTGCCAAGATTGAGTT
Found at i:168266 original size:21 final size:21
Alignment explanation
Indices: 168228--168268 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
168218 ATTCTTTTAA
* * *
168228 CCCACCAATAGTGGATGAATG
1 CCCACCAAGAGCGCATGAATG
168249 CCCACCAAGAGCGCATGAAT
1 CCCACCAAGAGCGCATGAAT
168269 ACTTTAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.22, T:0.15
Consensus pattern (21 bp):
CCCACCAAGAGCGCATGAATG
Found at i:168313 original size:27 final size:28
Alignment explanation
Indices: 168275--168340 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
168265 GAATACTTTA
* *
168275 AATACTTTTAAA-TACCAGGAGTGGATG
1 AATACTTTTAAACCACCAGGAGTGAATG
*
168302 AATACTTTTAAACCACTAGGAGTGAATG
1 AATACTTTTAAACCACCAGGAGTGAATG
168330 AATACTTTTAA
1 AATACTTTTAA
168341 CCATTATGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 12 0.34
28 23 0.66
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (28 bp):
AATACTTTTAAACCACCAGGAGTGAATG
Found at i:168351 original size:27 final size:28
Alignment explanation
Indices: 168275--168360 Score: 113
Period size: 27 Copynumber: 3.1 Consensus size: 28
168265 GAATACTTTA
* *
168275 AATACTTTTAAA-TACCAGGAGTGGATG
1 AATACTTTTAAACCACTAGGAGTGGATG
*
168302 AATACTTTTAAACCACTAGGAGTGAATG
1 AATACTTTTAAACCACTAGGAGTGGATG
* *
168330 AATACTTTT-AACCATTATGAGTGGATG
1 AATACTTTTAAACCACTAGGAGTGGATG
168357 AATA
1 AATA
168361 GTGAAAATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 31 0.60
28 21 0.40
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (28 bp):
AATACTTTTAAACCACTAGGAGTGGATG
Found at i:172679 original size:47 final size:46
Alignment explanation
Indices: 172569--172694 Score: 153
Period size: 47 Copynumber: 2.7 Consensus size: 46
172559 AATAAATTGA
* ** *
172569 AATGAACAAATAATAAATCAAAGCAAAGGTATTTTTTAAGTCAAAT
1 AATGAACAAATAATAAATCAAAGTAAAAATATTTTCTAAGTCAAAT
* * * *
172615 AATGAACAACTACTAAATCTAAGTAAAAATATTTTCCTAAGTCAAGT
1 AATGAACAAATAATAAATCAAAGTAAAAATATTTT-CTAAGTCAAAT
* *
172662 AATGAGCAAATAATAAATCAAAGTAAGAATATT
1 AATGAACAAATAATAAATCAAAGTAAAAATATT
172695 AATGAATCAA
Statistics
Matches: 66, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
46 29 0.44
47 37 0.56
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (46 bp):
AATGAACAAATAATAAATCAAAGTAAAAATATTTTCTAAGTCAAAT
Found at i:174244 original size:21 final size:20
Alignment explanation
Indices: 174198--174241 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
174188 ATTTAATTAT
174198 TTAATTAATTTAATAAAACC
1 TTAATTAATTTAATAAAACC
*
174218 TTAATTAATATTACT-AAACC
1 TTAATTAAT-TTAATAAAACC
174238 TTAA
1 TTAA
174242 ATTTTACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATTAATTTAATAAAACC
Found at i:174394 original size:27 final size:25
Alignment explanation
Indices: 174364--174420 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
174354 ATAAATATAA
*
174364 AATTAACTAAATTATTACTAAAACCTT
1 AATTAACTAAATTA--ACTAAAACATT
* *
174391 AATTAATTTAATTAACTAAAACATT
1 AATTAACTAAATTAACTAAAACATT
174416 -ATTAA
1 AATTAA
174421 ATTATCGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 5 0.19
25 10 0.37
27 12 0.44
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.39
Consensus pattern (25 bp):
AATTAACTAAATTAACTAAAACATT
Found at i:176423 original size:5 final size:6
Alignment explanation
Indices: 176409--176438 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
176399 TAAATTAGTC
*
176409 AAAATA AAAATA AAAATA AAAATA CAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA
176439 TGGCATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:176805 original size:15 final size:17
Alignment explanation
Indices: 176769--176805 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
176759 TTAAATAACA
176769 TATAATCATAGCTAATT
1 TATAATCATAGCTAATT
*
176786 TATAA-CATATCTAA-T
1 TATAATCATAGCTAATT
176801 TATAA
1 TATAA
176806 AAAGAGGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 8 0.42
17 5 0.26
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.41
Consensus pattern (17 bp):
TATAATCATAGCTAATT
Found at i:176886 original size:16 final size:16
Alignment explanation
Indices: 176867--176927 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
176857 GAGAAACTTA
176867 AAATAAAAAAAATAAT
1 AAATAAAAAAAATAAT
* * *
176883 AAATAAATAACATAAA
1 AAATAAAAAAAATAAT
176899 AAATAAATAATAAAATAAT
1 AAAT-AA-AA-AAAATAAT
176918 AAAATAAAAA
1 -AAATAAAAA
176928 TAAACTTCAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
16 17 0.49
17 3 0.09
18 3 0.09
19 8 0.23
20 4 0.11
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.20
Consensus pattern (16 bp):
AAATAAAAAAAATAAT
Found at i:176892 original size:20 final size:19
Alignment explanation
Indices: 176867--176925 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 19
176857 GAGAAACTTA
176867 AAATAAAAAAAATAATAAAT
1 AAATAAAAAAAA-AATAAAT
*
176887 AAATAACATAAAAAATAAAT
1 AAATAA-AAAAAAAATAAAT
176907 -AATAAAATAATAAAATAAA
1 AAATAAAA-AA-AAAATAAA
176926 AATAAACTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 1 0.03
19 7 0.21
20 21 0.62
21 5 0.15
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (19 bp):
AAATAAAAAAAAAATAAAT
Found at i:176906 original size:27 final size:26
Alignment explanation
Indices: 176865--176931 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
176855 AAGAGAAACT
176865 TAAAATAAAAA-AAATAAT-AAATAAA
1 TAAAATAAAAATAAATAATAAAAT-AA
*
176890 TAACATAAAAAATAAATAATAAAATAA
1 TAAAAT-AAAAATAAATAATAAAATAA
176917 TAAAATAAAAATAAA
1 TAAAATAAAAATAAA
176932 CTTCACCAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
25 5 0.14
26 14 0.38
27 14 0.38
28 4 0.11
ACGTcount: A:0.78, C:0.01, G:0.00, T:0.21
Consensus pattern (26 bp):
TAAAATAAAAATAAATAATAAAATAA
Found at i:181829 original size:29 final size:28
Alignment explanation
Indices: 181795--181889 Score: 100
Period size: 29 Copynumber: 3.3 Consensus size: 28
181785 AACATGTTTA
*
181795 TCTTAATTTAGATAAGAAAATATGTTTGG
1 TCTTAATTTAGATAAGAAAATATATTT-G
* *
181824 TCTTAATCTAGATAAGAAAACATATTTG
1 TCTTAATTTAGATAAGAAAATATATTTG
* * * *
181852 TCTCAATTTAGACAAGAAAAATTTTTTTTG
1 TCTTAATTTAGATAAG-AAAA-TATATTTG
181882 TCTTAATT
1 TCTTAATT
181890 AAAGACAAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
28 14 0.26
29 28 0.52
30 12 0.22
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (28 bp):
TCTTAATTTAGATAAGAAAATATATTTG
Found at i:181868 original size:28 final size:28
Alignment explanation
Indices: 181785--181871 Score: 111
Period size: 28 Copynumber: 3.1 Consensus size: 28
181775 TGACAACTTT
*
181785 AACATGTTTATCTTAATTTAGATAAGAA
1 AACATGTTTGTCTTAATTTAGATAAGAA
* *
181813 AATATGTTTGGTCTTAATCTAGATAAGAA
1 AACATGTTT-GTCTTAATTTAGATAAGAA
* * *
181842 AACATATTTGTCTCAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGATAAGAA
181870 AA
1 AA
181872 ATTTTTTTTG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
28 26 0.52
29 24 0.48
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGATAAGAA
Found at i:188066 original size:16 final size:17
Alignment explanation
Indices: 188030--188075 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
188020 CTTTGACTTG
*
188030 AGAAAAGTGAAAGGTAAA
1 AGAAAAGT-AGAGGTAAA
188048 AGAAAAGTAGAGG-AAA
1 AGAAAAGTAGAGGTAAA
*
188064 AGAAAAATAGAG
1 AGAAAAGTAGAG
188076 AACAATGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 14 0.54
17 4 0.15
18 8 0.31
ACGTcount: A:0.63, C:0.00, G:0.28, T:0.09
Consensus pattern (17 bp):
AGAAAAGTAGAGGTAAA
Found at i:188578 original size:19 final size:20
Alignment explanation
Indices: 188544--188594 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
188534 GTGAATGTCT
*
188544 ATTAT-ATTAATATTTAATGA
1 ATTATGATTATTATTTAAT-A
188564 A-TATGA-TATTATTTAATA
