Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1396
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: 309291
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 3
Found at i:123377 original size:26 final size:26
Alignment explanation
Indices: 123324--123384 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
123314 AAATTTATAT
* ** *
123324 ATATAATA-TTTTAAATATAATTATG
1 ATATAATATTTTTAAAAATAAACAAG
123349 ATATAATATTTTTAAAAATAAACAAG
1 ATATAATATTTTTAAAAATAAACAAG
123375 ATATGAATAT
1 ATAT-AATAT
123385 ATAAGTTCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 8 0.27
26 17 0.57
27 5 0.17
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (26 bp):
ATATAATATTTTTAAAAATAAACAAG
Found at i:125518 original size:3 final size:3
Alignment explanation
Indices: 125510--125553 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
125500 AGCTAGCTAG
125510 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
125554 TCATTGCTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:127426 original size:6 final size:6
Alignment explanation
Indices: 127406--127443 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
127396 ACATTAAAAA
*
127406 TTTCCT TTT-TT TTTCTT TTTCTT TTTCTT TTT-TT TTTC
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC
127444 AGTTGACTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 9 0.31
6 20 0.69
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:128559 original size:2 final size:2
Alignment explanation
Indices: 128552--128606 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
128542 ATTAAACTAC
* * * * * *
128552 TA TA TA TA TA TA TA TA TA CA CA CA CA CA CA 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
128594 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
128607 GGATTTTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (2 bp):
TA
Found at i:130182 original size:21 final size:22
Alignment explanation
Indices: 130140--130194 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
130130 ATTATCTAAC
* *
130140 TTATTTTTTGTATCATGCAGTTG
1 TTATTTTTTTTATCA-GAAGTTG
130163 TTATTTTTTTTATCA-AAGTTG
1 TTATTTTTTTTATCAGAAGTTG
*
130184 CTATTTTTTTT
1 TTATTTTTTTT
130195 TGTATTTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 15 0.52
23 14 0.48
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.64
Consensus pattern (22 bp):
TTATTTTTTTTATCAGAAGTTG
Found at i:131016 original size:27 final size:28
Alignment explanation
Indices: 130986--131039 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
130976 AAAATTATTG
130986 TTAAAAATAA-TTTTTATTTTAAAAATT
1 TTAAAAATAATTTTTTATTTTAAAAATT
*
131013 TTAAAAATAATTTTTTATTTTTAAAAT
1 TTAAAAATAATTTTTTATTTTAAAAAT
131040 ATAATTGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTAAAAATAATTTTTTATTTTAAAAATT
Found at i:131029 original size:14 final size:13
Alignment explanation
Indices: 130940--131027 Score: 67
Period size: 13 Copynumber: 6.8 Consensus size: 13
130930 ATTTTAAAAT
*
130940 AAATATTTTTTAA
1 AAATAATTTTTAA
130953 AAAT--TTTTTAA
1 AAATAATTTTTAA
* *
130964 AGATAATTTTAAA
1 AAATAATTTTTAA
* *
130977 AAATTATTGTTAA
1 AAATAATTTTTAA
*
130990 AAATAATTTTTATTTT
1 AAATAATTTTTA---A
131006 AAA-AA-TTTTAA
1 AAATAATTTTTAA
131017 AAATAATTTTT
1 AAATAATTTTT
131028 TATTTTTAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
11 13 0.22
12 2 0.03
13 33 0.57
14 5 0.09
15 2 0.03
16 3 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (13 bp):
AAATAATTTTTAA
Found at i:134681 original size:25 final size:24
Alignment explanation
Indices: 134630--134693 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
134620 TATTTTTTAA
134630 AAAT-TTAAT-TATAAAAATATAT
1 AAATATTAATATATAAAAATATAT
134652 AAATATTAATATATAAATAATATAT
1 AAATATTAATATATAAA-AATATAT
* *
134677 TAATATAAATA-ATAAAA
1 AAATATTAATATATAAAA
134694 TAAAATTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
22 4 0.11
23 6 0.16
24 11 0.30
25 16 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATATTAATATATAAAAATATAT
Found at i:134704 original size:25 final size:25
Alignment explanation
Indices: 134639--134704 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 25
134629 AAAATTTAAT
* * *
134639 TATAAA-AATATATAAATATTAATA
1 TATAAATAAAATATTAATATAAATA
*
134663 TATAAATAATATATTAATATAAATA
1 TATAAATAAAATATTAATATAAATA
*
134688 -ATAAAATAAAATTTTAA
1 TAT-AAATAAAATATTAA
134705 ATTATCTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 8 0.22
25 28 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TATAAATAAAATATTAATATAAATA
Found at i:136839 original size:16 final size:17
Alignment explanation
Indices: 136759--136839 Score: 57
Period size: 16 Copynumber: 5.0 Consensus size: 17
136749 ATATATGTAT
136759 TAAAAT-TTATATAATA
1 TAAAATATTATATAATA
** *
136775 TTCATTATTA-ATACAT-
1 TAAAATATTATATA-ATA
136791 TAAAAT-TTATATAAATA
1 TAAAATATTATAT-AATA
*
136808 TAAAATATTTTA-AATA
1 TAAAATATTATATAATA
*
136824 T-AATTATTATATAATA
1 TAAAATATTATATAATA
136840 AAATAAAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
15 11 0.22
16 22 0.45
17 12 0.24
18 4 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAATATTATATAATA
Found at i:137009 original size:6 final size:6
Alignment explanation
Indices: 136998--137033 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
136988 CCCAATATTA
136998 TGTGTC TGTGTC TGTGTC TGTGTC TGTGTC TGTGTC
1 TGTGTC TGTGTC TGTGTC TGTGTC TGTGTC TGTGTC
137034 CGTGCTAGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.17, G:0.33, T:0.50
Consensus pattern (6 bp):
TGTGTC
Found at i:139073 original size:20 final size:20
Alignment explanation
Indices: 139030--139073 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
139020 ATTTTTTTCT
* * **
139030 AATTTTTTATCGATTTAATT
1 AATTTTTTATCAATTCAAAA
139050 AATTTTTTATCAATTCAAAA
1 AATTTTTTATCAATTCAAAA
139070 AATT
1 AATT
139074 ACGGATGATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (20 bp):
AATTTTTTATCAATTCAAAA
Found at i:140743 original size:2 final size:2
Alignment explanation
Indices: 140736--140761 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
140726 TTTTGAAATA
140736 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
140762 CCTCATACTT
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:141092 original size:2 final size:2
Alignment explanation
Indices: 141085--141117 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
141075 ATTGAAAAAC
141085 AT 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 AT A
141118 AAGAGCATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:144508 original size:22 final size:22
Alignment explanation
Indices: 144462--144506 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
144452 GATTCATGTG
*
144462 AATTTAATTAATTTAAATATTA
1 AATTTAATTAATTAAAATATTA
*
144484 AATTTGATTAATTAAAAT-TTA
1 AATTTAATTAATTAAAATATTA
144505 AA
1 AA
144507 ATGATTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AATTTAATTAATTAAAATATTA
Found at i:144692 original size:2 final size:2
Alignment explanation
Indices: 144685--144713 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
144675 ATAAGAGAAT
144685 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
144714 GCTCAATAAC
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:151717 original size:16 final size:15
Alignment explanation
Indices: 151669--151722 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 15
151659 TTTAATCTAT
*
151669 ATTTAAAAAAT-AAA
1 ATTTAAAATATAAAA
**
151683 ATTTAAAATATAATT
1 ATTTAAAATATAAAA
151698 ATTTAAATATATAAAA
1 ATTTAAA-ATATAAAA
151714 ATTTTAAAA
1 A-TTTAAAA
151723 ATTTAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 10 0.31
15 8 0.25
16 8 0.25
17 6 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTTAAAATATAAAA
Found at i:152323 original size:13 final size:14
Alignment explanation
Indices: 152302--152334 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
