Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 80 of 126
Found at i:16234238 original size:12 final size:11
Alignment explanation
Indices: 16234219--16234253 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
16234209 AAAAAAAATT
16234219 TCGGGTTCGGG
1 TCGGGTTCGGG
16234230 TCAGGGTTCGGG
1 TC-GGGTTCGGG
*
16234242 TCGGGGTCGGG
1 TCGGGTTCGGG
16234253 T
1 T
16234254 TTTAAGCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.03, C:0.17, G:0.54, T:0.26
Consensus pattern (11 bp):
TCGGGTTCGGG
Found at i:16234311 original size:12 final size:14
Alignment explanation
Indices: 16234294--16234350 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
16234284 AAAATTATTT
16234294 TTTAATT-T-TATA
1 TTTAATTATATATA
16234306 TTTAATTATATATA
1 TTTAATTATATATA
*
16234320 TTT-TTTATATATA
1 TTTAATTATATATA
* *
16234333 TTTAATTTTATATT
1 TTTAATTATATATA
16234347 TTTA
1 TTTA
16234351 TTTAAAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
12 7 0.18
13 13 0.34
14 18 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTAATTATATATA
Found at i:16234343 original size:16 final size:16
Alignment explanation
Indices: 16234302--16234345 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 16
16234292 TTTTTAATTT
16234302 TATATTTAA--TTATA
1 TATATTTAATTTTATA
16234316 TATA-TT--TTTTATA
1 TATATTTAATTTTATA
16234329 TATATTTAATTTTATA
1 TATATTTAATTTTATA
16234345 T
1 T
16234346 TTTTATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.44
14 6 0.24
16 8 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATTTAATTTTATA
Found at i:16237539 original size:21 final size:21
Alignment explanation
Indices: 16237498--16237539 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
16237488 ATTTGAGATT
*
16237498 ATTAAAATTTAAATTCTAATA
1 ATTAAAATTAAAATTCTAATA
16237519 ATTAAAATTAAAAATTC-AATA
1 ATTAAAATT-AAAATTCTAATA
16237540 TTTTATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTAAAATTAAAATTCTAATA
Found at i:16239765 original size:23 final size:23
Alignment explanation
Indices: 16239720--16239765 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
16239710 TACACAAGAT
*
16239720 TATTATATAATAAGATAATATAA
1 TATTATATAATAAGATAAAATAA
16239743 TATTATA-AATAAGATTAAAATAA
1 TATTATATAATAAGA-TAAAATAA
16239766 ATAATATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (23 bp):
TATTATATAATAAGATAAAATAA
Found at i:16248506 original size:62 final size:63
Alignment explanation
Indices: 16248432--16248559 Score: 152
Period size: 63 Copynumber: 2.0 Consensus size: 63
16248422 TTCTTTTAAT
** *
16248432 TTTCATACCAAGTCAAACT-A-AAACAAAATAAGGGGATGAAGAGAGTAGTCATCAATATCACA
1 TTTCATACCAAGTCAAACTCAGAAA-AAAATAAGGGGACAAAAAGAGTAGTCATCAATATCACA
* * * ** *
16248494 TTTCATATCAAGTCAAATTCAGAAAAAAATAATGGTCCAAAAAGAGTAGTCATCGATATCACA
1 TTTCATACCAAGTCAAACTCAGAAAAAAATAAGGGGACAAAAAGAGTAGTCATCAATATCACA
16248557 TTT
1 TTT
16248560 ACACTTGTAC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
62 17 0.31
63 35 0.64
64 3 0.05
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (63 bp):
TTTCATACCAAGTCAAACTCAGAAAAAAATAAGGGGACAAAAAGAGTAGTCATCAATATCACA
Found at i:16250234 original size:9 final size:9
Alignment explanation
Indices: 16250211--16250240 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
16250201 AATCTTGAAT
16250211 TTATTCAAA
1 TTATTCAAA
16250220 -TATTCAAA
1 TTATTCAAA
16250228 TTATTCAAA
1 TTATTCAAA
16250237 TTAT
1 TTAT
16250241 AATTGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (9 bp):
TTATTCAAA
Found at i:16250290 original size:14 final size:14
Alignment explanation
Indices: 16250271--16250303 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16250261 TAATTATATT
16250271 TTTTAAAAT-TAAAA
1 TTTTAAAATAT-AAA
16250285 TTTTAAAATATAAA
1 TTTTAAAATATAAA
16250299 TTTTA
1 TTTTA
16250304 TCCAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.94
15 1 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTTAAAATATAAA
Found at i:16251365 original size:22 final size:22
Alignment explanation
Indices: 16251334--16251381 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
16251324 CACAAAAAAT
* *
16251334 TTTTATTTTTTAAAATTTAGTA
1 TTTTAGTTTTGAAAATTTAGTA
*
16251356 TTTTAGTTTTGAATATTTAGTA
1 TTTTAGTTTTGAAAATTTAGTA
16251378 TTTT
1 TTTT
16251382 TTTTCCTTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (22 bp):
TTTTAGTTTTGAAAATTTAGTA
Found at i:16252780 original size:7 final size:7
Alignment explanation
Indices: 16252759--16252796 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
16252749 ATATTATTGA
16252759 ATCAAAT
1 ATCAAAT
16252766 ACTCAAAT
1 A-TCAAAT
16252774 ATCAAAT
1 ATCAAAT
16252781 ATCAAAT
1 ATCAAAT
*
16252788 ATCATAT
1 ATCAAAT
16252795 AT
1 AT
16252797 TAACTTCATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (7 bp):
ATCAAAT
Found at i:16253170 original size:30 final size:30
Alignment explanation
Indices: 16253136--16253202 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
16253126 AAGTTAATAT
* *
16253136 TTTATTTGAAAATAAATTAAAG-ATTAAAGA
1 TTTATTTGAAAAT-AATAAAAGTATTAAAAA
* *
16253166 TTTATTTGCATATAATAAAAGTATTAAAAA
1 TTTATTTGAAAATAATAAAAGTATTAAAAA
16253196 TTTATTT
1 TTTATTT
16253203 TAGTAAAGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.43
Consensus pattern (30 bp):
TTTATTTGAAAATAATAAAAGTATTAAAAA
Found at i:16253302 original size:22 final size:23
Alignment explanation
Indices: 16253276--16253321 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
16253266 TAAGCTTTTT
16253276 TTATTTTGA-ATAAAAATAATTA
1 TTATTTTGATATAAAAATAATTA
16253298 TTATTTTGATATAAAAATAATTA
1 TTATTTTGATATAAAAATAATTA
16253321 T
1 T
16253322 ATAAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
TTATTTTGATATAAAAATAATTA
Found at i:16254849 original size:20 final size:22
Alignment explanation
Indices: 16254808--16254849 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
16254798 TGTATATTTA
16254808 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCTCTAGAATTAAG
16254830 TATTTGTATC-CTAG-ATTAAG
1 TATTTGTATCTCTAGAATTAAG
16254850 AAGTTTAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
21 4 0.20
22 10 0.50
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (22 bp):
TATTTGTATCTCTAGAATTAAG
Found at i:16255017 original size:25 final size:25
Alignment explanation
Indices: 16254989--16255053 Score: 130
Period size: 25 Copynumber: 2.6 Consensus size: 25
16254979 AAAATTTTCA
16254989 GCCTTCATTGCCGAATCCTGTTTAG
1 GCCTTCATTGCCGAATCCTGTTTAG
16255014 GCCTTCATTGCCGAATCCTGTTTAG
1 GCCTTCATTGCCGAATCCTGTTTAG
16255039 GCCTTCATTGCCGAA
1 GCCTTCATTGCCGAA
16255054 CCCTTTCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.17, C:0.29, G:0.20, T:0.34
Consensus pattern (25 bp):
GCCTTCATTGCCGAATCCTGTTTAG
Found at i:16255247 original size:18 final size:18
Alignment explanation
Indices: 16255224--16255258 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16255214 ATGTTCTTTG
*
16255224 GGTAAAGTTTCTAGTTCA
1 GGTAAAGCTTCTAGTTCA
*
16255242 GGTAAAGCTTCTGGTTC
1 GGTAAAGCTTCTAGTTC
16255259 TCATGGATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (18 bp):
GGTAAAGCTTCTAGTTCA
Found at i:16258715 original size:22 final size:22
Alignment explanation