1 ATTATGATTATTATTTAATA
188582 ATTATGATTATTA
1 ATTATGATTATTA
188595 ACATGTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.07
19 18 0.67
20 7 0.26
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (20 bp):
ATTATGATTATTATTTAATA
Found at i:194079 original size:27 final size:26
Alignment explanation
Indices: 194041--194141 Score: 96
Period size: 27 Copynumber: 3.7 Consensus size: 26
194031 TTAATAATAA
194041 GAATACTTTTAACCCACCAAGATGGAT
1 GAATACTTTTAA-CCACCAAGATGGAT
** *
194068 GAATACTTTTAAATACC-AGGTGTAGAT
1 GAATACTTTTAACCACCAAGATG--GAT
* *
194095 GAATACTTTTAAACCATCAAGAGTGAAT
1 GAATACTTTT-AACCACCAAGA-TGGAT
*
194123 GAATATTTTTAACCACCAA
1 GAATACTTTTAACCACCAA
194142 AAATAGATCA
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
25 4 0.07
26 3 0.05
27 33 0.56
28 15 0.25
29 2 0.03
30 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.30
Consensus pattern (26 bp):
GAATACTTTTAACCACCAAGATGGAT
Found at i:194149 original size:55 final size:54
Alignment explanation
Indices: 194041--194149 Score: 119
Period size: 55 Copynumber: 2.0 Consensus size: 54
194031 TTAATAATAA
* * * ****
194041 GAATACTTTTAACCCACCAAGATGGATGAATACTTTTAAATACCAGGTGTAGAT
1 GAATACTTTTAAACCACCAAGATGAATGAATACTTTTAAACACCAAAAATAGAT
* * *
194095 GAATACTTTTAAACCATCAAGAGTGAATGAATATTTTTAACCACCAAAAATAGAT
1 GAATACTTTTAAACCACCAAGA-TGAATGAATACTTTTAAACACCAAAAATAGAT
194150 CAGCAATAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
54 20 0.45
55 24 0.55
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (54 bp):
GAATACTTTTAAACCACCAAGATGAATGAATACTTTTAAACACCAAAAATAGAT
Found at i:195022 original size:29 final size:29
Alignment explanation
Indices: 194971--195138 Score: 111
Period size: 29 Copynumber: 6.0 Consensus size: 29
194961 ATTAAAGTAT
* * *
194971 AACAAAATGTTTTTGAATATGGCGTGTAAC
1 AACAATAT-TTTTTTAACATGGCGTGTAAC
* *
195001 AATAATATTTTTTTAACATGGCATGTAAC
1 AACAATATTTTTTTAACATGGCGTGTAAC
* *
195030 AACAATTTTTTTTTCAACATGGTGTGTAAC
1 AACAATATTTTTTT-AACATGGCGTGTAAC
*
195060 AAC----TTTTTTTAACCATGACGTGTAAC
1 AACAATATTTTTTTAA-CATGGCGTGTAAC
* * *
195086 -AC---GTTTTTGT-ACATGGTGTGTAAC
1 AACAATATTTTTTTAACATGGCGTGTAAC
* * *
195110 AACAATATTCTTTTCAACATAGCCTGTAA
1 AACAATATT-TTTTTAACATGGCGTGTAA
195139 TAACCTAACC
Statistics
Matches: 109, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
24 11 0.10
25 7 0.06
26 24 0.22
28 2 0.02
29 33 0.30
30 32 0.29
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (29 bp):
AACAATATTTTTTTAACATGGCGTGTAAC
Found at i:195076 original size:26 final size:26
Alignment explanation
Indices: 195008--195112 Score: 90
Period size: 26 Copynumber: 4.0 Consensus size: 26
194998 AACAATAATA
** *
195008 TTTTTTTAACATGGCATGTAACAACAATT
1 TTTTTTTAACATGGTGTGTAACAAC---G
195037 TTTTTTTCAACATGGTGTGTAACAAC-
1 TTTTTTT-AACATGGTGTGTAACAACG
**
195063 TTTTTTTAACCATGACGTGTAAC-ACG
1 TTTTTTTAA-CATGGTGTGTAACAACG
*
195089 TTTTTGT-ACATGGTGTGTAACAAC
1 TTTTTTTAACATGGTGTGTAACAAC
195113 AATATTCTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
24 11 0.17
25 7 0.11
26 24 0.37
29 7 0.11
30 16 0.25
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (26 bp):
TTTTTTTAACATGGTGTGTAACAACG
Found at i:195716 original size:15 final size:15
Alignment explanation
Indices: 195696--195725 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
195686 ATTCGATCTT
195696 GGTCACAAACACTTC
1 GGTCACAAACACTTC
195711 GGTCACAAACACTTC
1 GGTCACAAACACTTC
195726 CATTTCATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.20
Consensus pattern (15 bp):
GGTCACAAACACTTC
Found at i:197838 original size:60 final size:61
Alignment explanation
Indices: 197691--197855 Score: 192
Period size: 60 Copynumber: 2.7 Consensus size: 61
197681 TGGGAACCTC
* * * *
197691 CCACGCCACCATTTATAAATC-GGGATTTCAGGTCCCCCTTTTGATCTACTCATAGGAACTAG
1 CCACGCCACCATATATAAATCAGGG-CTTCAGGTCCCCCTTTT-ACCGACTCATAGGAACTAG
* * * *
197753 CCATGCCACCATATATAAATTAGGGCTTCAGGT-CCCCTTTTACCGACTCGT-GGAAACTAT
1 CCACGCCACCATATATAAATCAGGGCTTCAGGTCCCCCTTTTACCGACTCATAGG-AACTAG
* *
197813 CCACGCCACCCTATATAAATCAGGGCTTCAAGTCCCCCTTTTA
1 CCACGCCACCATATATAAATCAGGGCTTCAGGTCCCCCTTTTA
197856 TAATCAAAAA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
59 2 0.02
60 41 0.47
61 17 0.19
62 25 0.28
63 3 0.03
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (61 bp):
CCACGCCACCATATATAAATCAGGGCTTCAGGTCCCCCTTTTACCGACTCATAGGAACTAG
Found at i:198469 original size:3 final size:3
Alignment explanation
Indices: 198461--198499 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
198451 AGTGAAACCC
198461 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
198500 TTTCTTCCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:198661 original size:66 final size:65
Alignment explanation
Indices: 198586--198713 Score: 168
Period size: 66 Copynumber: 2.0 Consensus size: 65
198576 TCCCTCTCTC
* * * *
198586 TTTTTCTTCTCCATTTTCCTTCTCC-TCTGGCACCACTGCTCTCCCTCTCTTTTCCTTCTTCTTT
1 TTTTTCTTCTCCATCTACCTTCTCCTTC-AGCACCACTGCTCTCCCTCTCTCTTCCTTCTTCTTT
198650 T
65 T
* * *
198651 TTTTTCCTTCTCCCTCTACCTTCTCCTTCAGCACCACTGCTTTTCCTCTCTCTTCCTTCTTCT
1 TTTTT-CTTCTCCATCTACCTTCTCCTTCAGCACCACTGCTCTCCCTCTCTCTTCCTTCTTCT
198714 ATCTTCTTCT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
65 5 0.09
66 47 0.87
67 2 0.04
ACGTcount: A:0.05, C:0.41, G:0.04, T:0.50
Consensus pattern (65 bp):
TTTTTCTTCTCCATCTACCTTCTCCTTCAGCACCACTGCTCTCCCTCTCTCTTCCTTCTTCTTTT
Found at i:198801 original size:48 final size:48
Alignment explanation
Indices: 198695--198808 Score: 151
Period size: 48 Copynumber: 2.4 Consensus size: 48
198685 CACTGCTTTT
* *
198695 CCTCTCTCTTCCTTCTTCTATCTTCTTCTCCAGCACGCCGCTGCTCTC
1 CCTCTCTTTTCCTTTTTCTATCTTCTTCTCCAGCACGCCGCTGCTCTC
* *
198743 CCTCTCTTTTCCTTTTTCTTTCTTCTTCTCCAGCACGTCGCT-CTC-C
1 CCTCTCTTTTCCTTTTTCTATCTTCTTCTCCAGCACGCCGCTGCTCTC
* *
198789 CTTTCTCTTTTTCTTTTTCT
1 C-CTCTCTTTTCCTTTTTCT
198809 CTTTATTTCC
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
46 2 0.03
47 19 0.32
48 38 0.64
ACGTcount: A:0.04, C:0.40, G:0.06, T:0.49
Consensus pattern (48 bp):
CCTCTCTTTTCCTTTTTCTATCTTCTTCTCCAGCACGCCGCTGCTCTC
Found at i:198827 original size:17 final size:18
Alignment explanation
Indices: 198801--198853 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
198791 TTCTCTTTTT
198801 CTTT-TTCTCTTTATTTC
1 CTTTCTTCTCTTTATTTC
*
198818 C-TTCTTCTCTTTTCTTCTC
1 CTTTCTTCTC-TTTATT-TC
198837 CTTTCTTCT-TTTATTTC
1 CTTTCTTCTCTTTATTTC
198854 TCTTGGCCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
16 2 0.07
17 8 0.27
18 10 0.33
19 3 0.10
20 7 0.23
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (18 bp):
CTTTCTTCTCTTTATTTC
Found at i:203440 original size:61 final size:62
Alignment explanation
Indices: 203293--203504 Score: 263
Period size: 61 Copynumber: 3.5 Consensus size: 62
203283 AGACATCATC
* * * * *
203293 ACCTACTCGTGGAAACCT-CCCACTCTACCATATATAAATC-GAGACTTCAGGT-CCCCATTT
1 ACCTACTCGTGGGAA-CTACCCACGCCACCCTATATAAATCGGAGACTTCAGGTCCCCCTTTT
203353 ACCTACTCGTGGGAACTACCCACGCCACCCTATATAAATCGGAG-CTTCAGGTCCCCCTTTT
1 ACCTACTCGTGGGAACTACCCACGCCACCCTATATAAATCGGAGACTTCAGGTCCCCCTTTT
* * * * **
203414 ACCTACTCGTGGAAAATACCCCCGCCACCCTATATAAATCGG-GACTTCATGTCCCTTTTTT
1 ACCTACTCGTGGGAACTACCCACGCCACCCTATATAAATCGGAGACTTCAGGTCCCCCTTTT
* *
203475 ACTTACTCGTGGGAACTACCCAGGCCACCC
1 ACCTACTCGTGGGAACTACCCACGCCACCC
203505 ATAGTATTTC
Statistics
Matches: 132, Mismatches: 16, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
59 2 0.02
60 42 0.32
61 88 0.67
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.25
Consensus pattern (62 bp):
ACCTACTCGTGGGAACTACCCACGCCACCCTATATAAATCGGAGACTTCAGGTCCCCCTTTT
Found at i:204036 original size:3 final size:3