152292 ATGCATCATA
*
152302 TTTTAAAAATTATT
1 TTTTAAAATTTATT
152316 TTTTAAAATTTATT
1 TTTTAAAATTTATT
152330 TTTTA
1 TTTTA
152335 TGAATAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTAAAATTTATT
Found at i:152604 original size:17 final size:17
Alignment explanation
Indices: 152582--152614 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
152572 TATTGATTGA
152582 TATAAAATTTTAATTTT
1 TATAAAATTTTAATTTT
*
152599 TATAAAATTTTGATTT
1 TATAAAATTTTAATTT
152615 ATTTGATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TATAAAATTTTAATTTT
Found at i:153065 original size:37 final size:39
Alignment explanation
Indices: 153024--153105 Score: 107
Period size: 37 Copynumber: 2.2 Consensus size: 39
153014 TACATAACGT
*
153024 TTATTTGTTAAAATAAAATAAAATT-ATAATTA-AATAA
1 TTATTTATTAAAATAAAATAAAATTAATAATTATAATAA
* *
153061 TTATTTATTAAAATTAAATTAAATTAAATAATTATAATAA
1 TTATTTATTAAAATAAAATAAAATT-AATAATTATAATAA
153101 -TATTT
1 TTATTT
153106 TAATTTAGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
37 22 0.56
39 12 0.31
40 5 0.13
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (39 bp):
TTATTTATTAAAATAAAATAAAATTAATAATTATAATAA
Found at i:153095 original size:27 final size:27
Alignment explanation
Indices: 153042--153095 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
153032 TAAAATAAAA
* *
153042 TAAAATTATAATTAAATAATTATTTAT
1 TAAAATTATAATTAAATAAATAATTAT
153069 TAAAATTA-AATTAAATTAAATAATTAT
1 TAAAATTATAATTAAA-TAAATAATTAT
153096 AATAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TAAAATTATAATTAAATAAATAATTAT
Found at i:156962 original size:7 final size:7
Alignment explanation
Indices: 156944--156975 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
156934 TCTGCTTTAG
156944 CTGTCT-
1 CTGTCTC
156950 CTGTCTC
1 CTGTCTC
156957 CTGTCTC
1 CTGTCTC
156964 CTGTCTC
1 CTGTCTC
156971 CTGTC
1 CTGTC
156976 ACTGTCTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.00, C:0.41, G:0.16, T:0.44
Consensus pattern (7 bp):
CTGTCTC
Found at i:156969 original size:14 final size:13
Alignment explanation
Indices: 156944--156983 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
156934 TCTGCTTTAG
156944 CTGTCTCTGTCTC
1 CTGTCTCTGTCTC
156957 CTGTCTCCTGTCTC
1 CTGTCT-CTGTCTC
*
156971 CTGTCACTGTCTC
1 CTGTCTCTGTCTC
156984 ACTCTCCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.03, C:0.40, G:0.15, T:0.42
Consensus pattern (13 bp):
CTGTCTCTGTCTC
Found at i:163130 original size:20 final size:18
Alignment explanation
Indices: 163088--163131 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
163078 AAATTTTATC
163088 AAAAATAAAAAATATATATA
1 AAAAATAAAAAATATA-A-A
* *
163108 AAATATAAAAACTATAAA
1 AAAAATAAAAAATATAAA
163126 AAAAAT
1 AAAAAT
163132 TTAGTTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 1 0.05
20 14 0.67
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATAAAAAATATAAA
Found at i:164305 original size:2 final size:2
Alignment explanation
Indices: 164298--164343 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
164288 AGACCATGGA
164298 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
164340 AT AT
1 AT AT
164344 TAAAGACAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:168196 original size:2 final size:2
Alignment explanation
Indices: 168189--168214 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
168179 GTCCTATTAA
168189 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
168215 TTTTCAGTAT
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:168667 original size:52 final size:52
Alignment explanation
Indices: 168589--168692 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
168579 TACTGGAAGG
168589 ATTTTACTTTAGGATTTAGTTAATTTTGTTTAAGGATTAGTATAGCCTTTAA
1 ATTTTACTTTAGGATTTAGTTAATTTTGTTTAAGGATTAGTATAGCCTTTAA
*
168641 ATTTTACTTTAGGATTTAGTTAATTTTGTTTAAGGATTAGTGTAGCCTTTAA
1 ATTTTACTTTAGGATTTAGTTAATTTTGTTTAAGGATTAGTATAGCCTTTAA
168693 TTAATGCAGT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (52 bp):
ATTTTACTTTAGGATTTAGTTAATTTTGTTTAAGGATTAGTATAGCCTTTAA
Found at i:169091 original size:37 final size:37
Alignment explanation
Indices: 169049--169132 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
169039 GTCATTTTAG
* * *
169049 GTTTAACACTCAA-ATTAATTAGATTTTGATCAATCGA
1 GTTTAACACT-AAGATTAATTAAATTTAGATCAATCAA
*
169086 GTTTAACACTAAGGTTAATTAAATTTAGATCAATCAA
1 GTTTAACACTAAGATTAATTAAATTTAGATCAATCAA
169123 GTTTAACACT
1 GTTTAACACT
169133 TGGACTTTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 2 0.05
37 40 0.95
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (37 bp):
GTTTAACACTAAGATTAATTAAATTTAGATCAATCAA
Found at i:170895 original size:22 final size:22
Alignment explanation
Indices: 170867--170908 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
170857 TTAAAAATTT
*
170867 TATTTTTATAGTAAAATTTATA
1 TATTTTTATAATAAAATTTATA
*
170889 TATTTTTATAATTAAATTTA
1 TATTTTTATAATAAAATTTA
170909 AATAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTTTTATAATAAAATTTATA
Found at i:171088 original size:30 final size:30
Alignment explanation
Indices: 171048--171127 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
171038 CAAGTCTATG
*
171048 CTTAAATAAATCATTTAA-CTTTAATTTATA
1 CTTAAATAAAT-ATTTAATATTTAATTTATA
* *
171078 TTTGAATAAAT-TATTAATATTTAATTTATA
1 CTTAAATAAATAT-TTAATATTTAATTTATA
171108 CTTAAATAAATATTTAATAT
1 CTTAAATAAATATTTAATAT
171128 AAATAAACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
28 1 0.02
29 4 0.10
30 36 0.86
31 1 0.02
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.49
Consensus pattern (30 bp):
CTTAAATAAATATTTAATATTTAATTTATA
Found at i:171381 original size:34 final size:34
Alignment explanation
Indices: 171316--171382 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
171306 TATAATTTAT
*
171316 ATAAATAAAACATAAAATATAATAATAAAATTAA
1 ATAAATAAAACATAAAATAAAATAATAAAATTAA
* * *
171350 ATAAATAAAA-ATCATATAAAATATATGAAATTA
1 ATAAATAAAACATAAAATAAAATA-ATAAAATTA
171383 CGTTGTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 10 0.36
34 18 0.64
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.28
Consensus pattern (34 bp):
ATAAATAAAACATAAAATAAAATAATAAAATTAA
Found at i:171677 original size:50 final size:50
Alignment explanation
Indices: 171583--171679 Score: 128
Period size: 50 Copynumber: 1.9 Consensus size: 50
171573 TATTAATAAA
* *
171583 AAATAAAAATATTTTTATATTAATAATTATATATTTTAATAATTAAATTT
1 AAATAAAAATATTTTTATATTAATAATAATATATTTGAATAATTAAATTT
171633 AAATAAAAATATTTTTATTATT-A-AATAATA-ATTTGAATCGAATTAAA
1 AAATAAAAATATTTTTA-TATTAATAATAATATATTTGAAT--AATTAAA
171680 ATAGTTCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
48 7 0.17
49 6 0.14
50 25 0.60
51 4 0.10
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (50 bp):
AAATAAAAATATTTTTATATTAATAATAATATATTTGAATAATTAAATTT
Found at i:173066 original size:9 final size:9
Alignment explanation
Indices: 173054--173105 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
173044 ACATAAAAAT
173054 AATATAATA
1 AATATAATA
*
173063 AATATGATA
1 AATATAATA
**
173072 TAATATGTTTA
1 -AATAT-AATA
*
173083 AATATAATT
1 AATATAATA
173092 AATATAATA
1 AATATAATA
173101 AATAT
1 AATAT
173106 TTAATACACA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
9 22 0.65
10 10 0.29
11 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (9 bp):
AATATAATA
Found at i:173457 original size:13 final size:13
Alignment explanation
Indices: 173424--173461 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
173414 TTCATATCTG
*
173424 ATAT-ATTTAAAT
1 ATATAATTTAAAA
173436 ATA-AATTTAAAA
1 ATATAATTTAAAA
173448 ATATAATTTAAAA
1 ATATAATTTAAAA
173461 A
1 A
173462 AACTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATAATTTAAAA
Found at i:173462 original size:14 final size:14
Alignment explanation
Indices: 173432--173461 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