Indices: 16258689--16258732 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
16258679 TGTATATTTA
*
16258689 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
16258711 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
16258733 GAAGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:16269026 original size:16 final size:16
Alignment explanation
Indices: 16268998--16269047 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
16268988 AAAATTTTTC
16268998 AATTTA-AATAAAATTT
1 AATTTATAA-AAAATTT
16269014 AATTTATAAAAAATATT
1 AATTTATAAAAAAT-TT
16269031 -ATTTATCAAAACAATTT
1 AATTTAT-AAAA-AATTT
16269048 TTAAAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 17 0.57
17 10 0.33
18 3 0.10
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTTATAAAAAATTT
Found at i:16269686 original size:21 final size:21
Alignment explanation
Indices: 16269661--16269703 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
16269651 TTTGATGTTA
16269661 TTATATTAATAAATAAT-TATT
1 TTATATTAATAAA-AATATATT
*
16269682 TTATATTTATAAAAATATATT
1 TTATATTAATAAAAATATATT
16269703 T
1 T
16269704 AAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATATTAATAAAAATATATT
Found at i:16271848 original size:15 final size:16
Alignment explanation
Indices: 16271828--16271865 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
16271818 AATTTATTAT
16271828 TATTTATTTA-ATGTA
1 TATTTATTTATATGTA
*
16271843 TATTTATATATATGTA
1 TATTTATTTATATGTA
16271859 T-TTTATT
1 TATTTATT
16271866 AATAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (16 bp):
TATTTATTTATATGTA
Found at i:16274275 original size:14 final size:15
Alignment explanation
Indices: 16274239--16274279 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
16274229 ATATAATAAG
*
16274239 TAATCATTTATTATA
1 TAATTATTTATTATA
16274254 TAATTATTTCATTATA
1 TAATTATTT-ATTATA
16274270 T-A-TATTTATT
1 TAATTATTTATT
16274280 CAAATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.12
14 5 0.21
15 9 0.38
16 7 0.29
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (15 bp):
TAATTATTTATTATA
Found at i:16274986 original size:17 final size:16
Alignment explanation
Indices: 16274955--16274990 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
16274945 AAATTTTAAC
*
16274955 TGAAATATAATAAAAT
1 TGAAAAATAATAAAAT
16274971 TGAAAAATACATAAAAT
1 TGAAAAATA-ATAAAAT
16274988 TGA
1 TGA
16274991 TCATTTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (16 bp):
TGAAAAATAATAAAAT
Found at i:16275266 original size:48 final size:48
Alignment explanation
Indices: 16275214--16275314 Score: 193
Period size: 48 Copynumber: 2.1 Consensus size: 48
16275204 TCAATTAACA
16275214 AAAATAAAATAAAATAATTTGATTAATTTACTTTTCAAATAATTCATT
1 AAAATAAAATAAAATAATTTGATTAATTTACTTTTCAAATAATTCATT
*
16275262 AAAATAAAATTAAATAATTTGATTAATTTACTTTTCAAATAATTCATT
1 AAAATAAAATAAAATAATTTGATTAATTTACTTTTCAAATAATTCATT
16275310 AAAAT
1 AAAAT
16275315 TTAATCAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (48 bp):
AAAATAAAATAAAATAATTTGATTAATTTACTTTTCAAATAATTCATT
Found at i:16275310 original size:24 final size:25
Alignment explanation
Indices: 16275225--16275311 Score: 90
Period size: 24 Copynumber: 3.6 Consensus size: 25
16275215 AAATAAAATA
*
16275225 AAATAATTTGATTAATTTACTTTTC
1 AAATAATTTCATTAATTTACTTTTC
** ***
16275250 AAATAA-TTCATTAAAATAAAATT-
1 AAATAATTTCATTAATTTACTTTTC
*
16275273 AAATAATTTGATTAATTTACTTTTC
1 AAATAATTTCATTAATTTACTTTTC
16275298 AAATAA-TTCATTAA
1 AAATAATTTCATTAA
16275312 AATTTAATCA
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
23 6 0.13
24 29 0.62
25 12 0.26
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (25 bp):
AAATAATTTCATTAATTTACTTTTC
Found at i:16275465 original size:2 final size:2
Alignment explanation
Indices: 16275449--16275481 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
16275439 TTTAGGATTT
16275449 TA TA TGA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
16275482 CACATTCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:16276048 original size:20 final size:20
Alignment explanation
Indices: 16276008--16276046 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
16275998 TAACAATGAG
16276008 ATTAAAATTACAACGATAAA
1 ATTAAAATTACAACGATAAA
16276028 ATTAAAA-T-CAACGATAAA
1 ATTAAAATTACAACGATAAA
16276046 A
1 A
16276047 AAATATGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.58
19 1 0.05
20 7 0.37
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.23
Consensus pattern (20 bp):
ATTAAAATTACAACGATAAA
Found at i:16277765 original size:4 final size:4
Alignment explanation
Indices: 16277758--16277792 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
16277748 TATTCCTTCC
*
16277758 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTTT TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
16277793 GGCTTTTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:16278547 original size:18 final size:18
Alignment explanation
Indices: 16278505--16278561 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
16278495 TATATATGAA
*
16278505 TATCAAT-ATGATTATATTT
1 TATCAATAATGA-TA-ATTC
16278524 TATCAATAATGATAATTC
1 TATCAATAATGATAATTC
*
16278542 TATCAATAATGATAGTTC
1 TATCAATAATGATAATTC
16278560 TA
1 TA
16278562 ATAATGAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
18 22 0.63
19 9 0.26
20 4 0.11
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (18 bp):
TATCAATAATGATAATTC
Found at i:16279701 original size:22 final size:22
Alignment explanation
Indices: 16279660--16279701 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
16279650 AAACTCCAAA
*
16279660 TATCTATTCAATATTTTTTATT
1 TATCTATTCAATATTATTTATT
16279682 TATCTATTCAAT-TTAATTTA
1 TATCTATTCAATATT-ATTTA
16279702 GTTAAAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (22 bp):
TATCTATTCAATATTATTTATT
Found at i:16280222 original size:24 final size:24
Alignment explanation
Indices: 16280190--16280238 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
16280180 TATATCTCTC
* *
16280190 TTTAGATCAGTCCAAACAAATTTA
1 TTTACATCAGACCAAACAAATTTA
* *
16280214 TTTACATCAGACCTAATAAATTTA
1 TTTACATCAGACCAAACAAATTTA
16280238 T
1 T
16280239 AAAAAGTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (24 bp):
TTTACATCAGACCAAACAAATTTA
Found at i:16280939 original size:3 final size:3
Alignment explanation
Indices: 16280915--16280974 Score: 93
Period size: 3 Copynumber: 19.7 Consensus size: 3
16280905 ATTGTTGTTA
* *
16280915 TAT TAT ATAT TGT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16280961 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
16280975 GTTTTAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:16281062 original size:39 final size:37
Alignment explanation
Indices: 16281004--16281093 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
16280994 AAGAAGGAAA
* * * *
16281004 TTGGTGATTCACTCTCGGATCCGTTTTATAGCATGATTC
1 TTGGTGATTCAATCACGGAT-C-TGTTAGAGCATGATTC
*
16281043 TTGGTGATTCAATCACGGATCTGTTGGAGCATGATTC
1 TTGGTGATTCAATCACGGATCTGTTAGAGCATGATTC
* *
16281080 ATGGTGATTTAATC
1 TTGGTGATTCAATC
16281094 CCAAATTTGG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 25 0.57
38 1 0.02
39 18 0.41
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (37 bp):