Alignment explanation
Indices: 204028--204072 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
204018 AGTAAAACCC
* *
204028 ATT ATT ATT ATT ATT -TT A-T ATT TTT ATT ATT TTT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
204073 CATTTTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
ATT
Found at i:204316 original size:32 final size:32
Alignment explanation
Indices: 204281--204346 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
204271 GCACCACTGC
* *
204281 TCTCCCTCTCTCTTCCT-TCT-TGTTTCTTCT
1 TCTCTCTCTCTCTTCCTCTCTCTCTTTCTTCT
* *
204311 TCTCTCTCTTTCTTCTTCTCTCTCTTTCTTCT
1 TCTCTCTCTCTCTTCCTCTCTCTCTTTCTTCT
204343 TCTC
1 TCTC
204347 CAGCACGCCG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 14 0.47
31 3 0.10
32 13 0.43
ACGTcount: A:0.00, C:0.39, G:0.02, T:0.59
Consensus pattern (32 bp):
TCTCTCTCTCTCTTCCTCTCTCTCTTTCTTCT
Found at i:204323 original size:10 final size:9
Alignment explanation
Indices: 204286--204346 Score: 53
Period size: 8 Copynumber: 7.3 Consensus size: 9
204276 ACTGCTCTCC
204286 CTCTCTCTT
1 CTCTCTCTT
204295 C-CT-TCTT
1 CTCTCTCTT
* *
204302 GTTTCTTCTT
1 CTCTC-TCTT
204312 CTCTCTCTT
1 CTCTCTCTT
204321 -TCT-TCTT
1 CTCTCTCTT
204328 CTCTCTCTT
1 CTCTCTCTT
204337 -TCT-TCTT
1 CTCTCTCTT
204344 CTC
1 CTC
204347 CAGCACGCCG
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
7 12 0.29
8 14 0.33
9 9 0.21
10 7 0.17
ACGTcount: A:0.00, C:0.38, G:0.02, T:0.61
Consensus pattern (9 bp):
CTCTCTCTT
Found at i:204324 original size:16 final size:16
Alignment explanation
Indices: 204303--204346 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
204293 TTCCTTCTTG
204303 TTTCTTCTTCTCTCTC
1 TTTCTTCTTCTCTCTC
204319 TTTCTTCTTCTCTCTC
1 TTTCTTCTTCTCTCTC
204335 TTTCTTCTTCTC
1 TTTCTTCTTCTC
204347 CAGCACGCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTCTTCTTCTCTCTC
Found at i:204339 original size:26 final size:26
Alignment explanation
Indices: 204286--204344 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
204276 ACTGCTCTCC
* *
204286 CTCTCTCTTCCTTCTTGTTTCTTCTT
1 CTCTCTCTTCCTTCTTCTCTCTTCTT
*
204312 CTCTCTCTTTCTTCTTCTCTC-TCTT
1 CTCTCTCTTCCTTCTTCTCTCTTCTT
204337 -TCT-TCTTC
1 CTCTCTCTTC
204345 TCCAGCACGC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 4 0.14
24 3 0.10
25 4 0.14
26 18 0.62
ACGTcount: A:0.00, C:0.37, G:0.02, T:0.61
Consensus pattern (26 bp):
CTCTCTCTTCCTTCTTCTCTCTTCTT
Found at i:204364 original size:48 final size:50
Alignment explanation
Indices: 204312--204448 Score: 145
Period size: 48 Copynumber: 2.7 Consensus size: 50
204302 GTTTCTTCTT
* *
204312 CTCTCTCTTTCTTCTTCTCTCTCTTTCTTCTTCTCCAGCACG-C-CGCT-G
1 CTCTCTCTTTCTT-TTCTCTTTCTTTCTTCTTCTCCAGCACGCCACGCTCC
* * * *
204360 CTCTCCCTCTCTTTTCCTTTTTCTTTCTTCTTCTCCAGCACGCCACTCTCC
1 CTCTCTCTTTCTTTT-CTCTTTCTTTCTTCTTCTCCAGCACGCCACGCTCC
204411 CTTTCTCTCTTTCTTTTTCTCTTTCTTTCCTTCTTCTC
1 C--TCTCTCTTTC-TTTTCTCTTTCTTT-CTTCTTCTC
204449 TTTTCTTCTT
Statistics
Matches: 72, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
47 2 0.03
48 35 0.49
49 1 0.01
50 3 0.04
51 1 0.01
53 17 0.24
54 13 0.18
ACGTcount: A:0.04, C:0.41, G:0.04, T:0.51
Consensus pattern (50 bp):
CTCTCTCTTTCTTTTCTCTTTCTTTCTTCTTCTCCAGCACGCCACGCTCC
Found at i:204391 original size:80 final size:79
Alignment explanation
Indices: 204228--204394 Score: 212
Period size: 80 Copynumber: 2.1 Consensus size: 79
204218 CTCTCTTTTC
* * *
204228 CTTCTTCT-TCTTTTTTTTCCTTCTCCCTCTTCCTTCTCCTCCGGCACCACTGCTCTCCCTCTCT
1 CTTCTTCTCTCTCTTTCTTCCTTCTCCCTCTTCCTTCTCCTCCAGCACCACTGCTCTCCCTCTCT
*
204292 CTTCCTTCTTGTTT
66 CTTCCTTCTTCTTT
* * * *
204306 CTTCTTCTCTCTCTTTCTT-CTTCTCTCTCTTTCTTCTTCTCCAGCACGCCGCTGCTCTCCCTCT
1 CTTCTTCTCTCTCTTTCTTCCTTCTCCCTCTTCCTTCTCCTCCAGCA--CCACTGCTCTCCCTCT
* *
204370 CTTTTCCTTTTTCTTT
64 CTCTTCCTTCTTCTTT
204386 CTTCTTCTC
1 CTTCTTCTC
204395 CAGCACGCCA
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
78 31 0.41
79 8 0.11
80 37 0.49
ACGTcount: A:0.02, C:0.41, G:0.05, T:0.51
Consensus pattern (79 bp):
CTTCTTCTCTCTCTTTCTTCCTTCTCCCTCTTCCTTCTCCTCCAGCACCACTGCTCTCCCTCTCT
CTTCCTTCTTCTTT
Found at i:204449 original size:17 final size:16
Alignment explanation
Indices: 204418--204451 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
204408 TCCCTTTCTC
*
204418 TCTTTCTTTTTCTCTT
1 TCTTTCTTCTTCTCTT
204434 TCTTTCCTTCTTCTCTT
1 TCTTT-CTTCTTCTCTT
204451 T
1 T
204452 TCTTCTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TCTTTCTTCTTCTCTT
Found at i:209854 original size:28 final size:29
Alignment explanation
Indices: 209822--209880 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
209812 AAAACACTTC
*
209822 AAAATGATATT-TTGATCTCTTTTATT-TT
1 AAAATGATATTATTGAT-TCTTTGATTGTT
*
209850 AAAATGATGTTATTGATTCTTTGATTGTT
1 AAAATGATATTATTGATTCTTTGATTGTT
209879 AA
1 AA
209881 CATTGTTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.53
Consensus pattern (29 bp):
AAAATGATATTATTGATTCTTTGATTGTT
Found at i:213948 original size:22 final size:22
Alignment explanation
Indices: 213924--213964 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
213914 ATACAAAATA
*
213924 AAAAGTA-ATATATTTATATTT
1 AAAAGTACATATATATATATTT
213945 AAAAGTACATATATATATAT
1 AAAAGTACATATATATATAT
213965 ATGCACACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (22 bp):
AAAAGTACATATATATATATTT
Found at i:218034 original size:18 final size:17
Alignment explanation
Indices: 218007--218069 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 17
217997 ACTTTAAATT
218007 TTTTTAATTTATATTATTA
1 TTTTT-ATTTATATT-TTA
*
218026 TTTTTATTTATATTTTT
1 TTTTTATTTATATTTTA
*
218043 TTATTTGTTTAT-TTTTA
1 TT-TTTATTTATATTTTA
218060 -TTTTATTTAT
1 TTTTTATTTAT
218070 TCATATGTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 8 0.21
16 1 0.03
17 8 0.21
18 17 0.44
19 5 0.13
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTTATTTATATTTTA
Found at i:218041 original size:33 final size:33
Alignment explanation
Indices: 217999--218069 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
217989 CTTACTCAAC
*
217999 TTTAAATTTTTTTAATT-TATATTATTATTTTTA
1 TTTATATTTTTTTAATTGTATATTATTA-TTTTA
* * *
218032 TTTATATTTTTTTATTTGTTTATTTTTATTTTA
1 TTTATATTTTTTTAATTGTATATTATTATTTTA
218065 TTTAT
1 TTTAT
218070 TCATATGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 25 0.76
34 8 0.24
ACGTcount: A:0.24, C:0.00, G:0.01, T:0.75
Consensus pattern (33 bp):
TTTATATTTTTTTAATTGTATATTATTATTTTA
Found at i:218043 original size:14 final size:14
Alignment explanation
Indices: 218014--218066 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
218004 ATTTTTTTAA
*
218014 TTTATATTATTATT
1 TTTATTTTATTATT
218028 TTTATTTATATT-TT
1 TTTATTT-TATTATT
218042 TTTATTTGT-TTATT
1 TTTATTT-TATTATT
218056 TTTATTTTATT
1 TTTATTTTATT
218067 TATTCATATG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 3 0.09
14 27 0.79
15 4 0.12
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTATT
Found at i:218046 original size:28 final size:27
Alignment explanation
Indices: 218014--218067 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
218004 ATTTTTTTAA
218014 TTTATATT-ATTATTTTTATTTATATTTT
1 TTTAT-TTGATTATTTTTATTT-TATTTT
*
218042 TTTATTTGTTTATTTTTATTTTATTT
1 TTTATTTGATTATTTTTATTTTATTT
218068 ATTCATATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (27 bp):
TTTATTTGATTATTTTTATTTTATTTT
Found at i:218056 original size:22 final size:23
Alignment explanation
Indices: 218014--218070 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 23
218004 ATTTTTTTAA
*
218014 TTTATATTATTATTTTTATTTATAT
1 TTTAT-TTATT-TGTTTATTTATAT
*
218039 TTT-TTTATTTGTTTATTTTTAT
1 TTTATTTATTTGTTTATTTATAT
218061 TTTATTTATT
1 TTTATTTATT