173422 TGATATATTT
173432 AAATATAAATTTAA
1 AAATATAAATTTAA
173446 AAATAT-AATTTAA
1 AAATATAAATTTAA
173459 AAA
1 AAA
173462 AACTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATAAATTTAA
Found at i:173967 original size:6 final size:6
Alignment explanation
Indices: 173956--173981 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
173946 AGCCTCACAG
173956 CTAGAA CTAGAA CTAGAA CTAGAA CT
1 CTAGAA CTAGAA CTAGAA CTAGAA CT
173982 GCCATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.19
Consensus pattern (6 bp):
CTAGAA
Found at i:174852 original size:2 final size:2
Alignment explanation
Indices: 174845--174874 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
174835 AAGTGAATCT
174845 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
174875 CTTAAAAAAA
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):
TA
Found at i:175046 original size:16 final size:16
Alignment explanation
Indices: 175027--175095 Score: 52
Period size: 16 Copynumber: 4.2 Consensus size: 16
175017 ATATAATTAT
175027 ATTATTAAATTTAAAA
1 ATTATTAAATTTAAAA
**
175043 ATTATTTTA-TTAAAA
1 ATTATTAAATTTAAAA
* *
175058 TATTAAT-AATATAAAA
1 -ATTATTAAATTTAAAA
*
175074 ATTATAAAAATTTATAAA
1 ATTAT-TAAATTTA-AAA
175092 ATTA
1 ATTA
175096 ATTTAATTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
15 11 0.28
16 17 0.43
17 5 0.12
18 7 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTATTAAATTTAAAA
Found at i:175722 original size:16 final size:18
Alignment explanation
Indices: 175703--175735 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
175693 ATTTAACAAT
175703 TTAATT-TATT-AAAATA
1 TTAATTATATTCAAAATA
175719 TTAATTATATTCAAAAT
1 TTAATTATATTCAAAAT
175736 TTTTTTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAATTATATTCAAAATA
Found at i:175968 original size:4 final size:4
Alignment explanation
Indices: 175959--175983 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
175949 TAATTTTTAG
175959 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
175984 TTGCAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:176204 original size:14 final size:14
Alignment explanation
Indices: 176181--176210 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
176171 AATTTATAAA
*
176181 AATAATATATATTT
1 AATAAAATATATTT
176195 AATAAAATATATTT
1 AATAAAATATATTT
176209 AA
1 AA
176211 ACATAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATAAAATATATTT
Found at i:177147 original size:18 final size:16
Alignment explanation
Indices: 177124--177159 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
177114 TTGAATTTAA
177124 TTTGATTTAAAATTATTT
1 TTTGA-TTAAAA-TATTT
177142 TTTGATTAAAATATTT
1 TTTGATTAAAATATTT
177158 TT
1 TT
177160 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 6 0.33
18 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
TTTGATTAAAATATTT
Found at i:177440 original size:21 final size:22
Alignment explanation
Indices: 177377--177441 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
177367 TATATATTAT
* * **
177377 TTATAATTAATAATTAAAAATA
1 TTATATTTTATAATTAAATTTA
177399 TTATATTTTAT-ATTAATATTTA
1 TTATATTTTATAATTAA-ATTTA
177421 -TATATTTTATAATTAAATTTA
1 TTATATTTTATAATTAAATTTA
177442 AATAAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 20 0.54
22 17 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATATTTTATAATTAAATTTA
Found at i:177464 original size:22 final size:23
Alignment explanation
Indices: 177426--177488 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 23
177416 ATTTATATAT
177426 TTTATAATTAAATTTAAATAAA-AA
1 TTTATAA-TAAA-TTAAATAAATAA
*
177450 TATTTTAAT-AATTAAA-AAATAA
1 T-TTATAATAAATTAAATAAATAA
177472 TTTATAATAAATTAAAT
1 TTTATAATAAATTAAAT
177489 TAATTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
21 9 0.27
22 15 0.45
23 2 0.06
24 2 0.06
25 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTATAATAAATTAAATAAATAA
Found at i:177467 original size:18 final size:21
Alignment explanation
Indices: 177440--177509 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 21
177430 TAATTAAATT
177440 TAAA-TAAAAAT-ATTT-TAA
1 TAAATTAAAAATAATTTATAA
177458 T-AATTAAAAAATAATTTATAA
1 TAAATT-AAAAATAATTTATAA
*
177479 TAAATT-AAATTAATTTA-AA
1 TAAATTAAAAATAATTTATAA
* *
177498 TTAATAAAAAAT
1 TAAATTAAAAAT
177510 TTATTAAACG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
17 2 0.05
18 2 0.05
19 12 0.29
20 18 0.43
21 4 0.10
22 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATTAAAAATAATTTATAA
Found at i:177483 original size:39 final size:37
Alignment explanation
Indices: 177440--177542 Score: 88
Period size: 37 Copynumber: 2.7 Consensus size: 37
177430 TAATTAAATT
*
177440 TAAATAAAAATATTTTAATAATTAA-AAAATAATTTATAA
1 TAAATAAAAATAATTT-A-AATTAATAAAA-AATTTATAA
* *
177479 TAAATTAAATTAATTTAAATTAATAAAAAATTTAT--
1 TAAATAAAAATAATTTAAATTAATAAAAAATTTATAA
*
177514 TAAACGAAACGAATAATTT-AATTAATAAA
1 TAAA-TAAA--AATAATTTAAATTAATAAA
177543 GTAGTCAAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
35 4 0.07
36 2 0.04
37 23 0.43
38 12 0.22
39 13 0.24
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (37 bp):
TAAATAAAAATAATTTAAATTAATAAAAAATTTATAA
Found at i:179091 original size:210 final size:212
Alignment explanation
Indices: 178666--179091 Score: 610
Period size: 210 Copynumber: 2.0 Consensus size: 212
178656 CATAAACATT
* * *
178666 TTTTTATTAAGATAAAATTAACCATAAACTTATATAAGTGTCCATATTTTATTATAATTGTATGT
1 TTTTTATTAAGATAAAATTAACCATAAACTTATATAAGTATCAATATTTTATTATAATTATATGT
* * *
178731 ATTTTTTTACTAGAATAATTATATATGTCTAGTCATGTTCTTCCACCCTTATTTCCATTATTTTT
66 AATTTTTTACTAAAATAATTATATATGTCTAGTCATGTTATTCCACCCTTATTTCCATTATTTTT
* * * * *
178796 TAATTTAAAAGACATCACAAAATAAAAAATTTTTAGAGACGAGATAAGAGAACGAATAAAAGAAT
131 TAATTTAAAAGACATCACAAAATAAAAAAATTTTAAAGACAAGATAAGAGAACGAATAAAAAAAA
* *
178861 TATCCTTTTTATCTTGA
196 CATCATTTTTATCTTGA
**
178878 TTTTTATTAAGATAAAATTAACTTTAAACTTATATAAGTATCAATATTTTATTATAATTATATGT
1 TTTTTATTAAGATAAAATTAACCATAAACTTATATAAGTATCAATATTTTATTATAATTATATGT
* * *
178943 AATTTTTTACTAAAATAA-T-TATGTGTCTAGTCATGTTATTCCACCTTTCTTTCCATTATTTTT
66 AATTTTTTACTAAAATAATTATATATGTCTAGTCATGTTATTCCACCCTTATTTCCATTATTTTT
* *
179006 TAATTTAAAAGATATTACAAAATAAAAAAATTTTAAAGACAAGATAAGACG-AC-AATTAGAAAA
131 TAATTTAAAAGACATCACAAAATAAAAAAATTTTAAAGACAAGATAAGA-GAACGAA-TA-AAAA
179069 AAACATCATTTTTATC-TGA
193 AAACATCATTTTTATCTTGA
179088 TTTT
1 TTTT
179092 AGAGAATAAA
Statistics
Matches: 191, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
209 2 0.01
210 95 0.50
211 18 0.09
212 76 0.40
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (212 bp):
TTTTTATTAAGATAAAATTAACCATAAACTTATATAAGTATCAATATTTTATTATAATTATATGT
AATTTTTTACTAAAATAATTATATATGTCTAGTCATGTTATTCCACCCTTATTTCCATTATTTTT
TAATTTAAAAGACATCACAAAATAAAAAAATTTTAAAGACAAGATAAGAGAACGAATAAAAAAAA
CATCATTTTTATCTTGA
Found at i:179233 original size:21 final size:22
Alignment explanation
Indices: 179207--179247 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
179197 ATTCTTAAAA
179207 TTTTTAAAAATAATT-TTTAAT
1 TTTTTAAAAATAATTATTTAAT
*
179228 TTTTTAAAGATAATTATTTA
1 TTTTTAAAAATAATTATTTA
179248 CAATTTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTTTAAAAATAATTATTTAAT
Found at i:179514 original size:15 final size:16
Alignment explanation
Indices: 179456--179516 Score: 63
Period size: 15 Copynumber: 3.8 Consensus size: 16
179446 TTAAAAAAAT
179456 TTAAATAAAATTTTAAA
1 TTAAAT-AAATTTTAAA
* **
179473 TTTAATAAA-ACTAAA
1 TTAAATAAATTTTAAA
179488 TTAAATTAAATTTTAAA
1 TTAAA-TAAATTTTAAA
179505 -TAAATAAATTTT
1 TTAAATAAATTTT
179517 TTATTTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
15 16 0.44
16 11 0.31
17 9 0.25
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAATAAATTTTAAA
Found at i:179863 original size:20 final size:21
Alignment explanation