TTGGTGATTCAATCACGGATCTGTTAGAGCATGATTC
Found at i:16285309 original size:19 final size:19
Alignment explanation
Indices: 16285285--16285329 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
16285275 AGTAATGAGT
* * *
16285285 AAAATAATAATTAAAGATG
1 AAAATAATAATAAAAAATA
16285304 AAAATAATAATAAAAAATA
1 AAAATAATAATAAAAAATA
16285323 AAAATAA
1 AAAATAA
16285330 AAAATTTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (19 bp):
AAAATAATAATAAAAAATA
Found at i:16285322 original size:13 final size:13
Alignment explanation
Indices: 16285304--16285334 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
16285294 ATTAAAGATG
*
16285304 AAAATAATAATAA
1 AAAATAAAAATAA
16285317 AAAATAAAAATAA
1 AAAATAAAAATAA
16285330 AAAAT
1 AAAAT
16285335 TTGAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:16285374 original size:30 final size:30
Alignment explanation
Indices: 16285338--16285394 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
16285328 AAAAAATTTG
* *
16285338 AAAATAAAATGAAAAT-AAAATAGAAAAAGT
1 AAAATAAAA-CAAAATCAAAACAGAAAAAGT
16285368 AAAATAAAACAAAATCAAAACAGAAAA
1 AAAATAAAACAAAATCAAAACAGAAAA
16285395 TACGATGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.12
Consensus pattern (30 bp):
AAAATAAAACAAAATCAAAACAGAAAAAGT
Found at i:16285995 original size:28 final size:29
Alignment explanation
Indices: 16285946--16286002 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
16285936 GAAACTTTAA
16285946 TTAACTTTTAGAATTATCT-AAATTTTTC
1 TTAACTTTTAGAATTATCTAAAATTTTTC
* *
16285974 TTAATTTTTAGAATCT-TTTAAAATTTTTC
1 TTAACTTTTAGAAT-TATCTAAAATTTTTC
16286003 CAAATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.32, C:0.09, G:0.04, T:0.56
Consensus pattern (29 bp):
TTAACTTTTAGAATTATCTAAAATTTTTC
Found at i:16286194 original size:8 final size:9
Alignment explanation
Indices: 16286183--16286227 Score: 69
Period size: 8 Copynumber: 5.3 Consensus size: 9
16286173 ATTAAAATAT
16286183 ATAAA-AAG
1 ATAAATAAG
16286191 ATAAATAA-
1 ATAAATAAG
16286199 ATAAATAA-
1 ATAAATAAG
16286207 ATAAATAAG
1 ATAAATAAG
16286216 ATAAATAAG
1 ATAAATAAG
16286225 ATA
1 ATA
16286228 TAAAAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
8 21 0.60
9 14 0.40
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (9 bp):
ATAAATAAG
Found at i:16286200 original size:4 final size:4
Alignment explanation
Indices: 16286177--16286223 Score: 60
Period size: 4 Copynumber: 11.5 Consensus size: 4
16286167 TAAAATATTA
*
16286177 AAAT ATAT AAA- AAGAT AAAT AAAT AAAT AAAT AAAT AAGAT AAAT AA
1 AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AA
16286224 GATATAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 2 0.05
4 30 0.79
5 6 0.16
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:16286206 original size:12 final size:13
Alignment explanation
Indices: 16286183--16286223 Score: 68
Period size: 12 Copynumber: 3.3 Consensus size: 13
16286173 ATTAAAATAT
16286183 ATAAA-AAGATAA
1 ATAAATAAGATAA
16286195 ATAAATAA-ATAA
1 ATAAATAAGATAA
16286207 ATAAATAAGATAA
1 ATAAATAAGATAA
16286220 ATAA
1 ATAA
16286224 GATATAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (13 bp):
ATAAATAAGATAA
Found at i:16286557 original size:18 final size:18
Alignment explanation
Indices: 16286524--16286590 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 18
16286514 TGATTCATAA
* *
16286524 AAAATTTATAATGATTTC
1 AAAATTTGTAAAGATTTC
16286542 AAAATTTGTAAAGA-TTC
1 AAAATTTGTAAAGATTTC
* * *
16286559 AAGATTTGCAAAGGTTTTC
1 AAAATTTGTAAA-GATTTC
*
16286578 -AAATTCGTAAAGA
1 AAAATTTGTAAAGA
16286591 ATTTTAGATT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
17 14 0.37
18 21 0.55
19 3 0.08
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.36
Consensus pattern (18 bp):
AAAATTTGTAAAGATTTC
Found at i:16286688 original size:86 final size:85
Alignment explanation
Indices: 16286567--16286773 Score: 216
Period size: 86 Copynumber: 2.4 Consensus size: 85
16286557 TCAAGATTTG
* * * * *
16286567 CAAAGGTTTTCAAATTCGTAAAGAATTTTAGATTCACAAAAATGGAAGATTCGTAAAATTTGAAG
1 CAAAGG-TTTCAAATTCAT-AAGGATTTTAGATTCACAAAAATGGAAAATTCATAAAATTTGAAA
* * *
16286632 TTTCGTAGAGGTTTTAGATTCA
64 TTTCGCAGAGGTTCTAAATTCA
* * * *
16286654 CAAAGGTTTCAAATTCATAAGGATTTTCATATTCACAAGAATGGAAAATTCATAAGATTTTAAAT
1 CAAAGGTTTCAAATTCATAAGGATTTT-AGATTCACAAAAATGGAAAATTCATAAAATTTGAAAT
**
16286719 TTCGCAGAGGTTCTAAATTTG
65 TTCGCAGAGGTTCTAAATTCA
* * * *
16286740 TAAAGGTTTCAGATTCACAAGGACTTTTAAATTC
1 CAAAGGTTTCAAATTCATAAGGA-TTTTAGATTC
16286774 GTAAGAATGA
Statistics
Matches: 100, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
85 8 0.08
86 82 0.82
87 10 0.10
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (85 bp):
CAAAGGTTTCAAATTCATAAGGATTTTAGATTCACAAAAATGGAAAATTCATAAAATTTGAAATT
TCGCAGAGGTTCTAAATTCA
Found at i:16286842 original size:17 final size:17
Alignment explanation
Indices: 16286799--16286842 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
16286789 AAGATTCCAA
16286799 GTTTCGCAAAGGTTTTAG
1 GTTT-GCAAAGGTTTTAG
* *
16286817 ATTTACAAAGGTTTTAG
1 GTTTGCAAAGGTTTTAG
16286834 GTTTGCAAA
1 GTTTGCAAA
16286843 ATATTCAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.39
Consensus pattern (17 bp):
GTTTGCAAAGGTTTTAG
Found at i:16286939 original size:36 final size:36
Alignment explanation
Indices: 16286850--16287020 Score: 100
Period size: 36 Copynumber: 4.8 Consensus size: 36
16286840 AAAATATTCA
* * *
16286850 AAGATTTGCAAGAAATT-TAAGTTCGTAAGAAATTT
1 AAGATTTGCAAGAAATTCAAAGTTCGCAAAAAATTT
* * *
16286885 AAATATTTGTAAGCAATTCAAAGATTCGCAAAAAATTT
1 -AAGATTTGCAAGAAATTCAAAG-TTCGCAAAAAATTT
* * ** * *
16286923 -AGATTTGCAAGAAATTCATA-TTCGTAGGAACTTCA
1 AAGATTTGCAAGAAATTCAAAGTTCGCAAAAAATT-T
** * * *
16286958 AAGATTCACAAGAGATTC-AAGTTCACAAGAAATTT
1 AAGATTTGCAAGAAATTCAAAGTTCGCAAAAAATTT
* *
16286993 AAG-TTTGCAAAAAATTTAAAGATTCGCA
1 AAGATTTGCAAGAAATTCAAAG-TTCGCA
16287021 TTCAAAAGAT
Statistics
Matches: 98, Mismatches: 30, Indels: 14
0.69 0.21 0.10
Matches are distributed among these distances:
34 18 0.18
35 7 0.07
36 58 0.59
37 3 0.03
38 12 0.12
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (36 bp):
AAGATTTGCAAGAAATTCAAAGTTCGCAAAAAATTT
Found at i:16286984 original size:17 final size:17
Alignment explanation
Indices: 16286962--16286997 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
16286952 ACTTCAAAGA
*
16286962 TTCACAAGAGATTCAAG
1 TTCACAAGAAATTCAAG
*
16286979 TTCACAAGAAATTTAAG
1 TTCACAAGAAATTCAAG
16286996 TT
1 TT
16286998 TGCAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (17 bp):
TTCACAAGAAATTCAAG
Found at i:16287185 original size:44 final size:45
Alignment explanation
Indices: 16287107--16287244 Score: 118
Period size: 45 Copynumber: 3.1 Consensus size: 45
16287097 TTCTTGTATG
* * ** *
16287107 AAAAATTTCAGGGTCTCACATCCAAAAGTTAAAGATTTTCA-TTC
1 AAAAATTTTAGGATCTCACATCCAAAAGTTAAAGATTCACATTTA
* *
16287151 AAAAATTTTAGGAT-TCACATTCAAAATTTCAAAGATTCACATTTA
1 AAAAATTTTAGGATCTCACATCCAAAAGTT-AAAGATTCACATTTA
* * ** * * * *
16287196 AAAAATTTTAGGGTTTTGCATCCAAAATTTTAAGAATCTCATTTA
1 AAAAATTTTAGGATCTCACATCCAAAAGTTAAAGATTCACATTTA
16287241 AAAA
1 AAAA
16287245 GCTCCAATAA
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