218071 CATATGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 14 0.48
23 11 0.38
24 1 0.03
25 3 0.10
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTATTTATTTGTTTATTTATAT
Found at i:218078 original size:27 final size:28
Alignment explanation
Indices: 218023--218078 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
218013 ATTTATATTA
* * *
218023 TTATTTTTATTTATATTTTTTTATTTGT
1 TTATTTTTATTTATATTTATTCATATGT
218051 TTATTTTTATTT-TATTTATTCATATGT
1 TTATTTTTATTTATATTTATTCATATGT
218078 T
1 T
218079 ATAAGTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.75
Consensus pattern (28 bp):
TTATTTTTATTTATATTTATTCATATGT
Found at i:233940 original size:2 final size:2
Alignment explanation
Indices: 233933--233979 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
233923 GAGAAATAAG
233933 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
233975 AT AT A
1 AT AT A
233980 CTATCTTTAG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:236692 original size:103 final size:100
Alignment explanation
Indices: 236575--236797 Score: 338
Period size: 103 Copynumber: 2.2 Consensus size: 100
236565 TGCATAACCA
* ** * * *
236575 TTTTTAGCTAGAATTTGATGAATTTGAGTTGGGCTTTTGGTCTTTTTCTTTGAGATAATTCTTGG
1 TTTTTAGCTTGAATTTGATGAATTTGAGTTGGGCTGGTGGTCTCTTTCTTTAAGATAATTCTGGG
* *
236640 GATTTGAATGTTGATGAGTTAAAAGTTTTTTCCTTTT
66 GATTTGAAAGTTGATGAGTT-AAAGTTTCTTCC-TTT
*
236677 TTTTTAAGCTTGAATTTGATGAATTTGAGTTGGGCTGGTGGTCTCTTTCTTTAATATAATTCTGG
1 TTTTT-AGCTTGAATTTGATGAATTTGAGTTGGGCTGGTGGTCTCTTTCTTTAAGATAATTCTGG
236742 GGATTTGAAAGTTGATGAGTTAAAGTTTCTTCCTTT
65 GGATTTGAAAGTTGATGAGTTAAAGTTTCTTCCTTT
236778 TTTTTAGCTTGAATTTGATG
1 TTTTTAGCTTGAATTTGATG
236798 CTGTTTTTGA
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
100 15 0.14
101 8 0.07
102 16 0.14
103 72 0.65
ACGTcount: A:0.21, C:0.08, G:0.22, T:0.49
Consensus pattern (100 bp):
TTTTTAGCTTGAATTTGATGAATTTGAGTTGGGCTGGTGGTCTCTTTCTTTAAGATAATTCTGGG
GATTTGAAAGTTGATGAGTTAAAGTTTCTTCCTTT
Found at i:270791 original size:30 final size:30
Alignment explanation
Indices: 270752--270870 Score: 150
Period size: 30 Copynumber: 4.0 Consensus size: 30
270742 TGGTGGACTT
* *
270752 GGTGGCTTGTAAGGGGGTGTAGGAGTTGGC
1 GGTGCCTTGTAAGGAGGTGTAGGAGTTGGC
270782 GGTGCCTTGTAAGGAGGTGTAGGAGTTGGC
1 GGTGCCTTGTAAGGAGGTGTAGGAGTTGGC
**
270812 GGTGCCTTGTAAGGAGGTGCT-GGAGTTGTT
1 GGTGCCTTGTAAGGAGGTG-TAGGAGTTGGC
* * * *
270842 GGTGGCTTGTATGGGGGTGAAGGAGTTGG
1 GGTGCCTTGTAAGGAGGTGTAGGAGTTGG
270871 GGGTTTATAT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
30 77 0.99
31 1 0.01
ACGTcount: A:0.14, C:0.08, G:0.50, T:0.29
Consensus pattern (30 bp):
GGTGCCTTGTAAGGAGGTGTAGGAGTTGGC
Found at i:270924 original size:48 final size:48
Alignment explanation
Indices: 270853--271304 Score: 661
Period size: 48 Copynumber: 9.4 Consensus size: 48
270843 GTGGCTTGTA
* * * * ** **
270853 TGGGGGTGAAGGAGTTGGGGGTTTATATGGGGGAGCGGGAGCCTTGGT
1 TGGGGGTGCAGGACTTGGGGGTTTGTACGGGGGAGTAGGAGCCTTGAC
* * * *
270901 TGGGGGTGCAGGAGTTGGGGGTTTATATGGGGGAGTAGGAGCCTCGAC
1 TGGGGGTGCAGGACTTGGGGGTTTGTACGGGGGAGTAGGAGCCTTGAC
** *
270949 TGGGGGTGTGGGAGTTGGGGGTTTGTACGGGGGAGTAGGAGCCTTGAC
1 TGGGGGTGCAGGACTTGGGGGTTTGTACGGGGGAGTAGGAGCCTTGAC
*
270997 TGGAGGTGCAGGACTTGGGGGTTTGTACGGGGGAGTAGGAGCCTTGAC
1 TGGGGGTGCAGGACTTGGGGGTTTGTACGGGGGAGTAGGAGCCTTGAC
*
271045 TGGAGGTGCAGGACTTGGGGGTTTGTACGGGGGAGTAGGAGCCTTGAC
1 TGGGGGTGCAGGACTTGGGGGTTTGTACGGGGGAGTAGGAGCCTTGAC
*
271093 TGGAGGTGCAGGACTTGGGGGTTTGTACGGGGGAGTAGGAGCCTTGAC
1 TGGGGGTGCAGGACTTGGGGGTTTGTACGGGGGAGTAGGAGCCTTGAC
*
271141 TGGAGGTGCAGGACTTGGGGGTTTGTACGGGGGAGTAGGAGCCTTGAC
1 TGGGGGTGCAGGACTTGGGGGTTTGTACGGGGGAGTAGGAGCCTTGAC
* * * *
271189 TGGGGGTGTAGGAGTTGGGGGTTTATATGGGGGAGTAGGAGCCTTGAC
1 TGGGGGTGCAGGACTTGGGGGTTTGTACGGGGGAGTAGGAGCCTTGAC
* * * *
271237 TGGGGGTGTAGGAGTTGGGGGTTTGTATGGAGGAGTAGGAGCCTTGAC
1 TGGGGGTGCAGGACTTGGGGGTTTGTACGGGGGAGTAGGAGCCTTGAC
271285 TGGGGGTGCAGGACTTGGGG
1 TGGGGGTGCAGGACTTGGGG
271305 CTGTGTAAGG
Statistics
Matches: 380, Mismatches: 24, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 380 1.00
ACGTcount: A:0.16, C:0.10, G:0.50, T:0.24
Consensus pattern (48 bp):
TGGGGGTGCAGGACTTGGGGGTTTGTACGGGGGAGTAGGAGCCTTGAC
Found at i:271202 original size:27 final size:27
Alignment explanation
Indices: 271172--271251 Score: 64
Period size: 27 Copynumber: 3.2 Consensus size: 27
271162 TTTGTACGGG
271172 GGAGTAGGAGCCTTGACTGGGGGTGTA
1 GGAGTAGGAGCCTTGACTGGGGGTGTA
* ** * **
271199 GGAGTTGG-GGGTTTA-TATGGG-G--
1 GGAGTAGGAGCCTTGACTGGGGGTGTA
271221 -GAGTAGGAGCCTTGACTGGGGGTGTA
1 GGAGTAGGAGCCTTGACTGGGGGTGTA
271247 GGAGT
1 GGAGT
271252 TGGGGGTTTG
Statistics
Matches: 35, Mismatches: 12, Indels: 12
0.59 0.20 0.20
Matches are distributed among these distances:
21 6 0.17
22 4 0.11
23 4 0.11
24 2 0.06
25 4 0.11
26 4 0.11
27 11 0.31
ACGTcount: A:0.17, C:0.07, G:0.50, T:0.25
Consensus pattern (27 bp):
GGAGTAGGAGCCTTGACTGGGGGTGTA
Found at i:271297 original size:27 final size:27
Alignment explanation
Indices: 271267--271368 Score: 75
Period size: 27 Copynumber: 3.8 Consensus size: 27
271257 GTTTGTATGG
*
271267 AGGAGTAGGAGCCTTGACTGGGGGTGC
1 AGGAGTGGGAGCCTTGACTGGGGGTGC
* *
271294 AGGACTTGGG-G-CTGTGTA-AGGGGGTGC
1 AGGA-GTGGGAGCCT-TG-ACTGGGGGTGC
* * *
271321 TGGAGTGGGAGTCTTAACTGGGGGTGC
1 AGGAGTGGGAGCCTTGACTGGGGGTGC
* * *
271348 AGGGGTGGGTGCCTTCACTGG
1 AGGAGTGGGAGCCTTGACTGG
271369 TACTGGAGCT
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
26 7 0.12
27 44 0.77
28 6 0.11
ACGTcount: A:0.15, C:0.14, G:0.49, T:0.23
Consensus pattern (27 bp):
AGGAGTGGGAGCCTTGACTGGGGGTGC
Found at i:273400 original size:16 final size:14
Alignment explanation
Indices: 273373--273417 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 14
273363 TCCCTCCCAT
*
273373 AAAAGGAAAGAAAA
1 AAAAAGAAAGAAAA
273387 AAAACAGAAAAGAAACA
1 AAAA-AG-AAAGAAA-A
273404 AAAAAGAAAGAAAA
1 AAAAAGAAAGAAAA
273418 GGAAAGATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 5 0.19
15 8 0.30
16 9 0.33
17 5 0.19
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAGAAAA
Found at i:273406 original size:20 final size:20
Alignment explanation
Indices: 273373--273418 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
273363 TCCCTCCCAT
*
273373 AAAAGGAAAGAAAAAA-AACAG
1 AAAA-GAAACAAAAAAGAA-AG
273394 AAAAGAAACAAAAAAGAAAG
1 AAAAGAAACAAAAAAGAAAG
273414 AAAAG
1 AAAAG
273419 GAAAGATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAAGAAACAAAAAAGAAAG
Found at i:275722 original size:2 final size:2
Alignment explanation
Indices: 275715--275744 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
275705 ACATACATGA
275715 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
275745 GTATGTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:289943 original size:7 final size:7
Alignment explanation
Indices: 289914--289978 Score: 76
Period size: 7 Copynumber: 9.1 Consensus size: 7
289904 TCGTGTTATT
*
289914 TGTCACG
1 TGTCAAG
289921 TGTCAAG
1 TGTCAAG
* *
289928 ATCTAAAG
1 -TGTCAAG
289936 TGTCAAG
1 TGTCAAG
289943 TGTCAAG
1 TGTCAAG
289950 TGTCAAG
1 TGTCAAG
289957 TGTCAAG
1 TGTCAAG
* *
289964 TGTGAAA
1 TGTCAAG
289971 TGTCAAG
1 TGTCAAG
289978 T
1 T
289979 ATTACGTGTC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
7 43 0.90
8 5 0.10
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (7 bp):
TGTCAAG
Found at i:299639 original size:2 final size:2
Alignment explanation
Indices: 299580--299626 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
299570 ATTGTGATGN
299580 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
299622 TA TA T
1 TA TA T
299627 TGTGACAATA
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:326129 original size:17 final size:16