Indices: 179822--179866 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
179812 GATTTGATAA
* *
179822 ATTTAATTAAAATTATTATTT
1 ATTTAATAAAAATAATTATTT
179843 ATTTAATAAAAATAATT-TTT
1 ATTTAATAAAAATAATTATTT
179863 ATTT
1 ATTT
179867 TTAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTAATAAAAATAATTATTT
Found at i:180449 original size:19 final size:19
Alignment explanation
Indices: 180425--180465 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
180415 TTGATTAAAA
180425 TTAATTTAATTCGGTTCAT
1 TTAATTTAATTCGGTTCAT
* * *
180444 TTAATTTAGTTTGGTTGAT
1 TTAATTTAATTCGGTTCAT
180463 TTA
1 TTA
180466 GTAAATCGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.15, T:0.56
Consensus pattern (19 bp):
TTAATTTAATTCGGTTCAT
Found at i:180816 original size:15 final size:15
Alignment explanation
Indices: 180796--180830 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
180786 ATTTGATAAA
180796 TTGAAAAATTAAATG
1 TTGAAAAATTAAATG
*
180811 TTGAAAAATTAAGTG
1 TTGAAAAATTAAATG
180826 TTGAA
1 TTGAA
180831 TTTTTAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (15 bp):
TTGAAAAATTAAATG
Found at i:181864 original size:21 final size:22
Alignment explanation
Indices: 181825--181867 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
181815 AATAAGTATT
181825 AAATATATGTAATAATTAATAAA
1 AAATATATGTAAT-ATTAATAAA
*
181848 AAATATATGTAGT-TTAATAA
1 AAATATATGTAATATTAATAA
181868 TACATTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (22 bp):
AAATATATGTAATATTAATAAA
Found at i:182412 original size:2 final size:2
Alignment explanation
Indices: 182400--182430 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
182390 TTGAGAGTTA
182400 AT AT CAT 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
182431 TAATGTGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:182501 original size:13 final size:13
Alignment explanation
Indices: 182479--182508 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
182469 ATTTTAATAT
*
182479 ATATCTAATATAA
1 ATATCGAATATAA
182492 ATATCGAATATAA
1 ATATCGAATATAA
182505 ATAT
1 ATAT
182509 TTTAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (13 bp):
ATATCGAATATAA
Found at i:183102 original size:24 final size:24
Alignment explanation
Indices: 183070--183117 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
183060 AAACCTAAGG
183070 TGCAGACATGAACTTGATTGGCGA
1 TGCAGACATGAACTTGATTGGCGA
183094 TGCAGACATGAACTTGATTGGCGA
1 TGCAGACATGAACTTGATTGGCGA
183118 AGAGGAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (24 bp):
TGCAGACATGAACTTGATTGGCGA
Found at i:188103 original size:19 final size:22
Alignment explanation
Indices: 188065--188106 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
188055 AGTTCAATCG
188065 ATTTAATTGATAAAATTAAATT
1 ATTTAATTGATAAAATTAAATT
188087 ATTTAATT-A-AAAA-TAAATT
1 ATTTAATTGATAAAATTAAATT
188106 A
1 A
188107 AATATTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 4 0.20
21 1 0.05
22 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTTAATTGATAAAATTAAATT
Found at i:189286 original size:2 final size:2
Alignment explanation
Indices: 189275--189318 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
189265 ATTTATCTTT
189275 TA TA TA -A 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
189316 TA T
1 TA T
189319 TAGTATTTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:192602 original size:25 final size:26
Alignment explanation
Indices: 192574--192623 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
192564 TTATGTATTC
192574 GTATTGTGT-ATATATTATTTTTTTT
1 GTATTGTGTCATATATTATTTTTTTT
* *
192599 GTATTGTGTCATGTTTTATTTTTTT
1 GTATTGTGTCATATATTATTTTTTT
192624 ATATGTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (26 bp):
GTATTGTGTCATATATTATTTTTTTT
Found at i:192952 original size:150 final size:151
Alignment explanation
Indices: 192782--193077 Score: 540
Period size: 150 Copynumber: 2.0 Consensus size: 151
192772 TCCCCGTCGC
*
192782 GATAGGAACTTGAATTTTTTTTATATAATTTCAATTATATTAAATAGTGATTATTTATTTGAATA
1 GATAGGAACTTGAATTTTTTTTATATAATTTCAATTATATTAAATAGTGATTATTTATTTAAATA
*
192847 TTTGAATATATAAATTAATTATATTTTTAATATAAAATTAAATATTTGCAATTATATCTGCC-AA
66 TTTGAATATATAAATTAATTATATTTTTAATATAAAATTAAATATTTGAAATTATATCTGCCTAA
192911 AAAAAAAGTTTATTACGTTGT
131 AAAAAAAGTTTATTACGTTGT
192932 GATAGGAACTTGAATTTTTTTTATATAATTTCAATTATATTAAATAGTGATTATTTATTTAAATA
1 GATAGGAACTTGAATTTTTTTTATATAATTTCAATTATATTAAATAGTGATTATTTATTTAAATA
* * *
192997 TTTTAATATATAAATTAATTATATTTTTAATATAAAATTAAATATTTTAAATTATATCTGCCTCA
66 TTTGAATATATAAATTAATTATATTTTTAATATAAAATTAAATATTTGAAATTATATCTGCCTAA
193062 AAAAAAAGTTTATTAC
131 AAAAAAAGTTTATTAC
193078 CTAAATCAAT
Statistics
Matches: 140, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
150 123 0.88
151 17 0.12
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (151 bp):
GATAGGAACTTGAATTTTTTTTATATAATTTCAATTATATTAAATAGTGATTATTTATTTAAATA
TTTGAATATATAAATTAATTATATTTTTAATATAAAATTAAATATTTGAAATTATATCTGCCTAA
AAAAAAAGTTTATTACGTTGT
Found at i:193021 original size:23 final size:20
Alignment explanation
Indices: 192990--193046 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 20
192980 GATTATTTAT
192990 TTAAATATTTTAATATATAAA
1 TTAAATATTTTAATATA-AAA
193011 TTAATTATATTTTTAATATAAAA
1 TTAA--ATA-TTTTAATATAAAA
193034 TTAAATATTTTAA
1 TTAAATATTTTAA
193047 ATTATATCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
20 6 0.18
21 7 0.21
23 10 0.30
24 10 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAAATATTTTAATATAAAA
Found at i:193027 original size:24 final size:22
Alignment explanation
Indices: 192990--193053 Score: 78
Period size: 21 Copynumber: 2.9 Consensus size: 22
192980 GATTATTTAT
192990 TTAAATA-TTTTAATATATAAA
1 TTAAATATTTTTAATATATAAA
193011 TTAATTATATTTTTAATATA-AAA
1 TTAA--ATATTTTTAATATATAAA
*
193034 TTAAATATTTTAAATTATAT
1 TTAAATATTTTTAA-TATAT
193054 CTGCCTCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
21 13 0.35
22 4 0.11
23 10 0.27
24 10 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAAATATTTTTAATATATAAA
Found at i:193788 original size:15 final size:14
Alignment explanation
Indices: 193770--193821 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
193760 TATAAATAAA
193770 TATAATATTTAAATT
1 TATAA-ATTTAAATT
193785 TATAAA--T-AA-T
1 TATAAATTTAAATT
193795 T-TAAATTTAAATT
1 TATAAATTTAAATT
193808 TATAATATTTAAAT
1 TATAA-ATTTAAAT
193822 CCAAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
9 4 0.13
10 2 0.06
11 3 0.10
12 3 0.10
13 2 0.06
14 4 0.13
15 13 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATAAATTTAAATT
Found at i:194194 original size:17 final size:17
Alignment explanation
Indices: 194154--194197 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
194144 TAAAAAATTC
* *
194154 ATTAAAAATTATGAAAC
1 ATTAAAATTTATGAAAA
*
194171 A-TAAAATTTATTAAAA
1 ATTAAAATTTATGAAAA
194187 ATTAAAATTTA
1 ATTAAAATTTA
194198 ATATTATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
ATTAAAATTTATGAAAA
Found at i:194416 original size:16 final size:15
Alignment explanation
Indices: 194395--194429 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
194385 TTTTTAAACA
*
194395 AAATAAAATTAAAAAT
1 AAATAAAAAT-AAAAT
194411 AAATAAAAATAAAAT
1 AAATAAAAATAAAAT
194426 AAAT
1 AAAT
194430 TTTTATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAAAATAAAAT
Found at i:194796 original size:22 final size:22
Alignment explanation
Indices: 194749--194797 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
194739 TTAGAATCTT
* *
194749 AATTTTTAAATAAATTTAATTT
1 AATTTTAAAATAAATTTAATTA
*
194771 AATTTTAAAATAAACTTTTA-TA
1 AATTTTAAAATAAA-TTTAATTA
194793 AATTT
1 AATTT
194798 GAAATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTTTAAAATAAATTTAATTA
Found at i:194858 original size:16 final size:16
Alignment explanation
Indices: 194839--194878 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