43 13 0.17
44 21 0.27
45 31 0.40
46 12 0.16
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (45 bp):
AAAAATTTTAGGATCTCACATCCAAAAGTTAAAGATTCACATTTA
Found at i:16287187 original size:22 final size:21
Alignment explanation
Indices: 16287122--16287198 Score: 73
Period size: 22 Copynumber: 3.6 Consensus size: 21
16287112 TTTCAGGGTC
* *
16287122 TCACATCCAAAAGTTAAAGAT
1 TCACATTCAAAATTTAAAGAT
** * *
16287143 TTTCATTCAAAAATTTTAGGAT
1 TCACATTC-AAAATTTAAAGAT
16287165 TCACATTCAAAATTTCAAAGAT
1 TCACATTCAAAATTT-AAAGAT
*
16287187 TCACATTTAAAA
1 TCACATTCAAAA
16287199 AATTTTAGGG
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
21 12 0.28
22 31 0.72
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (21 bp):
TCACATTCAAAATTTAAAGAT
Found at i:16287207 original size:45 final size:44
Alignment explanation
Indices: 16287107--16287207 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 44
16287097 TTCTTGTATG
* * ** *
16287107 AAAAATTTCAGGGTCTCACATCCAAAAGTTAAAGATTTTCATTC
1 AAAAATTTTAGGATCTCACATCCAAAAGTTAAAGATTCACATTA
* *
16287151 AAAAATTTTAGGAT-TCACATTCAAAATTTCAAAGATTCACATTTA
1 AAAAATTTTAGGATCTCACATCCAAAAGTT-AAAGATTCACA-TTA
16287196 AAAAATTTTAGG
1 AAAAATTTTAGG
16287208 GTTTTGCATC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 13 0.27
44 21 0.44
45 14 0.29
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.34
Consensus pattern (44 bp):
AAAAATTTTAGGATCTCACATCCAAAAGTTAAAGATTCACATTA
Found at i:16287497 original size:20 final size:19
Alignment explanation
Indices: 16287451--16287499 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
16287441 AAATGTTGCA
*
16287451 AATGCCAATGTCCTACTAT
1 AATGCAAATGTCCTACTAT
*
16287470 AATTCAAATGTTCTCTAC-AT
1 AATGCAAATG-TC-CTACTAT
16287490 AATGCAAATG
1 AATGCAAATG
16287500 CATGTCCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 8 0.32
20 13 0.52
21 4 0.16
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (19 bp):
AATGCAAATGTCCTACTAT
Found at i:16288970 original size:17 final size:17
Alignment explanation
Indices: 16288929--16288971 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
16288919 TTTATTTCCT
*
16288929 TTTATTCAACAATCTTAA
1 TTTA-TCAACAATATTAA
**
16288947 TGAATCAACAATATTAA
1 TTTATCAACAATATTAA
16288964 TTTATCAA
1 TTTATCAA
16288972 TCATATCATC
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTATCAACAATATTAA
Found at i:16304742 original size:31 final size:31
Alignment explanation
Indices: 16304677--16304794 Score: 163
Period size: 31 Copynumber: 3.9 Consensus size: 31
16304667 AAGTCATGAC
* *
16304677 ATCATGCAAT-AATATTAAATTCA-TA-CAAA
1 ATCATGCAATAAATA-TAAAATCATTACCTAA
*
16304706 ATCATGAAATAAATATAAAATCATTACCTAA
1 ATCATGCAATAAATATAAAATCATTACCTAA
*
16304737 ATCATGCAGTAAATATAAAATCATTACCTAA
1 ATCATGCAATAAATATAAAATCATTACCTAA
16304768 ATCATGCAATAAATATAAAATC-TTACC
1 ATCATGCAATAAATATAAAATCATTACC
16304795 ATGCAAATAA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
29 16 0.20
30 11 0.14
31 53 0.66
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.30
Consensus pattern (31 bp):
ATCATGCAATAAATATAAAATCATTACCTAA
Found at i:16304846 original size:24 final size:24
Alignment explanation
Indices: 16304803--16304860 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
16304793 CCATGCAAAT
*
16304803 AATAAATA-ATAAATAATCATGCA
1 AATAAATATATAAATAATCATACA
* *
16304826 AATAAATATATTAATAATCATATA
1 AATAAATATATAAATAATCATACA
16304850 AATAAATATAT
1 AATAAATATAT
16304861 CATAAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 8 0.26
24 23 0.74
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (24 bp):
AATAAATATATAAATAATCATACA
Found at i:16304875 original size:24 final size:24
Alignment explanation
Indices: 16304803--16304876 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
16304793 CCATGCAAAT
**
16304803 AATAAATA-A-TAAATAATCATGCA
1 AATAAATATATTAAA-AATCATATA
*
16304826 AATAAATATATTAATAATCATATA
1 AATAAATATATTAAAAATCATATA
16304850 AATAAATATATCATAAAAAT-AT-TA
1 AATAAATATAT--TAAAAATCATATA
16304874 AAT
1 AAT
16304877 CACGCAGATT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
23 8 0.19
24 24 0.56
25 5 0.12
26 6 0.14
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.32
Consensus pattern (24 bp):
AATAAATATATTAAAAATCATATA
Found at i:16304905 original size:16 final size:16
Alignment explanation
Indices: 16304866--16304916 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
16304856 TATATCATAA
16304866 AAATATTAAATCACGC
1 AAATATTAAATCACGC
* *
16304882 --AGATTAAATCATGC
1 AAATATTAAATCACGC
*
16304896 AAATATTAAATCACAC
1 AAATATTAAATCACGC
16304912 AAATA
1 AAATA
16304917 AATTACTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 12 0.43
16 16 0.57
ACGTcount: A:0.53, C:0.16, G:0.06, T:0.25
Consensus pattern (16 bp):
AAATATTAAATCACGC
Found at i:16305904 original size:28 final size:28
Alignment explanation
Indices: 16305844--16305971 Score: 95
Period size: 28 Copynumber: 4.5 Consensus size: 28
16305834 GCATTAAAAG
* * *
16305844 AAAACTTTTAAAAATTCAAAAAAAATTTTA
1 AAAACTTTTAAAAA-TC-TAAAATATTATA
16305874 AAAACTTTTAAAAATCTAAAATATTATA
1 AAAACTTTTAAAAATCTAAAATATTATA
* * * *
16305902 AAAA--ATTAAAAATATATGAAATATTTTT
1 AAAACTTTTAAAAATCTA--AAATATTATA
*
16305930 AAAA-TTATAAAAAT-TAAAA-ATATATA
1 AAAACTTTTAAAAATCTAAAATAT-TATA
16305956 AGAAACTTTTAAAAAT
1 A-AAACTTTTAAAAAT
16305972 TCAAAAACCT
Statistics
Matches: 80, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
25 2 0.03
26 16 0.20
27 3 0.04
28 36 0.45
29 9 0.11
30 14 0.17
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (28 bp):
AAAACTTTTAAAAATCTAAAATATTATA
Found at i:16305971 original size:37 final size:37
Alignment explanation
Indices: 16305890--16305972 Score: 107
Period size: 36 Copynumber: 2.2 Consensus size: 37
16305880 TTTAAAAATC
16305890 TAAAATATTATAAAAAATTAAAAATATATGAAATATTT
1 TAAAA-ATTATAAAAAATTAAAAATATATGAAATATTT
* *
16305928 TTAAAATTAT-AAAAATTAAAAATATATAAGAAA-CTTT
1 TAAAAATTATAAAAAATTAAAAATATAT--GAAATATTT
16305965 TAAAAATT
1 TAAAAATT
16305973 CAAAAACCTC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
36 17 0.43
37 15 0.38
38 8 0.20
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.36
Consensus pattern (37 bp):
TAAAAATTATAAAAAATTAAAAATATATGAAATATTT
Found at i:16306029 original size:22 final size:20
Alignment explanation
Indices: 16305994--16306037 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
16305984 GAATTTTAAT
16305994 AAAAAATCCAAAAAATTCAAAA
1 AAAAAATCC-AAAAATT-AAAA
**
16306016 AAAAAATCTTAAAATTAAAA
1 AAAAAATCCAAAAATTAAAA
16306036 AA
1 AA
16306038 TACGAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 6 0.30
22 8 0.40
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (20 bp):
AAAAAATCCAAAAATTAAAA
Found at i:16306151 original size:36 final size:36
Alignment explanation
Indices: 16306099--16306189 Score: 98
Period size: 36 Copynumber: 2.6 Consensus size: 36
16306089 AAAAAACTTT
*
16306099 AAAAA-TTG-AAAA-TAAAAAAGCTAAAATGTTTTG
1 AAAAATTTGAAAAATTAAAAAAGCTAAAATCTTTTG
* * * *
16306132 AAAAATTTTAAAAATTAAAAAATCTAAATTCTTTTT
1 AAAAATTTGAAAAATTAAAAAAGCTAAAATCTTTTG
**
16306168 AAAAATTTGAAATTTTAAAAAA
1 AAAAATTTGAAAAATTAAAAAA