Alignment explanation
Indices: 326109--326145 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
326099 TTTTTTTTTT
326109 AAAAAATAAAATTTTGA
1 AAAAAAT-AAATTTTGA
*
326126 AAAAAATAACTTTTGA
1 AAAAAATAAATTTTGA
326142 AAAA
1 AAAA
326146 GCTCATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (16 bp):
AAAAAATAAATTTTGA
Found at i:329326 original size:16 final size:17
Alignment explanation
Indices: 329307--329342 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
329297 TAGTAATGCT
329307 TATGTATAAATA-AATA
1 TATGTATAAATATAATA
*
329323 TATGTATATATATAATA
1 TATGTATAAATATAATA
329340 TAT
1 TAT
329343 TACTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
TATGTATAAATATAATA
Found at i:329681 original size:84 final size:84
Alignment explanation
Indices: 329569--329742 Score: 303
Period size: 84 Copynumber: 2.1 Consensus size: 84
329559 ATACAATTAT
329569 ATATATATTCATAACTTTTTATGTTATGAAACATTACTAAAGTGTAATAATTATAAAATATTAAT
1 ATATATATTCATAACTTTTTATGTTATGAAACATTACTAAAGTGTAATAATTATAAAATATTAAT
*
329634 ATGTAGGATATTTACTATN
66 ATGTAGGATATTTACTATC
* * * *
329653 ATATATATTCATAACTTTTTATGTTATGAAACATTATTAAGGTGTATTAATTATAATATATTAAT
1 ATATATATTCATAACTTTTTATGTTATGAAACATTACTAAAGTGTAATAATTATAAAATATTAAT
329718 ATGTAGGATATTTACTATC
66 ATGTAGGATATTTACTATC
329737 ATATAT
1 ATATAT
329743 TATAATATTA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (84 bp):
ATATATATTCATAACTTTTTATGTTATGAAACATTACTAAAGTGTAATAATTATAAAATATTAAT
ATGTAGGATATTTACTATC
Found at i:330394 original size:21 final size:21
Alignment explanation
Indices: 330360--330400 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
330350 GACACTCATT
330360 TAAAAATAATAATAAAATAAA
1 TAAAAATAATAATAAAATAAA
330381 TAAAATATAA-AATAAAATAA
1 TAAAA-ATAATAATAAAATAA
330401 TGAGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAAAATAATAATAAAATAAA
Found at i:330408 original size:16 final size:15
Alignment explanation
Indices: 330362--330401 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
330352 CACTCATTTA
330362 AAAATAATAATAAAAT
1 AAAATAAT-ATAAAAT
*
330378 AAATAAAATATAAAAT
1 AAA-ATAATATAAAAT
330394 AAAATAAT
1 AAAATAAT
330402 GAGAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 4 0.19
16 13 0.62
17 4 0.19
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATAATATAAAAT
Found at i:331618 original size:27 final size:27
Alignment explanation
Indices: 331531--331618 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 27
331521 ATAATGTTTT
* * * * *
331531 AGAAAAAAATACTAATAAAAATATTAA
1 AGAAAATAATAATAATAACAATAATCA
** *
331558 ACGAAAATAATAATAATAATGATAATTA
1 A-GAAAATAATAATAATAACAATAATCA
331586 AGAAAATAATAATAAATAACAATAA-CA
1 AGAAAATAATAAT-AATAACAATAATCA
*
331613 ATAAAA
1 AGAAAA
331619 ATGATATAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
27 19 0.39
28 30 0.61
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (27 bp):
AGAAAATAATAATAATAACAATAATCA
Found at i:335371 original size:23 final size:23
Alignment explanation
Indices: 335345--335390 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
335335 TAGAATAACA
335345 ATTCCTAATTATATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
*
335368 ATTCTTAATTATATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
335391 GTTATTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (23 bp):
ATTCCTAATTATATTAGGATAAG
Found at i:338707 original size:23 final size:23
Alignment explanation
Indices: 338676--338721 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
338666 TAGAGTAACA
*
338676 ATTCCTAATTATATTAGGATAAG
1 ATTCATAATTATATTAGGATAAG
338699 ATTCATAATTATATTAGGATAAG
1 ATTCATAATTATATTAGGATAAG
338722 GTTATTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (23 bp):
ATTCATAATTATATTAGGATAAG
Found at i:343482 original size:85 final size:85
Alignment explanation
Indices: 343244--343727 Score: 396
Period size: 86 Copynumber: 5.6 Consensus size: 85
343234 TTTGGTTAGA
* * * ** * *
343244 AATCATTATGAAGCACTATTTATGCACGTGTATTAAATTGTTTAAATTTATTAAACTTAAAATCG
1 AATCATTATGAAGTACTATTT-TGCACATGCATTAAATTGTACAAACTTATCAAACTTAAAATCG
343309 TGTATATATAACTATTCAAGC
65 TGTATATATAACTATTCAAGC
* * * * * * *
343330 AATAATTATGAAGTATTGTTTAGACACATTCATTAAATCT-TACAAACTTATCAAATTTGAAATC
1 AATCATTATGAAGTACTATTTTG-CACATGCATTAAAT-TGTACAAACTTATCAAACTTAAAATC
*
343394 GTGTATATATAACTACTCAAGC
64 GTGTATATATAACTATTCAAGC
* * *
343416 GATCATTATCAAGTACTATTTTGCACATGCATTAAATTGTACAAACTTGTCAAACTTAAAATCGT
1 AATCATTATGAAGTACTATTTTGCACATGCATTAAATTGTACAAACTTATCAAACTTAAAATCGT
343481 GTATATATAACTATTCAAGC
66 GTATATATAACTATTCAAGC
* * * ** ** * * * * *
343501 AATTATTATGAAATACTATTTGGGCACATATATTAAGCTATACAAACTTATTAAATTTAGAATTG
1 AATCATTATGAAGTACTATTT-TGCACATGCATTAAATTGTACAAACTTATCAAACTTAAAATCG
** * * *
343566 TACATATATAATTGTTCAAAC
65 TGTATATATAACTATTCAAGC
* * ** * * * ** *
343587 AATCATTATGAATTACTATTTAAGCACATAAAGTAAACTGTTA-AAACTTATCAAATTTGGAATT
1 AATCATTATGAAGTACTATTT-TGCACATGCATTAAATTG-TACAAACTTATCAAACTTAAAATC
* * *
343651 ATGCATATATAGCTATTCAAGC
64 GTGTATATATAACTATTCAAGC
* * * * * * *
343673 AATTATTATAAAATACTATTTAGACACATACATTAAACTGTACAAACCTATCAAA
1 AATCATTATGAAGTACTATTTTG-CACATGCATTAAATTGTACAAACTTATCAAA
343728 TTTGAATATA
Statistics
Matches: 323, Mismatches: 68, Indels: 14
0.80 0.17 0.03
Matches are distributed among these distances:
84 1 0.00
85 77 0.24
86 242 0.75
87 3 0.01
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.36
Consensus pattern (85 bp):
AATCATTATGAAGTACTATTTTGCACATGCATTAAATTGTACAAACTTATCAAACTTAAAATCGT
GTATATATAACTATTCAAGC
Found at i:343575 original size:171 final size:169
Alignment explanation
Indices: 343244--343734 Score: 527
Period size: 171 Copynumber: 2.9 Consensus size: 169
343234 TTTGGTTAGA
* * * * * *
343244 AATCATTATGAAGCACTATTTATGCACGTGTATTAAATTGTTTAAATTTATTAAACTTAAAATCG
1 AATCATTATGAAGTACTATTTATGCACATGAATTAAATTG-TAAAACTTATCAAACTTAAAATCG
* * * *
343309 TGTATATATAACTATTCAAGCAATAATTATGAAGTATTGTTTAGACACAT-TCATTAAATCTTAC
65 TGTATATATAACTATTCAAGCAATTATTATGAAATACTATTTAGACACATAT-ATTAAA-CTTAC
** *
343373 AAACTTATCAAATTTGAAATCGTGTATATATAACTACTCAAGC
128 AAACTTATCAAATTTG-AATCGTACATATATAACTACTCAAAC
* * * *
343416 GATCATTATCAAGTACTATTT-TGCACATGCATTAAATTGTACAAACTTGTCAAACTTAAAATCG
1 AATCATTATGAAGTACTATTTATGCACATGAATTAAATTGTA-AAACTTATCAAACTTAAAATCG
* * *
343480 TGTATATATAACTATTCAAGCAATTATTATGAAATACTATTTGGGCACATATATTAAGCTATACA
65 TGTATATATAACTATTCAAGCAATTATTATGAAATACTATTTAGACACATATATTAAACT-TACA
* * * **
343545 AACTTATTAAATTTAGAATTGTACATATATAATTGTTCAAAC
129 AACTTATCAAATTT-GAATCGTACATATATAACTACTCAAAC
* * * * * * ** **
343587 AATCATTATGAATTACTATTTAAGCACATAAAGTAAACTGTTAAAACTTATCAAATTTGGAATTA
1 AATCATTATGAAGTACTATTTATGCACATGAATTAAATTG-TAAAACTTATCAAACTTAAAATCG
* * * *
343652 TGCATATATAGCTATTCAAGCAATTATTATAAAATACTATTTAGACACATACATTAAACTGTACA
65 TGTATATATAACTATTCAAGCAATTATTATGAAATACTATTTAGACACATATATTAAACT-TACA
*
343717 AACCTATCAAATTTGAAT
129 AACTTATCAAATTTGAAT
343735 ATATATATAT
Statistics
Matches: 265, Mismatches: 48, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
170 3 0.01
171 142 0.54
172 118 0.45
173 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.36
Consensus pattern (169 bp):
AATCATTATGAAGTACTATTTATGCACATGAATTAAATTGTAAAACTTATCAAACTTAAAATCGT
GTATATATAACTATTCAAGCAATTATTATGAAATACTATTTAGACACATATATTAAACTTACAAA
CTTATCAAATTTGAATCGTACATATATAACTACTCAAAC
Found at i:343728 original size:86 final size:86
Alignment explanation
Indices: 343303--343733 Score: 431
Period size: 86 Copynumber: 5.0 Consensus size: 86
343293 ATTAAACTTA
* * * * * *
343303 AAATCGTGTATATATAACTATTCAAGCAATAATTATGAAGTATTGTTTAGACACATTCATTAAAT
1 AAATCGTGCATATATAACTATTCAAGCAATCATTATGAAATACTATTTAGACACATACATTAAA-
343368 CT-TACAAACTTATCAAATTTG