194829 TCGAATAAAA
*
194839 TTAAATTTAAAATATT
1 TTAAATTTAAAATAAT
194855 TTAAATTT-AAATAAT
1 TTAAATTTAAAATAAT
194870 TT-AATTTAA
1 TTAAATTTAA
194879 TTTAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 9 0.41
16 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATTTAAAATAAT
Found at i:194916 original size:35 final size:35
Alignment explanation
Indices: 194839--194922 Score: 86
Period size: 35 Copynumber: 2.4 Consensus size: 35
194829 TCGAATAAAA
* **
194839 TTAAATTTAAAATATTTTAAATTTAAATAATTTAAT
1 TTAAATTTAAATTATTTTAAAAATAAATAATTT-AT
194875 TT-AATTTAAATTATTTTAATAAATAAA-AATATT-T
1 TTAAATTTAAATTATTTTAA-AAATAAATAAT-TTAT
194909 TTAAATTT-AATTAT
1 TTAAATTTAAATTAT
194923 AAACTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
34 9 0.21
35 24 0.57
36 9 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
TTAAATTTAAATTATTTTAAAAATAAATAATTTAT
Found at i:195428 original size:15 final size:15
Alignment explanation
Indices: 195408--195441 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
195398 CAAAACCCTC
*
195408 TTTTTTTTATC-TTG
1 TTTTTTTTTTCGTTG
195422 TTTTTTTTTTCGTTG
1 TTTTTTTTTTCGTTG
195437 TTTTT
1 TTTTT
195442 GTTGTGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.03, C:0.06, G:0.09, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTCGTTG
Found at i:196637 original size:3 final size:3
Alignment explanation
Indices: 196629--196653 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
196619 GTACTCAAAA
196629 GTT GTT GTT GTT GTT GTT GTT GTT G
1 GTT GTT GTT GTT GTT GTT GTT GTT G
196654 GTGGCTGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (3 bp):
GTT
Found at i:197271 original size:5 final size:5
Alignment explanation
Indices: 197261--197285 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
197251 ACATAAATGA
197261 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
197286 ATTTATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:198972 original size:33 final size:33
Alignment explanation
Indices: 198935--199000 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
198925 TCATTATTTC
*
198935 AAACTTAGGGTATTAACAATTATTGTCTTTCCA
1 AAACTTAAGGTATTAACAATTATTGTCTTTCCA
*
198968 AAACTTAAGGTATTGACAATTATTGTCTTTCCA
1 AAACTTAAGGTATTAACAATTATTGTCTTTCCA
199001 GTAATCAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (33 bp):
AAACTTAAGGTATTAACAATTATTGTCTTTCCA
Found at i:200069 original size:33 final size:33
Alignment explanation
Indices: 200032--200098 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
200022 TTCAACGATT
200032 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
200065 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
200098 T
1 T
200099 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:200070 original size:13 final size:13
Alignment explanation
Indices: 200052--200076 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
200042 CATAAAATGT
200052 TGTATCGATACAA
1 TGTATCGATACAA
200065 TGTATCGATACA
1 TGTATCGATACA
200077 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:200157 original size:13 final size:13
Alignment explanation
Indices: 200139--200163 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
200129 ATTACTCAAA
200139 TGTATCGATACAT
1 TGTATCGATACAT
200152 TGTATCGATACA
1 TGTATCGATACA
200164 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:200228 original size:52 final size:52
Alignment explanation
Indices: 200172--200300 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
200162 CACTGATCTT
*
200172 TGTATCGATACATGCAGGCAAATTTGCACAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCACAGATGTATCGATACACTATAAAA
* *
200224 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCACAGATGTATCGATACACTATAAAA
*
200276 TGTATCGATACATACAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
200301 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCACAGATGTATCGATACACTATAAAA
Found at i:208519 original size:31 final size:29
Alignment explanation
Indices: 208481--208679 Score: 192
Period size: 30 Copynumber: 6.7 Consensus size: 29
208471 ATACCTTTTT
208481 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGC-AT-TCTTCTC
208512 AAAGTCCACGACTCAGT-G-A--C-TCTC
1 AAAGTCCACGACTCAGTGGCATTCTTCTC
* **
208536 AAAGTCCACGACTCAGTGACAATCTCTGGTC
1 AAAGTCCACGACTCAGTGGC-AT-TCTTCTC
* *
208567 AAAGTCCACGACTCAGTGGCATCTTTTCCTTT
1 AAAGTCCACGACTCAGTGGCAT-TCTT-C-TC
* *
208599 AAAGTCCACGACTCAGTGGCATTTTGTCTT
1 AAAGTCCACGACTCAGTGGCATTCT-TCTC
*
208629 AAAGTCCACGACTCAGTGGCATTTTGTCTC
1 AAAGTCCACGACTCAGTGGCATTCT-TCTC
* *
208659 AAAGTCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCA
208680 CCTTTTTCTG
Statistics
Matches: 147, Mismatches: 11, Indels: 21
0.82 0.06 0.12
Matches are distributed among these distances:
24 21 0.14
25 1 0.01
27 1 0.01
28 1 0.01
30 57 0.39
31 42 0.29
32 24 0.16
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (29 bp):
AAAGTCCACGACTCAGTGGCATTCTTCTC
Found at i:208539 original size:24 final size:24
Alignment explanation
Indices: 208508--208555 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
208498 GGCAATCTCT
208508 TCTCAAAGTCCACGACTCAGTGAC
1 TCTCAAAGTCCACGACTCAGTGAC
208532 TCTCAAAGTCCACGACTCAGTGAC
1 TCTCAAAGTCCACGACTCAGTGAC
208556 AATCTCTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (24 bp):
TCTCAAAGTCCACGACTCAGTGAC
Found at i:208546 original size:55 final size:60
Alignment explanation
Indices: 208481--208679 Score: 198
Period size: 55 Copynumber: 3.4 Consensus size: 60
208471 ATACCTTTTT
208481 AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTG-A-C-T-C-TC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGCATCTTCCTTC
* ** *
208536 AAAGTCCACGACTCAGTGACAATCTCTGGTCAAAGTCCACGACTCAGTGGCATCTTTTCCTTT
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGT-GCATC--TTCCTTC
* * **
208599 AAAGTCCACGACTCAGTGGC-AT-TTTGTCTTAAAGTCCACGACTCAGTGGCAT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCT-TCTCAAAGTCCACGACTCAGT-GCATCTTCCT-TC
* *
208659 AAAGTCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCA
208680 CCTTTTTCTG
Statistics
Matches: 119, Mismatches: 14, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
55 45 0.38
56 1 0.01
57 1 0.01
58 1 0.01
59 3 0.03
60 19 0.16
61 3 0.03
62 26 0.22
63 20 0.17
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (60 bp):
AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGCATCTTCCTTC
Found at i:208703 original size:34 final size:33
Alignment explanation
Indices: 208659--208823 Score: 215
Period size: 34 Copynumber: 4.8 Consensus size: 33
208649 ATTTTGTCTC
*
208659 AAAGTCCACAACTCCGTGGCACCTTTTTCTGTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTT
208693 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTT
*
208729 CAAAGCCCACAACTCCGTGGCACTTTTTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
208763 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTT
* *
208799 -AAGTCCACAACTCCGTGGCATCTTT
1 AAAGCCCACAACTCCGTGGCACCTTT
208824 CTCCCTTCCT
Statistics
Matches: 119, Mismatches: 5, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
33 22 0.18
34 35 0.29
35 25 0.21
36 13 0.11
37 24 0.20
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (33 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
Found at i:208783 original size:70 final size:71
Alignment explanation
Indices: 208657--208823 Score: 286
Period size: 70 Copynumber: 2.4 Consensus size: 71
208647 GCATTTTGTC
*
208657 TCAAAGTCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 TCAAAGTCCACAACTCCGTGGCACTTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
208722 CCCTTT
66 CCCTTT
*
208728 TCAAAGCCCACAACTCCGTGGCACTTTTTTCT-TTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 TCAAAGTCCACAACTCCGTGGCACTTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
208792 CCCTTT
66 CCCTTT
208798 T--AAGTCCACAACTCCGTGGCATCTTT