16306190 ATTCTTAAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
33 5 0.11
34 2 0.04
35 4 0.09
36 36 0.77
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.34
Consensus pattern (36 bp):
AAAAATTTGAAAAATTAAAAAAGCTAAAATCTTTTG
Found at i:16306413 original size:12 final size:12
Alignment explanation
Indices: 16306398--16306422 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16306388 ATTTTTTAAG
16306398 TTTTTTTGAATT
1 TTTTTTTGAATT
16306410 TTTTTTTGAATT
1 TTTTTTTGAATT
16306422 T
1 T
16306423 AAAGAAAAAT
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:16306536 original size:19 final size:19
Alignment explanation
Indices: 16306514--16306571 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 19
16306504 ATTTTGAATT
16306514 TTTTTTTAAATTTTTTAAG
1 TTTTTTTAAATTTTTTAAG
**
16306533 TTTTAAT-AATTGTTTTAA-
1 TTTTTTTAAATT-TTTTAAG
* *
16306551 TTTTTTAAAATATTTT-AG
1 TTTTTTTAAATTTTTTAAG
16306569 TTT
1 TTT
16306572 GTAATTTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
17 1 0.03
18 15 0.50
19 14 0.47
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTTTTTAAATTTTTTAAG
Found at i:16306543 original size:18 final size:18
Alignment explanation
Indices: 16306522--16306576 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
16306512 TTTTTTTTTA
16306522 AATTTTTTAAGTTTTAAT
1 AATTTTTTAAGTTTTAAT
*
16306540 AATTGTTTTAATTTTTTAA-
1 AATT-TTTTAA-GTTTTAAT
*
16306559 AATATTTT-AGTTTGTAAT
1 AATTTTTTAAGTTT-TAAT
16306577 TTTATAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
16 3 0.10
17 4 0.13
18 8 0.27
19 9 0.30
20 6 0.20
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (18 bp):
AATTTTTTAAGTTTTAAT
Found at i:16306610 original size:9 final size:9
Alignment explanation
Indices: 16306576--16306637 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
16306566 TAGTTTGTAA
*
16306576 TTTTATAAT
1 TTTTAAAAT
*
16306585 TTCTAAAAT
1 TTTTAAAAT
* *
16306594 ATTCAAAAT
1 TTTTAAAAT
16306603 TTTTAAAATT
1 TTTTAAAA-T
16306613 TGTTTAGAAAT
1 T-TTTA-AAAT
16306624 TTTTAAAAAT
1 TTTT-AAAAT
16306634 TTTT
1 TTTT
16306638 TTGCAAGTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
9 19 0.45
10 13 0.31
11 7 0.17
12 3 0.07
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:16306632 original size:22 final size:22
Alignment explanation
Indices: 16306599--16306658 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
16306589 AAAATATTCA
16306599 AAATTTTT-AAAATTTGTTTAG-
1 AAATTTTTAAAAATTT-TTTAGC
*
16306620 AAATTTTTAAAAATTTTTTTGC
1 AAATTTTTAAAAATTTTTTAGC
*
16306642 AAGTTTTTAGAAAATTT
1 AAATTTTTA-AAAATTT
16306659 CTTTTAATGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.35
22 15 0.44
23 7 0.21
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (22 bp):
AAATTTTTAAAAATTTTTTAGC
Found at i:16306633 original size:10 final size:10
Alignment explanation
Indices: 16306598--16306637 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
16306588 TAAAATATTC
16306598 AAAATTTTTA
1 AAAATTTTTA
*
16306608 AAATTTGTTTA
1 AAAATT-TTTA
*
16306619 GAAATTTTTA
1 AAAATTTTTA
16306629 AAAATTTTT
1 AAAATTTTT
16306638 TTGCAAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (10 bp):
AAAATTTTTA
Found at i:16308158 original size:21 final size:21
Alignment explanation
Indices: 16308125--16308166 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
16308115 ACAGTAGCAA
16308125 CAATATTATTATTATTT-TTAT
1 CAATATTATTATT-TTTATTAT
16308146 CAAT-TTATCTATTTTTATTAT
1 CAATATTAT-TATTTTTATTAT
16308167 TATACAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
CAATATTATTATTTTTATTAT
Found at i:16310915 original size:41 final size:42
Alignment explanation
Indices: 16310858--16311087 Score: 190
Period size: 41 Copynumber: 5.6 Consensus size: 42
16310848 AAGGTTTTTT
* *
16310858 AAAATCACTTAAAAATCTAAGATTTTACC-CGAAGATCTTTG
1 AAAATCATTTAAAAATCTAAGATTTTGCCTCGAAGATCTTTG
* * *
16310899 AAAATCATTAAAAAATCTAAAATTTTGCCTCGAAG--CATT-
1 AAAATCATTTAAAAATCTAAGATTTTGCCTCGAAGATCTTTG
* ** * *
16310938 AAAGATCATTCAAAGTTTTAAGATTTTGCCTGGAAG-TCTTTTG
1 AAA-ATCATTTAAAAATCTAAGATTTTGCCTCGAAGATC-TTTG
* * * * *
16310981 -AAATCATTTAAAAATATGAGATTTTTCCTTG-AGATCTTTT
1 AAAATCATTTAAAAATCTAAGATTTTGCCTCGAAGATCTTTG
* * *
16311021 TAAATCATTTAAAAATCTAAGATTTTGCCT-GGAGGTCTTTTG
1 AAAATCATTTAAAAATCTAAGATTTTGCCTCGAAGATC-TTTG
* *
16311063 -AAATCATTTAAAAATATGAGATTTT
1 AAAATCATTTAAAAATCTAAGATTTT
16311088 TCCCTGAGAT
Statistics
Matches: 153, Mismatches: 27, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
39 3 0.02
40 35 0.23
41 103 0.67
42 12 0.08
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (42 bp):
AAAATCATTTAAAAATCTAAGATTTTGCCTCGAAGATCTTTG
Found at i:16311045 original size:82 final size:82
Alignment explanation
Indices: 16310956--16311106 Score: 284
Period size: 82 Copynumber: 1.8 Consensus size: 82
16310946 TTCAAAGTTT
*
16310956 TAAGATTTTGCCTGGAAGTCTTTTGAAATCATTTAAAAATATGAGATTTTTCCTTGAGATCTTTT
1 TAAGATTTTGCCTGGAAGTCTTTTGAAATCATTTAAAAATATGAGATTTTTCCCTGAGATCTTTT
16311021 TAAATCATTTAAAAATC
66 TAAATCATTTAAAAATC
*
16311038 TAAGATTTTGCCTGGAGGTCTTTTGAAATCATTTAAAAATATGAGATTTTTCCCTGAGATCTTTT
1 TAAGATTTTGCCTGGAAGTCTTTTGAAATCATTTAAAAATATGAGATTTTTCCCTGAGATCTTTT
16311103 TAAA
66 TAAA
16311107 GGTCTTTGAA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 67 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.42
Consensus pattern (82 bp):
TAAGATTTTGCCTGGAAGTCTTTTGAAATCATTTAAAAATATGAGATTTTTCCCTGAGATCTTTT
TAAATCATTTAAAAATC
Found at i:16311101 original size:41 final size:41
Alignment explanation
Indices: 16310974--16311102 Score: 188
Period size: 41 Copynumber: 3.1 Consensus size: 41
16310964 TGCCTGGAAG
*
16310974 TCTTTTGAAATCATTTAAAAATATGAGATTTTTCCTTGAGA
1 TCTTTTGAAATCATTTAAAAATATGAGATTTTTCCCTGAGA
* * * * *
16311015 TCTTTTTAAATCATTTAAAAATCTAAGA-TTTTGCCTGGAGG
1 TCTTTTGAAATCATTTAAAAATATGAGATTTTTCCCT-GAGA
16311056 TCTTTTGAAATCATTTAAAAATATGAGATTTTTCCCTGAGA
1 TCTTTTGAAATCATTTAAAAATATGAGATTTTTCCCTGAGA
16311097 TCTTTT
1 TCTTTT
16311103 TAAAGGTCTT
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 6 0.08
41 62 0.83
42 7 0.09
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (41 bp):
TCTTTTGAAATCATTTAAAAATATGAGATTTTTCCCTGAGA
Found at i:16311873 original size:17 final size:17
Alignment explanation
Indices: 16311853--16311886 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16311843 TAAAAACATT
* *
16311853 TTTTTTTCTTTTTTTTC
1 TTTTTTTATTTCTTTTC
16311870 TTTTTTTATTTCTTTTC
1 TTTTTTTATTTCTTTTC
16311887 AACATCATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTATTTCTTTTC
Found at i:16311885 original size:9 final size:9
Alignment explanation
Indices: 16311852--16311876 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16311842 TTAAAAACAT
16311852 TTTTTTTTC
1 TTTTTTTTC
16311861 TTTTTTTTC
1 TTTTTTTTC
16311870 TTTTTTT
1 TTTTTTT
16311877 ATTTCTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:16312998 original size:14 final size:14
Alignment explanation
Indices: 16312954--16313016 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 14
16312944 CTTATTCATT
16312954 TTTTTTCTTTTT-C
1 TTTTTTCTTTTTCC
* *
16312967 TTTCTTT-TGTTTCA
1 TTT-TTTCTTTTTCC
16312981 TTTTTTCTTTTTCC
1 TTTTTTCTTTTTCC
* *
16312995 TTTTCTC-TTTACC