65 CTGTACAAACTTATCAAATTTG
* * * * * * * *
343389 AAATCGTGTATATATAACTACTCAAGCGATCATTATCAAGTACTATTTTG-CACATGCATTAAAT
1 AAATCGTGCATATATAACTATTCAAGCAATCATTATGAAATACTATTTAGACACATACATTAAAC
* * *
343453 TGTACAAACTTGTCAAACTTA
66 TGTACAAACTTATCAAATTTG
* * * * * *
343474 AAATCGTGTATATATAACTATTCAAGCAATTATTATGAAATACTATTTGGGCACATATATTAAGC
1 AAATCGTGCATATATAACTATTCAAGCAATCATTATGAAATACTATTTAGACACATACATTAAAC
* *
343539 TATACAAACTTATTAAATTT-
66 TGTACAAACTTATCAAATTTG
* * * * * * * *
343559 AGAATTGTACATATATAATTGTTCAAACAATCATTATGAATTACTATTTA-AGCACATAAAGTAA
1 A-AATCGTGCATATATAACTATTCAAGCAATCATTATGAAATACTATTTAGA-CACATACATTAA
343623 ACTGTTA-AAACTTATCAAATTTG
64 ACTG-TACAAACTTATCAAATTTG
* ** * * *
343646 GAATTATGCATATATAGCTATTCAAGCAATTATTATAAAATACTATTTAGACACATACATTAAAC
1 AAATCGTGCATATATAACTATTCAAGCAATCATTATGAAATACTATTTAGACACATACATTAAAC
*
343711 TGTACAAACCTATCAAATTTG
66 TGTACAAACTTATCAAATTTG
343732 AA
1 AA
343734 TATATATATA
Statistics
Matches: 282, Mismatches: 55, Indels: 16
0.80 0.16 0.05
Matches are distributed among these distances:
84 1 0.00
85 75 0.27
86 203 0.72
87 3 0.01
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (86 bp):
AAATCGTGCATATATAACTATTCAAGCAATCATTATGAAATACTATTTAGACACATACATTAAAC
TGTACAAACTTATCAAATTTG
Found at i:343740 original size:2 final size:2
Alignment explanation
Indices: 343733--343814 Score: 127
Period size: 2 Copynumber: 43.0 Consensus size: 2
343723 TCAAATTTGA
343733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
343773 A- AT AN A- 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
343813 AT
1 AT
343815 TTAAACAATC
Statistics
Matches: 75, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
1 4 0.05
2 71 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:349778 original size:2 final size:2
Alignment explanation
Indices: 349773--349798 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
349763 ACACACATAC
349773 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
349799 TGGTTTTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:353113 original size:13 final size:12
Alignment explanation
Indices: 353070--353114 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
353060 TTTTGAGATG
353070 TAAAATTTTTAA
1 TAAAATTTTTAA
*
353082 TAAATTTTTATAA
1 TAAAATTTT-TAA
353095 TCAAAATTTTCTAA
1 T-AAAATTTT-TAA
353109 TAAAAT
1 TAAAAT
353115 ATAAATTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 8 0.29
13 9 0.32
14 11 0.39
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (12 bp):
TAAAATTTTTAA
Found at i:353608 original size:18 final size:19
Alignment explanation
Indices: 353576--353619 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
353566 TTTTATTAAT
*
353576 TATTTTTTACTTTTATATA
1 TATTTTTTACATTTATATA
353595 TATTTTTTA-ATTTATATA
1 TATTTTTTACATTTATATA
353613 TATTTTT
1 TATTTTT
353620 AATATAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TATTTTTTACATTTATATA
Found at i:353631 original size:15 final size:17
Alignment explanation
Indices: 353589--353625 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
353579 TTTTTACTTT
353589 TATATATAT-TTTTTAA
1 TATATATATATTTTTAA
*
353605 TTTATATATATTTTTAA
1 TATATATATATTTTTAA
353622 TATA
1 TATA
353626 ATTATTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATATATATTTTTAA
Found at i:353843 original size:19 final size:19
Alignment explanation
Indices: 353819--353857 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
353809 TTCATCATAG
353819 TTATTATATATTGGTTTCA
1 TTATTATATATTGGTTTCA
353838 TTATTATATATTGGTTTCA
1 TTATTATATATTGGTTTCA
353857 T
1 T
353858 AATATCCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.59
Consensus pattern (19 bp):
TTATTATATATTGGTTTCA
Found at i:354168 original size:13 final size:14
Alignment explanation
Indices: 354142--354173 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
354132 CCAATAAATT
354142 TAAAA-ATTTAAAA
1 TAAAATATTTAAAA
354155 TAAAATATTT-AAA
1 TAAAATATTTAAAA
354168 TAAAAT
1 TAAAAT
354174 TTTTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAAATATTTAAAA
Found at i:354185 original size:32 final size:32
Alignment explanation
Indices: 354149--354272 Score: 116
Period size: 33 Copynumber: 3.9 Consensus size: 32
354139 ATTTAAAAAT
* *
354149 TTAAAA-TAAAATATTTAAATAAAATTTTTTTA
1 TTAAAATTAAAAAAATTAAA-AAAATTTTTTTA
354181 TTAAAATTAAAAAAATTAAGAAAAATTTTATTT-
1 TTAAAATTAAAAAAATTAA-AAAAATTTT-TTTA
**
354214 TT----TTATTAAAATTAAAAAAAATTATTTTTTA
1 TTAAAATTAAAAAAATT-AAAAAAA-T-TTTTTTA
354245 TTAAAATTAAAAAAATTAAAAAAATTTT
1 TTAAAATTAAAAAAATTAAAAAAATTTT
354273 ATTTTTTTAA
Statistics
Matches: 75, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
29 14 0.19
30 6 0.08
31 5 0.07
32 9 0.12
33 21 0.28
34 11 0.15
35 9 0.12
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.44
Consensus pattern (32 bp):
TTAAAATTAAAAAAATTAAAAAAATTTTTTTA
Found at i:354241 original size:26 final size:28
Alignment explanation
Indices: 354192--354260 Score: 106
Period size: 26 Copynumber: 2.5 Consensus size: 28
354182 TAAAATTAAA
*
354192 AAAATTAAGAAAAATTTTATTTTTTTATT
1 AAAATTAA-AAAAATATTATTTTTTTATT
354221 AAAATTAAAAAAA-ATTA-TTTTTTATT
1 AAAATTAAAAAAATATTATTTTTTTATT
354247 AAAATTAAAAAAAT
1 AAAATTAAAAAAAT
354261 TAAAAAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
26 22 0.58
27 3 0.08
28 5 0.13
29 8 0.21
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (28 bp):
AAAATTAAAAAAATATTATTTTTTTATT
Found at i:354273 original size:29 final size:29
Alignment explanation
Indices: 354176--354275 Score: 85
Period size: 29 Copynumber: 3.2 Consensus size: 29
354166 AATAAAATTT
354176 TTTTATTAAAATTAAAAAAATTAAGAAAAA
1 TTTTATTAAAATTAAAAAAATTAA-AAAAA
*** **
354206 TTTTATT-TTTTTATTAAAATTAAAAAAAATTA
1 TTTTATTAAAATTAAAAAAATT--AAAAAA--A
354238 TTTTTTATTAAAATTAAAAAAATTAAAAAAA
1 --TTTTATTAAAATTAAAAAAATTAAAAAAA
354269 TTTTATT
1 TTTTATT
354276 TTTTTAAATT
Statistics
Matches: 53, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
29 16 0.30
30 11 0.21
31 3 0.06
32 1 0.02
33 6 0.11
34 7 0.13
35 9 0.17
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (29 bp):
TTTTATTAAAATTAAAAAAATTAAAAAAA
Found at i:354513 original size:24 final size:24
Alignment explanation
Indices: 354455--354513 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
354445 GTTGATTGAA
* * *
354455 AATAAAAA-ATATAATTAAAAATT
1 AATAAAAATTTATAAATAAAAAAT
* *
354478 AATAATATTTTATAAATAAAAAAT
1 AATAAAAATTTATAAATAAAAAAT
354502 AATAAAAATTTA
1 AATAAAAATTTA
354514 AATTTATTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
AATAAAAATTTATAAATAAAAAAT
Found at i:362307 original size:24 final size:23
Alignment explanation
Indices: 362264--362319 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
362254 ATATAATTTA
*
362264 AATTAATATAATTATTAATTTATT
1 AATTAA-ATAATTATTAATTAATT
362288 AATTAAATAA-TATCTCAATTAATT
1 AATTAAATAATTAT-T-AATTAATT
*
362312 AATAAAAT
1 AATTAAAT
362320 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.11
23 5 0.18
24 20 0.71
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTAAATAATTATTAATTAATT
Found at i:362974 original size:1 final size:1
Alignment explanation
Indices: 362970--363027 Score: 116
Period size: 1 Copynumber: 58.0 Consensus size: 1
362960 AAATAATAAT
362970 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
363028 TATTTAAAAN
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:363804 original size:20 final size:20
Alignment explanation
Indices: 363781--363819 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
363771 ACATTATACT
363781 ATTGTCCTATATTTTATAAC
1 ATTGTCCTATATTTTATAAC
**
363801 ATTGTTTTATATTTTATAA
1 ATTGTCCTATATTTTATAA
363820 TTGTTTATCT