1 TCAAAGTCCACAACTCCGTGGCA-CTTT
208824 CTCCCTTCCT
Statistics
Matches: 92, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
68 19 0.21
69 4 0.04
70 39 0.42
71 30 0.33
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.34
Consensus pattern (71 bp):
TCAAAGTCCACAACTCCGTGGCACTTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
CCCTTT
Found at i:208829 original size:34 final size:34
Alignment explanation
Indices: 208567--208830 Score: 244
Period size: 30 Copynumber: 8.0 Consensus size: 34
208557 ATCTCTGGTC
* *
208567 AAAGTCCACGACTCAGTGGCATC-TTTT-CCTTT
1 AAAGTCCACAACTCCGTGGCATCTTTTTCCCTTT
* * *
208599 AAAGTCCACGACTCAGTGGCAT-TTTGT--C-TT
1 AAAGTCCACAACTCCGTGGCATCTTTTTCCCTTT
* * * *
208629 AAAGTCCACGACTCAGTGGCAT-TTTGT--C-TC
1 AAAGTCCACAACTCCGTGGCATCTTTTTCCCTTT
* **
208659 AAAGTCCACAACTCCGTGGCACCTTTTTCTGTTT
1 AAAGTCCACAACTCCGTGGCATCTTTTTCCCTTT
*
208693 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGTCCACAACTCCGTGGCA-TCTTTTTCCC-TTT
* * *
208729 CAAAGCCCACAACTCCGTGGCA-CTTTTTTCTTTT
1 -AAAGTCCACAACTCCGTGGCATCTTTTTCCCTTT
*
208763 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
1 AAAGTCCACAACTCCGTGGCA-TCTTTTTCCCTTT
* *
208798 TAAGTCCACAACTCCGTGGCATCTTTCTCCCTT
1 AAAGTCCACAACTCCGTGGCATCTTTTTCCCTT
208831 CCTAAAGCCC
Statistics
Matches: 203, Mismatches: 19, Indels: 18
0.85 0.08 0.08
Matches are distributed among these distances:
30 50 0.25
31 5 0.02
32 25 0.12
33 21 0.10
34 35 0.17
35 43 0.21
36 3 0.01
37 21 0.10
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.33
Consensus pattern (34 bp):
AAAGTCCACAACTCCGTGGCATCTTTTTCCCTTT
Found at i:208936 original size:49 final size:49
Alignment explanation
Indices: 208864--209397 Score: 534
Period size: 49 Copynumber: 11.0 Consensus size: 49
208854 GCGACCCTTC
* *
208864 TAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACATTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * * * *
208913 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
208962 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * *
209011 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C-----CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
209054 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* ** * * * * *
209103 TAAGACCAAGGTAGCTGGCCTTGACTCAGCACATTGGCCCCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * * *
209152 TAAGCCCGATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTTTCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * *
209201 TAAGTCCAATGTAGCTGGCCTTAAATCAGCACATT-G-A-C---ATTTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
209244 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTT
* * * * ** *
209296 TAAGTTCAATGTAGCTGGCTTTGAACCAGCACGTTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC---TT-T-ATCTT
* * * * * *
209351 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
209398 ACTTTTCTCA
Statistics
Matches: 393, Mismatches: 73, Indels: 38
0.78 0.14 0.08
Matches are distributed among these distances:
43 74 0.19
44 2 0.01
45 1 0.00
46 2 0.01
47 1 0.00
48 2 0.01
49 232 0.59
50 1 0.00
51 2 0.01
52 36 0.09
53 2 0.01
54 1 0.00
55 36 0.09
56 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
Found at i:209033 original size:98 final size:94
Alignment explanation
Indices: 208864--209342 Score: 644
Period size: 98 Copynumber: 5.0 Consensus size: 94
208854 GCGACCCTTC
* *
208864 TAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACATTTATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
*
208929 GGCCTTGACTCAGCACATTGGCACCTTCACCAT
66 GGCCTTGACTCAGCACATTGGCACCTT----TT
208962 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
209027 GGCCTTGACTCAGCACATTGGCACC--TT
66 GGCCTTGACTCAGCACATTGGCACCTTTT
* *
209054 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAAGGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
*
209119 GGCCTTGACTCAGCACATTGGCCCCTTCACCTT
66 GGCCTTGACTCAGCACATTGGCACCTT----TT
* * * * *
209152 TAAGCCCGATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
* * *
209217 GGCCTTAAATCAGCACATT-G-ACATTTT
66 GGCCTTGACTCAGCACATTGGCACCTTTT
*
209244 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGTA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTTTAAGTCCAATGTA
* * *
209309 GCTGGCTTTGAAC-CAGCACGTTGACATCCTTTT
63 GCTGGCCTTG-ACTCAGCACATTGGCA-CCTTTT
209342 T
1 T
209343 CTCATCTTTA
Statistics
Matches: 339, Mismatches: 29, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
92 127 0.37
93 3 0.01
95 32 0.09
96 4 0.01
97 2 0.01
98 171 0.50
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (94 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
GGCCTTGACTCAGCACATTGGCACCTTTT
Found at i:209082 original size:92 final size:92
Alignment explanation
Indices: 208956--209327 Score: 512
Period size: 92 Copynumber: 3.9 Consensus size: 92
208946 TTGGCACCTT
*
208956 CACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAAT
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAAT
209021 GTAGCTGGCCTTGACTCAGCACATTGG
66 GTAGCTGGCCTTGACTCAGCACATTGG
* *
209048 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAAG
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAAT
209113 GTAGCTGGCCTTGACTCAGCACATTGG
66 GTAGCTGGCCTTGACTCAGCACATTGG
* * * * *
209140 CCCCTTCACCTTTAAGCCCGATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAG
1 ------CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAG
* * *
209205 TCCAATGTAGCTGGCCTTAAATCAGCACATTGA
60 TCCAATGTAGCTGGCCTTGACTCAGCACATTGG
** *
209238 CATTTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTC
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTTTAAGTCC
*
209303 AATGTAGCTGGCTTTGAAC-CAGCAC
63 AATGTAGCTGGCCTTG-ACTCAGCAC
209328 GTTGACATCC
Statistics
Matches: 246, Mismatches: 24, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
92 130 0.53
93 3 0.01
95 30 0.12
96 1 0.00
98 82 0.33
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (92 bp):
CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAAT
GTAGCTGGCCTTGACTCAGCACATTGG
Found at i:209187 original size:190 final size:190
Alignment explanation
Indices: 208859--209397 Score: 747
Period size: 190 Copynumber: 2.8 Consensus size: 190
208849 CGGTGGCGAC
* *
208859 CCTTCTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACATTTATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
* * * * *
208924 TAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATC
65 TAGCTGGCCTTGACTCAGCACATTGGCCCCTTCACCTTTAAGCCCAATATCGTTGGCCTTGAATC
* * *
208989 AGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA
130 AGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTAAATCAGCACATTGACA
* *
209050 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAAGGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
*
209115 AGCTGGCCTTGACTCAGCACATTGGCCCCTTCACCTTTAAGCCCGATATCGTTGGCCTTGAATCA
66 AGCTGGCCTTGACTCAGCACATTGGCCCCTTCACCTTTAAGCCCAATATCGTTGGCCTTGAATCA
*
209180 GCATATTGGCACCTTTTTCTTTAAGTCCAATGTAGCTGGCCTTAAATCAGCACATTGACA
131 GCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTAAATCAGCACATTGACA
** *
209240 TTTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTTTAAGTCCAA
* * * * *
209305 TGTAGCTGGCTTTGAAC-CAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGG
63 TGTAGCTGGCCTTG-ACTCAGCACATTGGC--CC---CT-TCACCTTTAAGCCCAATATCGTTGG
* * *
209369 CCATGAATCAACATATTGGCATCTTTATC
121 CCTTGAATCAGCATATTGGCACCTTTATC
209398 ACTTTTCTCA
Statistics
Matches: 309, Mismatches: 29, Indels: 12
0.88 0.08 0.03
Matches are distributed among these distances:
190 215 0.70
191 7 0.02
193 34 0.11
194 2 0.01
195 2 0.01
198 1 0.00
199 48 0.16
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (190 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
AGCTGGCCTTGACTCAGCACATTGGCCCCTTCACCTTTAAGCCCAATATCGTTGGCCTTGAATCA
GCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTAAATCAGCACATTGACA
Found at i:209320 original size:52 final size:55
Alignment explanation
Indices: 209242--209362 Score: 149
Period size: 52 Copynumber: 2.3 Consensus size: 55
209232 CATTGACATT
* * *
209242 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CATC
1 TTTAAGTCCAATATAGCTGGCCTTGAACCAGCACATTGACATCCTTTTTCTCATC
* * * *
209294 TTTAAGTTCAATGTAGCTGGCTTTGAACCAGCACGTTGACATCCTTTTTCTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAACCAGCACATTGACATCCTTTTTCTCATC
*
209349 TTTAAGCCCAATAT
1 TTTAAGTCCAATAT
209363 CGTTGGCCAT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
52 34 0.61
53 2 0.04
54 5 0.09
55 15 0.27
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (55 bp):
TTTAAGTCCAATATAGCTGGCCTTGAACCAGCACATTGACATCCTTTTTCTCATC
Found at i:209452 original size:67 final size:68
Alignment explanation
Indices: 209344--209470 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
209334 ATCCTTTTTC
* * *
209344 TCATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
209408 TCT
66 TCT
* * * *
209411 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTT
209471 AAAACCCAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCT
Found at i:210202 original size:33 final size:33
Alignment explanation
Indices: 210165--210231 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
210155 TTCAACGATT
210165 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
210198 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
210231 T
1 T
210232 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:210203 original size:13 final size:13
Alignment explanation
Indices: 210185--210209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
210175 CATAAAATGT
210185 TGTATCGATACAA
1 TGTATCGATACAA
210198 TGTATCGATACA
1 TGTATCGATACA
210210 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:210290 original size:13 final size:13
Alignment explanation
Indices: 210272--210296 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
210262 ATTACTCAAA
210272 TGTATCGATACAT
1 TGTATCGATACAT
210285 TGTATCGATACA
1 TGTATCGATACA
210297 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:210361 original size:52 final size:52
Alignment explanation
Indices: 210305--210433 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
210295 CACTGATCTT
*
210305 TGTATCGATACATGCAGGCAAATTTGCACAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCACAGATGTATCGATACACTATAAAA
* *
210357 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCACAGATGTATCGATACACTATAAAA
*
210409 TGTATCGATACATACAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
210434 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCACAGATGTATCGATACACTATAAAA
Found at i:214723 original size:12 final size:12
Alignment explanation
Indices: 214671--214723 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
214661 TCAAATGTTC
*
214671 ATTTCACTAATT
1 ATTTTACTAATT
214683 ATTTCTACTAATT
1 ATTT-TACTAATT
* *
214696 ATTTTTC-AAAT
1 ATTTTACTAATT
214707 ATTTTACTAATT
1 ATTTTACTAATT
214719 ATTTT
1 ATTTT
214724 TTGGATGTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
11 9 0.26
12 14 0.41
13 11 0.32
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (12 bp):
ATTTTACTAATT
Found at i:215011 original size:2 final size:2
Alignment explanation
Indices: 215004--215043 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
214994 GCACATTGAC
* *
215004 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AC 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
215044 GTATGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:217270 original size:31 final size:31
Alignment explanation
Indices: 217234--217300 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
217224 AATACATAAA
*
217234 ATAAAATA-AAT-TATTAATATGTAAAAAATAT
1 ATAAAATATAATATATTAA-ATATAAAAAA-AT
*
217265 ATAAAATATAATATTTTAAATATAAAAAAAT
1 ATAAAATATAATATATTAAATATAAAAAAAT
217296 ATAAA
1 ATAAA
217301 TACAAACATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 15 0.47
32 12 0.38
33 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (31 bp):
ATAAAATATAATATATTAAATATAAAAAAAT
Found at i:217270 original size:36 final size:32
Alignment explanation
Indices: 217214--217300 Score: 88
Period size: 36 Copynumber: 2.7 Consensus size: 32
217204 CTCTCATATA
* *
217214 TAAA-ATAACAAATACATAAAATAAAATAAATTAT
1 TAAATATAAAAAATATATAAAATAAAAT--ATT-T
* *
217248 TAATATGTAAAAAATATATAAAATATAATATTT
1 TAA-ATATAAAAAATATATAAAATAAAATATTT
217281 TAAATATAAAAAA-ATATAAA
1 TAAATATAAAAAATATATAAA
217301 TACAAACATA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
31 7 0.15
32 9 0.20
33 4 0.09
34 6 0.13
35 1 0.02
36 19 0.41
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (32 bp):
TAAATATAAAAAATATATAAAATAAAATATTT
Found at i:218644 original size:4 final size:4
Alignment explanation
Indices: 218635--218675 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
218625 ATAAAATTAT
* *
218635 TTTC TTTC TTT- TTTT TTTC TTT- TTTT TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
218676 TCAGCAAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 6 0.18
4 27 0.82
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (4 bp):
TTTC
Found at i:218653 original size:11 final size:11
Alignment explanation
Indices: 218634--218677 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
218624 CATAAAATTA
*
218634 TTTTCTTTCTT
1 TTTTTTTTCTT
218645 TTTTTTTTCTT
1 TTTTTTTTCTT
218656 TTTTTTTTCTT
1 TTTTTTTTCTT
218667 TCTTTCTTTTC
1 T-TTT-TTTTC
218678 AGCAAAACGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 22 0.73
12 3 0.10
13 5 0.17
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:218654 original size:15 final size:15
Alignment explanation
Indices: 218634--218676 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
218624 CATAAAATTA
218634 TTTTCTTTCTTTTTT
1 TTTTCTTTCTTTTTT
218649 TTTTCTTT-TTTTTT
1 TTTTCTTTCTTTTTT
218663 TCTTTCTTTCTTTT
1 T-TTTCTTTCTTTT
218677 CAGCAAAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.27
15 15 0.58
16 4 0.15
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTCTTTCTTTTTT
Found at i:219662 original size:22 final size:22
Alignment explanation
Indices: 219618--219658 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
219608 ATTTTTTATT
219618 TAAATTTAATTATGAAAATATA
1 TAAATTTAATTATGAAAATATA
219640 TAAATATTAATT-T-AAAATA
1 TAAAT-TTAATTATGAAAATA
219659 ATATTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 6 0.33
23 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TAAATTTAATTATGAAAATATA
Found at i:220065 original size:29 final size:34
Alignment explanation
Indices: 220024--220089 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 34
220014 TAAATATATT
220024 TTTTTCATAAATATATTT-AAA-AT-TTTTTAAA
1 TTTTTCATAAATATATTTGAAATATATTTTTAAA
*
220055 TTTTT-AT-AATATATTTGAAATATATTTTTATA
1 TTTTTCATAAATATATTTGAAATATATTTTTAAA
220087 TTT
1 TTT
220090 ATATCCAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
29 9 0.29
30 5 0.16
31 7 0.23
32 10 0.32
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (34 bp):
TTTTTCATAAATATATTTGAAATATATTTTTAAA
Found at i:225317 original size:18 final size:20
Alignment explanation
Indices: 225286--225328 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
225276 TATTTATATG
*
225286 ATATATGTATATAAATTTTT
1 ATATATGTATATAAATTTTA
225306 ATATAT-TA-ATAAATTTTA
1 ATATATGTATATAAATTTTA
225324 ATATA
1 ATATA
225329 ATATATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.64
19 2 0.09
20 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATATATGTATATAAATTTTA
Found at i:225387 original size:23 final size:23
Alignment explanation
Indices: 225351--225396 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
225341 TCATATTGTT
*
225351 TTATTTTTATATTATATTATTTA
1 TTATTTTTATATTAAATTATTTA
*
225374 TTATATTTTA-ATTAAATTTTTTA