1 TTTTTTCTTTTTCC
16313008 -TTTTTCTTT
1 TTTTTTCTTT
16313017 ATCATTCTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
12 5 0.13
13 17 0.44
14 17 0.44
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTTTTCTTTTTCC
Found at i:16313012 original size:27 final size:27
Alignment explanation
Indices: 16312954--16313004 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
16312944 CTTATTCATT
* * *
16312954 TTTTTTCTTTTTCTTTCTTTTGTTTCA
1 TTTTTTCTTTTTCCTTCTTCTCTTTCA
16312981 TTTTTTCTTTTTCCTT-TTCTCTTT
1 TTTTTTCTTTTTCCTTCTTCTCTTT
16313005 ACCTTTTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (27 bp):
TTTTTTCTTTTTCCTTCTTCTCTTTCA
Found at i:16313509 original size:10 final size:10
Alignment explanation
Indices: 16313495--16313538 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
16313485 TTTTTTATCA
16313495 TTTTTCTTTC
1 TTTTTCTTTC
*
16313505 CTTTT-TTTC
1 TTTTTCTTTC
16313514 TTTTTCTTTC
1 TTTTTCTTTC
*
16313524 TTTTTCTTTA
1 TTTTTCTTTC
16313534 TTTTT
1 TTTTT
16313539 GATATGTCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:16313517 original size:19 final size:20
Alignment explanation
Indices: 16313485--16313528 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
16313475 CAAAACTATT
16313485 TTTTTTATCATTTTTCTTTCC
1 TTTTTTATCATTTTTCTTT-C
16313506 TTTTTT-TC-TTTTTCTTTC
1 TTTTTTATCATTTTTCTTTC
16313524 TTTTT
1 TTTTT
16313529 CTTTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.26
19 9 0.39
20 2 0.09
21 6 0.26
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTATCATTTTTCTTTC
Found at i:16314936 original size:34 final size:34
Alignment explanation
Indices: 16314898--16314991 Score: 90
Period size: 34 Copynumber: 2.9 Consensus size: 34
16314888 TGTTTCAAGC
**
16314898 ATTTTAATTTTCTATGTTATTTAAATTTTATTTA
1 ATTTTAATTTTCTATGTTATTTAAATTTTATGCA
* *
16314932 ATTTTAATTATT-GATATTATTTAAA-TTTATGCA
1 ATTTTAATT-TTCTATGTTATTTAAATTTTATGCA
* *
16314965 A-TTTACTTTTCT-TGTAATTT-AATTTTA
1 ATTTTAATTTTCTATGTTATTTAAATTTTA
16314992 ACTGTTTAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
30 2 0.04
31 12 0.24
32 6 0.12
33 7 0.14
34 20 0.41
35 2 0.04
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (34 bp):
ATTTTAATTTTCTATGTTATTTAAATTTTATGCA
Found at i:16315039 original size:16 final size:16
Alignment explanation
Indices: 16315015--16315050 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16315005 CATGCCCTCA
*
16315015 TTTACTTTTTATGCAG
1 TTTACTTTTTATGCAC
*
16315031 TTTATTTTTTATGCAC
1 TTTACTTTTTATGCAC
16315047 TTTA
1 TTTA
16315051 AATTTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.11, G:0.08, T:0.61
Consensus pattern (16 bp):
TTTACTTTTTATGCAC
Found at i:16315103 original size:48 final size:49
Alignment explanation
Indices: 16315042--16315135 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
16315032 TTATTTTTTA
* *
16315042 TGCACTTTAAATTT-AT-ATAATTTAATATTTTCATGCACTTTAATTATT
1 TGCAATTTAAATTTAATGATAATTTAA-ATTTTCAAGCACTTTAATTATT
* * *
16315090 TGCAATTTAAATTTAATGTTTATTTAAATTTTCAAGCTCTTTAATT
1 TGCAATTTAAATTTAATGATAATTTAAATTTTCAAGCACTTTAATT
16315136 TTTATTAGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
48 13 0.33
49 19 0.49
50 7 0.18
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (49 bp):
TGCAATTTAAATTTAATGATAATTTAAATTTTCAAGCACTTTAATTATT
Found at i:16317758 original size:3 final size:3
Alignment explanation
Indices: 16317750--16317778 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
16317740 AACACATGGT
16317750 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
16317779 TTATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:16318724 original size:19 final size:19
Alignment explanation
Indices: 16318699--16318743 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
16318689 TTAAAAAAAC
*
16318699 TTAAA-ATAAAGAAAATTAAA
1 TTAAATATAAA-AAAACT-AA
16318719 TTAAATATAAAAAAACTAA
1 TTAAATATAAAAAAACTAA
16318738 TTAAAT
1 TTAAAT
16318744 CCAAAACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 10 0.43
21 5 0.22
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
TTAAATATAAAAAAACTAA
Found at i:16319405 original size:20 final size:20
Alignment explanation
Indices: 16319380--16319421 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
16319370 AGAAATATTA
*
16319380 TTTTG-AATTTATTTATTTTT
1 TTTTGAAATTAATTT-TTTTT
16319400 TTTTGAAATTAATTTTTTTT
1 TTTTGAAATTAATTTTTTTT
16319420 TT
1 TT
16319422 AAAATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTTGAAATTAATTTTTTTT
Found at i:16319416 original size:18 final size:17
Alignment explanation
Indices: 16319394--16319430 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
16319384 GAATTTATTT
* *
16319394 ATTTTTTTTTGAAATTA
1 ATTTTTTTTTTAAAATA
16319411 ATTTTTTTTTTAAAATA
1 ATTTTTTTTTTAAAATA
16319428 ATT
1 ATT
16319431 AAATAACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
ATTTTTTTTTTAAAATA
Found at i:16319937 original size:20 final size:19
Alignment explanation
Indices: 16319901--16319951 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
16319891 ACATAAAGTT
16319901 TTAAGG-TTTAGGTTCTCAC
1 TTAAGGTTTTA-GTTCTCAC
**
16319920 TTAAGGTTTTAGTATCTCTT
1 TTAAGGTTTTAGT-TCTCAC
*
16319940 TTAGGGTTTTAG
1 TTAAGGTTTTAG
16319952 GATTTACCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.20, C:0.10, G:0.22, T:0.49
Consensus pattern (19 bp):
TTAAGGTTTTAGTTCTCAC
Found at i:16320132 original size:3 final size:3
Alignment explanation
Indices: 16320124--16320152 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
16320114 ATTAAAAATT
16320124 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
16320153 TTAATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16320250 original size:3 final size:3
Alignment explanation
Indices: 16320237--16320265 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
16320227 GGGATTTAAA
16320237 TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16320266 ATTTTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:16321712 original size:16 final size:15
Alignment explanation
Indices: 16321686--16321715 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
16321676 CTTTTTTTTT
16321686 TTATATTTATATTTA
1 TTATATTTATATTTA
16321701 TTATATTTTATATTT
1 TTATA-TTTATATTT
16321716 GGTTTCTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATATTTATATTTA
Found at i:16322066 original size:6 final size:6
Alignment explanation
Indices: 16322055--16322116 Score: 52
Period size: 7 Copynumber: 9.5 Consensus size: 6
16322045 TTTTTTCTTC
* *
16322055 TTGTTT TTGTTTT TTGTTTT TTGTTT TTCGTTT TTGCTTT GTAGCTT TTGTTT
1 TTGTTT TTG-TTT TTG-TTT TTGTTT TT-GTTT TTG-TTT -TTGTTT TTGTTT
*
16322108 TTGTCT TTG
1 TTGTTT TTG
16322117 GAAGACTCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
6 21 0.45
7 24 0.51
8 2 0.04
ACGTcount: A:0.02, C:0.06, G:0.18, T:0.74
Consensus pattern (6 bp):
TTGTTT
Found at i:16322068 original size:20 final size:21
Alignment explanation
Indices: 16322043--16322089 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
16322033 TTTTTTTTGG
16322043 GTTTTTT-TCTTCTTGTTTTT-
1 GTTTTTTGT-TTCTTGTTTTTC
*
16322063 GTTTTTTGTTTTTTGTTTTTC
1 GTTTTTTGTTTCTTGTTTTTC
16322084 GTTTTT
1 GTTTTT