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:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTGTCCTATATTTTATAAC
Found at i:365661 original size:13 final size:13
Alignment explanation
Indices: 365643--365667 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
365633 TTTCAGAAAA
365643 TTTATAAAATCAT
1 TTTATAAAATCAT
365656 TTTATAAAATCA
1 TTTATAAAATCA
365668 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:373386 original size:20 final size:20
Alignment explanation
Indices: 373361--373429 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
373351 TCTAATTTCA
373361 AAATATAATATTTTATTAAT
1 AAATATAATATTTTATTAAT
**
373381 AAATATAAT-TTAAATTAAT
1 AAATATAATATTTTATTAAT
* *
373400 ATAAT-TATTAATTTATTAAT
1 A-AATATAATATTTTATTAAT
*
373420 TAA-ATAATAT
1 AAATATAATAT
373430 CTCAATTAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
19 18 0.49
20 19 0.51
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATATAATATTTTATTAAT
Found at i:373436 original size:24 final size:23
Alignment explanation
Indices: 373393--373448 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
373383 ATATAATTTA
*
373393 AATTAATATAATTATTAATTTATT
1 AATTAA-ATAATTATTAATTAATT
373417 AATTAAATAA-TATCTCAATTAATT
1 AATTAAATAATTAT-T-AATTAATT
*
373441 AATAAAAT
1 AATTAAAT
373449 TTTAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.11
23 5 0.18
24 20 0.71
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTAAATAATTATTAATTAATT
Found at i:392921 original size:129 final size:130
Alignment explanation
Indices: 392686--392936 Score: 425
Period size: 129 Copynumber: 1.9 Consensus size: 130
392676 TCATAACAAC
* * *
392686 AGAGTTTTCATCCTTTTCCAAACTGAACTGGAGAAAATAATAAGCATCTCAAAAATGCAGAATTT
1 AGAGTTTTCATACTTCTCCAAACTGAACTGGAGAAAATAATAAGCATCTCAAAAATGCACAATTT
* *
392751 TCTATGACATGCAGTTTTGGAGCTTAAGTACATACTATCCTCAATCTTCCCAAATTCCATTTGCT
66 TCTAGGACATGCAGTTTTGGAGCTTAAGTACATAATATCCTCAATCTTCCCAAATTCCATTTGCT
392816 AGAGTTTTCATACTTCTCCAAACTGAACTGGAGAAAAT-ATAAGCATCTCAAAAATGCACAATTT
1 AGAGTTTTCATACTTCTCCAAACTGAACTGGAGAAAATAATAAGCATCTCAAAAATGCACAATTT
*
392880 TCTAGGACATGCAGTTTT-GATGCTTAAGTACATAATGTCCTCAATCTTCCCAAATTC
66 TCTAGGACATGCAGTTTTGGA-GCTTAAGTACATAATATCCTCAATCTTCCCAAATTC
392937 TACAATTGCT
Statistics
Matches: 114, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
128 2 0.02
129 76 0.67
130 36 0.32
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (130 bp):
AGAGTTTTCATACTTCTCCAAACTGAACTGGAGAAAATAATAAGCATCTCAAAAATGCACAATTT
TCTAGGACATGCAGTTTTGGAGCTTAAGTACATAATATCCTCAATCTTCCCAAATTCCATTTGCT
Found at i:440224 original size:35 final size:36
Alignment explanation
Indices: 440175--440271 Score: 110
Period size: 35 Copynumber: 2.8 Consensus size: 36
440165 TGAAACACTA
440175 TTTTATACAAAACAACTAAAACAAGTGACA-CGTTAC
1 TTTTATACAAAACAACTAAAACAAGTGA-AGCGTTAC
* *
440211 TTTT-TACAGAACAACTAGAACAAGTGAAGCGTTAC
1 TTTTATACAAAACAACTAAAACAAGTGAAGCGTTAC
* * * *
440246 -TTCATGCAAAACAATTAAAATAAGTG
1 TTTTATACAAAACAACTAAAACAAGTG
440272 GAACACTACT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
34 3 0.06
35 44 0.86
36 4 0.08
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.26
Consensus pattern (36 bp):
TTTTATACAAAACAACTAAAACAAGTGAAGCGTTAC
Found at i:442401 original size:2 final size:2
Alignment explanation
Indices: 442385--442419 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
442375 GTAACATTGA
* *
442385 TC TC TC CC TC CC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
442420 GGAGTGAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:447949 original size:57 final size:57
Alignment explanation
Indices: 447842--447956 Score: 142
Period size: 57 Copynumber: 2.0 Consensus size: 57
447832 CAGTGAGGAG
* ** *
447842 CCATTAATCGTACATTGTGGAGGATATCATAGTCCTAGTGAAGCGTCATAAATCCTA
1 CCATTAATCGTACATTGTGGAGGATATCATAGTCCTAATGAAAAGCCATAAATCCTA
* * * *
447899 CCATTAATCTTATATTGTGGAGGAT-TCCATGGTTCTAATGAAAAGCCATAAATCCTA
1 CCATTAATCGTACATTGTGGAGGATAT-CATAGTCCTAATGAAAAGCCATAAATCCTA
447956 C
1 C
447957 ATCAATTGTG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
56 1 0.02
57 48 0.98
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (57 bp):
CCATTAATCGTACATTGTGGAGGATATCATAGTCCTAATGAAAAGCCATAAATCCTA
Found at i:448129 original size:60 final size:60
Alignment explanation
Indices: 448030--448204 Score: 192
Period size: 63 Copynumber: 2.9 Consensus size: 60
448020 ACCGACTAAC
* * * *
448030 AGGCCAAAACAGACAATACCTTACAGGATTATGATAGTTGGGTATCAAAGT-AAGGCC-AG
1 AGGCCAAAGCAGACAATACTTTACAGGACTATGACAGTTGGGTATCAAAGTGAA-GCCAAG
* * * *
448089 CGAGCCAAAGCAGACAATACTTTACAAGACTATGACAGTTGGGTATTAAAACTGTGAAGCCAAT
1 AG-GCCAAAGCAGACAATACTTTACAGGACTATGACAGTTGGGTA-TCAAA--GTGAAGCCAAG
* * *
448153 AGGCCAAAGCAGACAATACTTTGCAGGACCATGACAGTTGGGTATCGAAGTG
1 AGGCCAAAGCAGACAATACTTTACAGGACTATGACAGTTGGGTATCAAAGTG
448205 GGCTCTAAGG
Statistics
Matches: 96, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
59 1 0.01
60 40 0.42
61 4 0.04
62 3 0.03
63 44 0.46
64 4 0.04
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (60 bp):
AGGCCAAAGCAGACAATACTTTACAGGACTATGACAGTTGGGTATCAAAGTGAAGCCAAG
Found at i:448531 original size:45 final size:45
Alignment explanation
Indices: 448442--448542 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 45
448432 AGGAGCCGTT
* * * *
448442 AATCCTACATCATGGAGGATGTCTTGGTCCCAACGAAGATCCATG
1 AATCCTACATCATGAAGGATGCCATGGTCCCAACGAAGAGCCATG
* *
448487 AATCCTACATCATGAAGGATGCCATGGTCCTAGCG-AGAAGCCATG
1 AATCCTACATCATGAAGGATGCCATGGTCCCAACGAAG-AGCCATG
* *
448532 CATCTTACATC
1 AATCCTACATC
448543 GGTTGTGTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 2 0.04
45 45 0.96
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (45 bp):
AATCCTACATCATGAAGGATGCCATGGTCCCAACGAAGAGCCATG
Found at i:449336 original size:28 final size:28
Alignment explanation
Indices: 449301--449354 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
449291 ACATATTACA
*
449301 AACAAATAAATTATACCAAACATAAAAG
1 AACAAATAAATTACACCAAACATAAAAG
*
449329 AACAAATAAATTACATCAAACATAAA
1 AACAAATAAATTACACCAAACATAAA
449355 TAAAGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.65, C:0.15, G:0.02, T:0.19
Consensus pattern (28 bp):
AACAAATAAATTACACCAAACATAAAAG
Found at i:449696 original size:18 final size:18
Alignment explanation
Indices: 449673--449707 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
449663 AGTAAATATA
449673 TAAAATTATTAAATTAAC
1 TAAAATTATTAAATTAAC
*
449691 TAAAATTATTAATTTAA
1 TAAAATTATTAAATTAA
449708 TTTTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAATTATTAAATTAAC
Found at i:504026 original size:2 final size:2
Alignment explanation
Indices: 504014--504063 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
504004 TGAATTGAAC
*
504014 TA TA TA CA 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
504056 TA TA TA TA
1 TA TA TA TA
504064 NNNNNNNNNN
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:504085 original size:2 final size:2
Alignment explanation
Indices: 504078--504125 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
504068 NNNNNNNNNN
504078 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
504120 AT AT AT
1 AT AT AT
504126 CTGATGATGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:505271 original size:9 final size:10
Alignment explanation
Indices: 505258--505295 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
505248 TATAATTAAT
505258 TATATTAAAAA
1 TATA-TAAAAA
505269 TATATAAAAA
1 TATATAAAAA
505279 T-TA-AAAAA
1 TATATAAAAA
505287 TATATAAAA
1 TATATAAAA
505296 GTAAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 6 0.24
9 4 0.16
10 11 0.44
11 4 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TATATAAAAA
Found at i:505280 original size:26 final size:27