1 TTAT-TTTTATATTAAATTATTTA
225397 AATTAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTATTTTTATATTAAATTATTTA
Found at i:225616 original size:18 final size:18
Alignment explanation
Indices: 225579--225616 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
225569 TATTTTTTAA
*
225579 AATTAATATATTAAATAT
1 AATTAATATATTAAACAT
225597 AATTAATA-ATTAAAACAT
1 AATTAATATATT-AAACAT
225615 AA
1 AA
225617 ATATGTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AATTAATATATTAAACAT
Found at i:225944 original size:24 final size:24
Alignment explanation
Indices: 225905--225960 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
225895 TTTGAGTATT
225905 TTAATA-A-TATTCTTAA-AATTAA
1 TTAATATATTATTCTTAATAA-TAA
*
225927 TTAATATATTATTTTTAATAATAA
1 TTAATATATTATTCTTAATAATAA
225951 TT-ATATATTA
1 TTAATATATTA
225961 AATATAGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 6 0.20
23 9 0.30
24 13 0.43
25 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TTAATATATTATTCTTAATAATAA
Found at i:226672 original size:21 final size:21
Alignment explanation
Indices: 226646--226689 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
226636 ATTCAAATAT
226646 AATATTAAATTTAATAATAAA
1 AATATTAAATTTAATAATAAA
226667 AATATTAAATTTAATAATAAA
1 AATATTAAATTTAATAATAAA
226688 AA
1 AA
226690 AAACTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AATATTAAATTTAATAATAAA
Found at i:227596 original size:8 final size:8
Alignment explanation
Indices: 227585--227630 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
227575 CCTTTTGAAG
227585 TTTTTATT
1 TTTTTATT
*
227593 TTTTAATT
1 TTTTTATT
*
227601 TAAATTTATT
1 T--TTTTATT
227611 TTTTTATT
1 TTTTTATT
227619 TTTTTATT
1 TTTTTATT
227627 TTTT
1 TTTT
227631 AAAATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 26 0.81
10 6 0.19
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTATT
Found at i:228284 original size:15 final size:14
Alignment explanation
Indices: 228257--228292 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
228247 AGATTATTTA
228257 TTAATTTAATAAAT
1 TTAATTTAATAAAT
228271 TTAATTTCAATAAAT
1 TTAATTT-AATAAAT
*
228286 TAAATTT
1 TTAATTT
228293 TTAATAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAATTTAATAAAT
Found at i:232702 original size:23 final size:21
Alignment explanation
Indices: 232639--232704 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 21
232629 ATTTTTGTTT
*
232639 TAAATTTTAATTAATATTTTAAA
1 TAAATTTTTATT-AT-TTTTAAA
*
232662 T-AATTTTTATGTAATTTTAAA
1 TAAATTTTTAT-TATTTTTAAA
232683 TGTAAATTTTTATTATTTTTAA
1 --TAAATTTTTATTATTTTTAA
232705 TATTATAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 7 0.19
22 9 0.25
23 11 0.31
24 9 0.25
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (21 bp):
TAAATTTTTATTATTTTTAAA
Found at i:232714 original size:24 final size:25
Alignment explanation
Indices: 232661--232714 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
232651 AATATTTTAA
232661 ATAATTTTTATGTAATTTTAAATGT
1 ATAATTTTTATGTAATTTTAAATGT
*
232686 A-AATTTTTAT-TATTTTTAATAT-T
1 ATAATTTTTATGTAATTTTAA-ATGT
232709 ATAATT
1 ATAATT
232715 ATATTTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 10 0.38
24 15 0.58
25 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
ATAATTTTTATGTAATTTTAAATGT
Found at i:233443 original size:17 final size:17
Alignment explanation
Indices: 233407--233447 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
233397 CTTTTTATAA
*
233407 AATATAAAAATAAATAT
1 AATATAATAATAAATAT
233424 AATATAATAATATAAT-T
1 AATATAATAATA-AATAT
233441 AAT-TAAT
1 AATATAAT
233448 TAAAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 15 0.68
18 3 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATATAATAATAAATAT
Found at i:238720 original size:17 final size:17
Alignment explanation
Indices: 238684--238724 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
238674 CATTTCATAA
*
238684 AATATAAAAATAAATAT
1 AATATAATAATAAATAT
238701 AATATAATAATATAAT-T
1 AATATAATAATA-AATAT
238718 AAT-TAAT
1 AATATAAT
238725 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 15 0.68
18 3 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATATAATAATAAATAT
Found at i:239435 original size:2 final size:2
Alignment explanation
Indices: 239422--239451 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
239412 TTAATAATAA
*
239422 AT AT AT AC 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
239452 TTTGAGAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:239534 original size:9 final size:9
Alignment explanation
Indices: 239493--239564 Score: 60
Period size: 9 Copynumber: 7.9 Consensus size: 9
239483 CTAATTTAAA
239493 TTTATATATT
1 TTTATAT-TT
239503 TTTATAATTT
1 TTTAT-ATTT
**
239513 TTTATATGA
1 TTTATATTT
239522 TTTATATTT
1 TTTATATTT
239531 TTTA-ATTT
1 TTTATATTT
*
239539 AATTAT-TTT
1 -TTTATATTT
239548 ATTT-TATTT
1 -TTTATATTT
239557 TTTATATT
1 TTTATATT
239565 CGTATACACA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
8 8 0.16
9 29 0.57
10 12 0.24
11 2 0.04
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (9 bp):
TTTATATTT
Found at i:239547 original size:14 final size:14
Alignment explanation
Indices: 239521--239560 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
239511 TTTTTATATG
239521 ATTTATATTTTTTA
1 ATTTATATTTTTTA
239535 ATTTA-ATTATTTT-
1 ATTTATATT-TTTTA
239548 ATTT-TATTTTTTA
1 ATTTATATTTTTTA
239561 TATTCGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 4 0.17
13 10 0.43
14 9 0.39
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTTATATTTTTTA
Found at i:239555 original size:26 final size:26
Alignment explanation
Indices: 239497--239560 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
239487 TTTAAATTTA
*
239497 TATATTTTTATAATTTTTTATATGATT
1 TATATTTTT-TAATTTATTATATGATT
* *
239524 TATATTTTTTAATTTAATTATTTTATT
1 TATATTTTTTAATTT-ATTATATGATT
239551 T-TATTTTTTA
1 TATATTTTTTA
239561 TATTCGTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.45
27 18 0.55
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (26 bp):
TATATTTTTTAATTTATTATATGATT
Found at i:240105 original size:31 final size:33
Alignment explanation
Indices: 240067--240127 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
240057 TTCATGGAGA
* *
240067 TAAAAAAAT-TAATTTT-ATATAAATATAATAT
1 TAAAAAAATAAAATTTTGATAAAAATATAATAT
240098 TAAAAAAATAAAATTTTGATAAAAATATAA
1 TAAAAAAATAAAATTTTGATAAAAATATAA
240128 AAAATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 9 0.35
32 6 0.23
33 11 0.42
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (33 bp):
TAAAAAAATAAAATTTTGATAAAAATATAATAT
Found at i:241214 original size:2 final size:2
Alignment explanation
Indices: 241207--241244 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
241197 GCAAATCATA
241207 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
241245 CTATTCGATT
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:243086 original size:20 final size:20
Alignment explanation
Indices: 243061--243103 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
243051 TTCAAAAATT
243061 TTTTTAAATAAA-TAAATAAA
1 TTTTTAAA-AAATTAAATAAA
*
243081 TTTTTAAAAAATTAAATATA
1 TTTTTAAAAAATTAAATAAA
243101 TTT
1 TTT
243104 GTATCAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTTTAAAAAATTAAATAAA
Found at i:245158 original size:25 final size:25
Alignment explanation
Indices: 245094--245158 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
245084 ATATCATATA
* * *
245094 TAATTTATTTATAATTGATTTTATT
1 TAATTTATTAATATTTAATTTTATT
* * *
245119 TGAA-GTATGAGTATTTAATTTTATT
1 T-AATTTATTAATATTTAATTTTATT
245144 TAATTTATTAATATT
1 TAATTTATTAATATT
245159 ATTTTTAAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
24 2 0.07
25 25 0.86
26 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (25 bp):
TAATTTATTAATATTTAATTTTATT
Done.