16322090 GCTTTGTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.00, C:0.06, G:0.13, T:0.81
Consensus pattern (21 bp):
GTTTTTTGTTTCTTGTTTTTC
Found at i:16322070 original size:7 final size:7
Alignment explanation
Indices: 16322058--16322089 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
16322048 TTTCTTCTTG
16322058 TTTTTGT
1 TTTTTGT
16322065 TTTTTGT
1 TTTTTGT
16322072 TTTTTGT
1 TTTTTGT
*
16322079 TTTTCGT
1 TTTTTGT
16322086 TTTT
1 TTTT
16322090 GCTTTGTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.84
Consensus pattern (7 bp):
TTTTTGT
Found at i:16339540 original size:16 final size:16
Alignment explanation
Indices: 16339521--16339560 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
16339511 ACTTACATGT
16339521 TTAAAATAT-ATATAAA
1 TTAAAATATAATAT-AA
16339537 TT-AAATATAATATAA
1 TTAAAATATAATATAA
16339552 TTAAAATAT
1 TTAAAATAT
16339561 CAAATCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAAATATAATATAA
Found at i:16339544 original size:15 final size:16
Alignment explanation
Indices: 16339524--16339560 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
16339514 TACATGTTTA
16339524 AAATATATATA-AATT
1 AAATATATATATAATT
16339539 AAATATA-ATATAATT
1 AAATATATATATAATT
16339554 AAA-ATAT
1 AAATATAT
16339561 CAAATCATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATATATATAATT
Found at i:16339903 original size:23 final size:24
Alignment explanation
Indices: 16339872--16339919 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
16339862 ATTCAACATT
*
16339872 TATTGTTAAAT-TGACAAAGAAAA
1 TATTATTAAATATGACAAAGAAAA
*
16339895 TATTATTAAATACTTACAAAGAAAA
1 TATTATTAAATA-TGACAAAGAAAA
16339920 AATAGATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
25 11 0.52
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.31
Consensus pattern (24 bp):
TATTATTAAATATGACAAAGAAAA
Found at i:16341821 original size:2 final size:2
Alignment explanation
Indices: 16341809--16341873 Score: 51
Period size: 2 Copynumber: 33.0 Consensus size: 2
16341799 CAAATATCTT
* * * * * * * *
16341809 TA TA T- TA TA TA TA TA TG TA TG TG TG TG TA TG TA TA CA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16341850 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
16341874 GCACTTAAGC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (2 bp):
TA
Found at i:16343223 original size:2 final size:2
Alignment explanation
Indices: 16343218--16343242 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16343208 ATTAAAAAAT
16343218 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16343243 TAGTAAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16343762 original size:17 final size:18
Alignment explanation
Indices: 16343742--16343779 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
16343732 TTATTATGAG
16343742 TAAA-GATTTTATGATTA
1 TAAAGGATTTTATGATTA
16343759 TAAAGGATTTTATGATTA
1 TAAAGGATTTTATGATTA
16343777 TAA
1 TAA
16343780 TTAAACCACG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (18 bp):
TAAAGGATTTTATGATTA
Found at i:16346420 original size:24 final size:25
Alignment explanation
Indices: 16346387--16346435 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
16346377 ATACATATTA
16346387 TAATAATTATATAAATTAATAATTT
1 TAATAATTATATAAATTAATAATTT
* *
16346412 TAAT-ATTATTTAAGTTAATAATTT
1 TAATAATTATATAAATTAATAATTT
16346436 GTAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TAATAATTATATAAATTAATAATTT
Found at i:16346613 original size:19 final size:19
Alignment explanation
Indices: 16346570--16346606 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
16346560 AATATAATCT
16346570 ATTAAATTCATTATAAAAA
1 ATTAAATTCATTATAAAAA
16346589 ATTAAATT-ATATATAAAA
1 ATTAAATTCAT-TATAAAA
16346607 TGTTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTAAATTCATTATAAAAA
Found at i:16346687 original size:14 final size:16
Alignment explanation
Indices: 16346670--16346702 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
16346660 TTAACTTCAA
16346670 AATAT-AAA-AATTAT
1 AATATAAAATAATTAT
16346684 AATATAAAATAATTAT
1 AATATAAAATAATTAT
16346700 AAT
1 AAT
16346703 TTTAAGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 3 0.18
16 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATATAAAATAATTAT
Found at i:16347360 original size:2 final size:2
Alignment explanation
Indices: 16347353--16347386 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16347343 TTGTTTTAAC
16347353 GA GA GA GA 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 GA GA GA GA
16347387 CCTGGTTGCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:16348159 original size:80 final size:80
Alignment explanation
Indices: 16348025--16348186 Score: 315
Period size: 80 Copynumber: 2.0 Consensus size: 80
16348015 ATGTTAAAGA
16348025 AGACTTTGCGAAGACTGGGACGAGCTTCTACAACTCAGCAGCTTTCCGTCTGAGTTTTAATTTGG
1 AGACTTTGCGAAGACTGGGACGAGCTTCTACAACTCAGCAGCTTTCCGTCTGAGTTTTAATTTGG
16348090 AGTTGGAACTTCAAT
66 AGTTGGAACTTCAAT
*
16348105 AGACTTTGCGAAGACTGGGACGAGCTTCTACAACTCAGCAGCTTTCCGTTTGAGTTTTAATTTGG
1 AGACTTTGCGAAGACTGGGACGAGCTTCTACAACTCAGCAGCTTTCCGTCTGAGTTTTAATTTGG
16348170 AGTTGGAACTTCAAT
66 AGTTGGAACTTCAAT
16348185 AG
1 AG
16348187 CGTGGCTTCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (80 bp):
AGACTTTGCGAAGACTGGGACGAGCTTCTACAACTCAGCAGCTTTCCGTCTGAGTTTTAATTTGG
AGTTGGAACTTCAAT
Found at i:16348470 original size:16 final size:16
Alignment explanation
Indices: 16348445--16348475 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16348435 GTCAATTTAG
*
16348445 ATTTAGATTATTTTGA
1 ATTTAAATTATTTTGA
16348461 ATTTAAATTATTTTG
1 ATTTAAATTATTTTG
16348476 GATTCATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (16 bp):
ATTTAAATTATTTTGA
Found at i:16351480 original size:95 final size:97
Alignment explanation
Indices: 16351310--16351502 Score: 363
Period size: 95 Copynumber: 2.0 Consensus size: 97
16351300 ACTAGTGTCG
16351310 GTGTTTTAAAGTTTTGAGTTGTTAATAAATATTAAAAAAAAAAAAGGAAAGAAAAGAATAAAGCC
1 GTGTTTTAAAGTTTTGAGTTGTTAATAAATATT-AAAAAAAAAAAGGAAAGAAAAGAATAAAGCC
16351375 GGTTTTTCTTTTGTTATAAATATTGATCAACAA
65 GGTTTTTCTTTTGTTATAAATATTGATCAACAA
16351408 GTGTTTTAAAGTTTTGAGTTGTTAATAAATA-T-AAAAAAAAAAGGAAAGAAAAGAATAAAGCCG
1 GTGTTTTAAAGTTTTGAGTTGTTAATAAATATTAAAAAAAAAAAGGAAAGAAAAGAATAAAGCCG
16351471 GTTTTTCTTTTGTTATAAATATTGATCAACAA
66 GTTTTTCTTTTGTTATAAATATTGATCAACAA
16351503 ATCTTTCTTT
Statistics
Matches: 95, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
95 63 0.66
97 1 0.01
98 31 0.33
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.35
Consensus pattern (97 bp):
GTGTTTTAAAGTTTTGAGTTGTTAATAAATATTAAAAAAAAAAAGGAAAGAAAAGAATAAAGCCG
GTTTTTCTTTTGTTATAAATATTGATCAACAA
Found at i:16352505 original size:81 final size:81
Alignment explanation
Indices: 16352370--16352520 Score: 284
Period size: 81 Copynumber: 1.9 Consensus size: 81
16352360 TTAAAGAGCT
*
16352370 TAAATTCAGAAACTGAAATTAATATAAACTTAATTCACGTTTAAATATGCATCTAATTAATACAA
1 TAAATTCAAAAACTGAAATTAATATAAACTTAATTCACGTTTAAATATGCATCTAATTAATACAA
16352435 AGTTTAACAATTAATA
66 AGTTTAACAATTAATA
*
16352451 TAAATTCAAAAACTGAAATTAATATAAACTTAATTCATGTTTAAATATGCATCTAATTAATACAA
1 TAAATTCAAAAACTGAAATTAATATAAACTTAATTCACGTTTAAATATGCATCTAATTAATACAA