Alignment explanation
Indices: 505220--505282 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
505210 AAATTTAGAG
* *
505220 AAAATTCATTATTTTATAATAATTATA
1 AAAATTAATTATATTATAATAATTATA
505247 ATATAATTAATTATATTA-AA-AATATATA
1 A-A-AATTAATTATATTATAATAAT-TATA
505275 AAAATTAA
1 AAAATTAA
505283 AAAATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
26 6 0.19
27 5 0.16
28 8 0.26
29 12 0.39
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
AAAATTAATTATATTATAATAATTATA
Found at i:505283 original size:17 final size:17
Alignment explanation
Indices: 505261--505310 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
505251 AATTAATTAT
505261 ATTAAAAATATATAAAA
1 ATTAAAAATATATAAAA
505278 ATTAAAAAATATATAAAA
1 ATT-AAAAATATATAAAA
* * *
505296 GTAAAAAATAAATAA
1 ATTAAAAATATATAA
505311 TAAAATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
ATTAAAAATATATAAAA
Found at i:505287 original size:18 final size:18
Alignment explanation
Indices: 505264--505310 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
505254 TAATTATATT
*
505264 AAAAATATATAAAAATTA
1 AAAAATATATAAAAAGTA
505282 AAAAATATAT-AAAAGTA
1 AAAAATATATAAAAAGTA
*
505299 AAAAATAAATAA
1 AAAAATATATAA
505311 TAAAATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (18 bp):
AAAAATATATAAAAAGTA
Found at i:511932 original size:30 final size:29
Alignment explanation
Indices: 511896--511971 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
511886 TATTAATCAC
511896 AAAAATTTATTTAATTTAAAATAAAAATAT
1 AAAAATTTATTTAATTTAAAATAAAAA-AT
* * *
511926 AAAAATTTAATTAA-ATATAATAAAAAAT
1 AAAAATTTATTTAATTTAAAATAAAAAAT
*
511954 AATAATTTATTTACATTT
1 AAAAATTTATTTA-ATTT
511972 TTAAAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
28 13 0.34
29 11 0.29
30 14 0.37
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAAATTTATTTAATTTAAAATAAAAAAT
Found at i:517657 original size:4 final size:4
Alignment explanation
Indices: 517648--517675 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
517638 TCATTTCTAG
517648 AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA
517676 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:521234 original size:23 final size:23
Alignment explanation
Indices: 521212--521259 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
521202 TAATAGTATA
521212 AATAAAGTTTAT-TATAAGTTAT
1 AATAAAGTTTATGTATAAGTTAT
* * *
521234 AGTAATGTTTATGTATAAATTA-
1 AATAAAGTTTATGTATAAGTTAT
521256 AATA
1 AATA
521260 TATGTATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (23 bp):
AATAAAGTTTATGTATAAGTTAT
Found at i:521642 original size:218 final size:213
Alignment explanation
Indices: 521068--521708 Score: 936
Period size: 211 Copynumber: 3.0 Consensus size: 213
521058 TTTATCCATA
* *
521068 ATTATAT-C-TATATATGAAATTAATGATATAACTTATATGTTATAATGTTTTATATCACAATTT
1 ATTATATACATATATATGAAATTAATGACATAACTTATATGTTATAATGTTTTATATCAAAATTT
* *
521131 GTATAAATAATAACTAATTATAAACAATATGTTATAAAATCTAAAGTGATAGCTAATAAACTTAT
66 GTATAAATAATAACTAATTATAAACAATATGTTATAAAATCTAAAGTGATAACTAATAAAGTTAT
521196 TAAGTGTAATAGTATAAATAAAGTTTATTATAAGTTATAGTAATGTTTATGTATAAATTAAATAT
131 TAAGTGTAATA-TATAAATAAAGTTTATTATAAGTTATAGTAATGTTT-TGTATAAATTAAATAT
521261 ATGTATATATAATATATTTT
194 ATGTATATATAATATATTTT
* * * *
521281 TTTAT-TATATATATAT--AATTAATGAACA-AA-TTATATGTTAAAATGTTTTATATCAAAGTT
1 ATTATATACATATATATGAAATTAATG-ACATAACTTATATGTTATAATGTTTTATATCAAAATT
* * * *
521341 TGTATAAATAATAATTAATTATAAACAATATGTTATAAAATCTAATGTAACAACTAATAAAGTTA
65 TGTATAAATAATAACTAATTATAAACAATATGTTATAAAATCTAAAGTGATAACTAATAAAGTTA
* *
521406 TTAAGTGTAATAATATAAATAAAGTCTATTATAAGTTATAGTAATACTTTTGTATAAATTAAATA
130 TTAAGTGTAAT-ATATAAATAAAGTTTATTATAAGTTATAGTAAT-GTTTTGTATAAATTAAATA
521471 TATGTATATATAATATATGACTTT
193 TATGTATATATAATATAT---TTT
521495 ATTATATACATATATATGAAATTAATGACATAACTTATATGTTATAATGTTTTATATCAAAATTT
1 ATTATATACATATATATGAAATTAATGACATAACTTATATGTTATAATGTTTTATATCAAAATTT
* * *
521560 GTACAAATAATAACTAATTATAAACAATATGTTATAAAATCTAAGGTGATAACTAATAAAGTTAC
66 GTATAAATAATAACTAATTATAAACAATATGTTATAAAATCTAAAGTGATAACTAATAAAGTTAT
* * * * *
521625 CAAATGTAATCATATAAATCAAGTTTATTATAAATTATAGTAATGTGTATGTATAAATTAAATAT
131 TAAGTGTAAT-ATATAAATAAAGTTTATTATAAGTTATAGTAATGT-TTTGTATAAATTAAATAT
*
521690 ATGTACATATAATATATTT
194 ATGTATATATAATATATTT
521709 ATACAATTAT
Statistics
Matches: 381, Mismatches: 33, Indels: 26
0.87 0.08 0.06
Matches are distributed among these distances:
211 161 0.42
212 15 0.04
213 6 0.02
214 14 0.04
215 12 0.03
216 3 0.01
217 11 0.03
218 159 0.42
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (213 bp):
ATTATATACATATATATGAAATTAATGACATAACTTATATGTTATAATGTTTTATATCAAAATTT
GTATAAATAATAACTAATTATAAACAATATGTTATAAAATCTAAAGTGATAACTAATAAAGTTAT
TAAGTGTAATATATAAATAAAGTTTATTATAAGTTATAGTAATGTTTTGTATAAATTAAATATAT
GTATATATAATATATTTT
Found at i:522018 original size:16 final size:17
Alignment explanation
Indices: 521996--522044 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
521986 ATTCTTTTTA
521996 ATATATATAAAAAATAT
1 ATATATATAAAAAATAT
* *
522013 -TATATATATTAATATAT
1 ATATATATA-AAAAATAT
*
522030 ATATTTATAAAAAAT
1 ATATATATAAAAAAT
522045 TAATTTGATT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
16 8 0.32
17 10 0.40
18 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATATATAAAAAATAT
Found at i:530433 original size:27 final size:27
Alignment explanation
Indices: 530394--530446 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
530384 CACACTACAT
530394 AGTGTATCAGAAGTTGAAGCTAAGAAG
1 AGTGTATCAGAAGTTGAAGCTAAGAAG
*
530421 AGTGTATCGGAAGTTGAAGCTAAGAA
1 AGTGTATCAGAAGTTGAAGCTAAGAA
530447 AATGGGTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.30, T:0.23
Consensus pattern (27 bp):
AGTGTATCAGAAGTTGAAGCTAAGAAG
Found at i:534498 original size:21 final size:21
Alignment explanation
Indices: 534474--534513 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
534464 TTAAGTATAA
**
534474 TATTTTAACTTTTTTAAAAAT
1 TATTTTAAAATTTTTAAAAAT
534495 TATTTTAAAATTTTTAAAA
1 TATTTTAAAATTTTTAAAA
534514 TAAATATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTTAAAATTTTTAAAAAT
Found at i:535582 original size:12 final size:12
Alignment explanation
Indices: 535565--535589 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
535555 TTATTTATTT
535565 TTTTTATAATTA
1 TTTTTATAATTA
535577 TTTTTATAATTA
1 TTTTTATAATTA
535589 T
1 T
535590 AGATTTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTATAATTA
Found at i:535677 original size:18 final size:18
Alignment explanation
Indices: 535640--535679 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
535630 ATATTTTTAT
**
535640 TTAATCGTGTAAAATGTG
1 TTAATCGTGTAAAACATG
*
535658 TTAATTGTGTAAAACATG
1 TTAATCGTGTAAAACATG
535676 TTAA
1 TTAA
535680 AAGAGTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (18 bp):
TTAATCGTGTAAAACATG
Found at i:545463 original size:2 final size:2
Alignment explanation
Indices: 545456--545491 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
545446 AAAATCAATA
*
545456 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
545492 GGATGATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:546131 original size:33 final size:30
Alignment explanation
Indices: 546050--546128 Score: 122
Period size: 30 Copynumber: 2.6 Consensus size: 30
546040 CAAGAGCAAA
* **
546050 AAGAAGATAAACGACAACACCATCATCAAG
1 AAGAAGATAAACAACAACAGAATCATCAAG
546080 AAGAAGATAAACAACAACAGAATCATCAAG
1 AAGAAGATAAACAACAACAGAATCATCAAG
*
546110 AAGAAGATAAAGAACAACA
1 AAGAAGATAAACAACAACA
546129 ACAAGAACGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.59, C:0.18, G:0.14, T:0.09
Consensus pattern (30 bp):
AAGAAGATAAACAACAACAGAATCATCAAG
Done.