16352516 AGTTT
66 AGTTT
16352521 TAAATATTCT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 68 1.00
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.36
Consensus pattern (81 bp):
TAAATTCAAAAACTGAAATTAATATAAACTTAATTCACGTTTAAATATGCATCTAATTAATACAA
AGTTTAACAATTAATA
Found at i:16352509 original size:38 final size:38
Alignment explanation
Indices: 16352386--16352512 Score: 93
Period size: 38 Copynumber: 3.2 Consensus size: 38
16352376 CAGAAACTGA
*
16352386 AATTAATATAAACTTAATTCACGTTTAAATATGCATCT
1 AATTAATATAAACTTAATTCATGTTTAAATATGCATCT
* * *
16352424 AATTAATACAAAGTTTAA--CAAT-TAATATAAAT-T-CAAAAACT
1 AATTAATATAAA-CTTAATTC-ATGT--T-TAAATATGC---ATCT
16352465 GAAATTAATATAAACTTAATTCATGTTTAAATATGCATCT
1 --AATTAATATAAACTTAATTCATGTTTAAATATGCATCT
16352505 AATTAATA
1 AATTAATA
16352513 CAAAGTTTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 30
0.64 0.07 0.29
Matches are distributed among these distances:
37 2 0.03
38 21 0.31
39 6 0.09
40 8 0.12
41 8 0.12
42 6 0.09
43 14 0.21
44 2 0.03
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (38 bp):
AATTAATATAAACTTAATTCATGTTTAAATATGCATCT
Found at i:16362126 original size:80 final size:78
Alignment explanation
Indices: 16361995--16362243 Score: 311
Period size: 80 Copynumber: 3.1 Consensus size: 78
16361985 AATATTATGG
* *
16361995 TTTGCTGAACCTTGTTGTCTGATATTATTTTACTGAATGGTATTGTATGATATTAGGGGATGGAA
1 TTTGCTGAACCTTATTGTCTGATATTATTTTACTGAATGGTATT-TTTGATATTAGGGGAT-GAA
* *
16362060 TCGTATGCTGAATGG
64 TCATATGCTGAATGA
*
16362075 TTTGCTGAACCTTATTGTCTGATATTATTTTACTGAATGGTATTATTTGATATTGAGGGGTTGAA
1 TTTGCTGAACCTTATTGTCTGATATTATTTTACTGAATGGTATT-TTTGATATT-AGGGGATGAA
*
16362140 TCATATGCTAAATGA
64 TCATATGCTGAATGA
* * * * *
16362155 TTTGTTGAACCTTATTATCTGATATTGTTTTGCTGAATGG-ATTTGTATGATATTGGGGGACTGA
1 TTTGCTGAACCTTATTGTCTGATATTATTTTACTGAATGGTATTT-T-TGATATTAGGGGA-TGA
*
16362219 ATCATATGATGAATGA
63 ATCATATGCTGAATGA
*
16362235 TTTGTTGAA
1 TTTGCTGAA
16362244 TGGTGTTTCT
Statistics
Matches: 150, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
78 1 0.01
79 8 0.05
80 135 0.90
81 6 0.04
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43
Consensus pattern (78 bp):
TTTGCTGAACCTTATTGTCTGATATTATTTTACTGAATGGTATTTTTGATATTAGGGGATGAATC
ATATGCTGAATGA
Found at i:16367860 original size:131 final size:130
Alignment explanation
Indices: 16367596--16367847 Score: 330
Period size: 131 Copynumber: 1.9 Consensus size: 130
16367586 TTTAAGTTTT
* * *
16367596 AATGCATTGCATTCATGGAAGATTTGTCAATATTTGGTACTTACTGTTTCCTTAAAAAAAAAAGT
1 AATGCATTGCATCCATGGAAGACTTGTCAATATTTGGTACTAACTGTTTCCTTAAAAAAAAAAGT
* * ** **
16367661 ACATTATCAATCAAAGTGATTTCACTTGTTTGTTTTGGATGTAAAATGCATATATGATAAAAAAA
66 ACAGTATCAATCAAAGTAAAATCACTTACTTGTTTTGGATGTAAAATG-ATATATGATAAAAAAA
16367726 A
130 A
16367727 AATGCATTGCATCCATGGAAGACTTGTCAAGT-TTTGGTACTAACTGTTTCCTTAACAGAAAAAG
1 AATGCATTGCATCCATGGAAGACTTGTCAA-TATTTGGTACTAACTGTTTCCTTAA-A-AAAAA-
*
16367791 AA-TAGCAGTATCAATCAAAGTAAAATCCCTTACTTGTTTTGGATGT-AAATGTATATA
62 AAGTA-CAGTATCAATCAAAGTAAAATCACTTACTTGTTTTGGATGTAAAATG-ATATA
16367848 AAGAGAACAA
Statistics
Matches: 105, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
131 50 0.48
132 2 0.02
133 17 0.16
134 36 0.34
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (130 bp):
AATGCATTGCATCCATGGAAGACTTGTCAATATTTGGTACTAACTGTTTCCTTAAAAAAAAAAGT
ACAGTATCAATCAAAGTAAAATCACTTACTTGTTTTGGATGTAAAATGATATATGATAAAAAAAA
Found at i:16391227 original size:16 final size:16
Alignment explanation
Indices: 16391199--16391248 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
16391189 AAATTTTTTC
16391199 AATTTA-AATAAAATTT
1 AATTTATAA-AAAATTT
16391215 AATTTATAAAAAATATT
1 AATTTATAAAAAAT-TT
16391232 -ATTTATGAAAATAATTT
1 AATTTAT-AAAA-AATTT
16391249 TTAAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 17 0.57
17 10 0.33
18 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
AATTTATAAAAAATTT
Found at i:16391443 original size:18 final size:19
Alignment explanation
Indices: 16391429--16391468 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
16391419 ATAATTATAT
16391429 ATTTTATA-TTTATTAAAA
1 ATTTTATATTTTATTAAAA
*
16391447 ATTTTATATTTTATTAATA
1 ATTTTATATTTTATTAAAA
16391466 ATT
1 ATT
16391469 AAAATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTATATTTTATTAAAA
Found at i:16391478 original size:26 final size:25
Alignment explanation
Indices: 16391421--16391477 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
16391411 TTGTTAGTAT
* * *
16391421 AATTATATATTTTATATTTATTAAA
1 AATTTTATATTTTATAATAATTAAA
16391446 AATTTTATATTTTATTAATAATTAAA
1 AATTTTATATTTTA-TAATAATTAAA
16391472 ATATTT
1 A-ATTT
16391478 ACATTTACAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 13 0.48
26 10 0.37
27 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
AATTTTATATTTTATAATAATTAAA
Found at i:16391932 original size:19 final size:20
Alignment explanation
Indices: 16391892--16391932 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
16391882 TATATTTAAA
16391892 ATATTTATATAAAATTTTTT
1 ATATTTATATAAAATTTTTT
16391912 ATATTTA-AT-AAATTTTATT
1 ATATTTATATAAAATTTT-TT
16391931 AT
1 AT
16391933 GTATTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 6 0.30
20 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATTTATATAAAATTTTTT
Found at i:16391945 original size:21 final size:18
Alignment explanation
Indices: 16391892--16391945 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 18
16391882 TATATTTAAA
16391892 ATATTTATATAAAATTTTTT
1 ATATTTA-A-AAAATTTTTT
*
16391912 ATATTTAATAAATTTTATT
1 ATATTTAAAAAATTTT-TT
16391931 ATGTATTTAAAAAAT
1 A--TATTTAAAAAAT
16391946 CAACAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 7 0.24
19 4 0.14
20 7 0.24
21 11 0.38
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATATTTAAAAAATTTTTT
Found at i:16393019 original size:24 final size:24
Alignment explanation
Indices: 16392987--16393035 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
16392977 TATATCTCTC
* *
16392987 TTTAGATCAATCCAAACAAATTTA
1 TTTACATCAAACCAAACAAATTTA
* *
16393011 TTTACATCAAACCTAATAAATTTA
1 TTTACATCAAACCAAACAAATTTA
16393035 T
1 T
16393036 AAAAAATTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.37
Consensus pattern (24 bp):
TTTACATCAAACCAAACAAATTTA
Found at i:16394658 original size:22 final size:21
Alignment explanation
Indices: 16394628--16394669 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
16394618 CTCTCCCTTT
*
16394628 TTTTCTCTCTATTTTTTTGGC
1 TTTTCTCTCTATTTTCTTGGC
*
16394649 TTTTCTTCTCTCTTTTCTTGG
1 TTTTC-TCTCTATTTTCTTGG
16394670 TTTACGACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.02, C:0.21, G:0.10, T:0.67
Consensus pattern (21 bp):
TTTTCTCTCTATTTTCTTGGC
Found at i:16399407 original size:21 final size:21
Alignment explanation
Indices: 16399376--16399417 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
16399366 TCTCTTTTCT
16399376 CTTTTTTCTCTATTTT-TTGG
1 CTTTTTTCTCTATTTTCTTGG
*
16399396 CTTTTCTTCTCTCTTTTCTTGG
1 CTTTT-TTCTCTATTTTCTTGG
16399418 TCTGCGACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 10 0.53
22 4 0.21
ACGTcount: A:0.02, C:0.21, G:0.10, T:0.67
Consensus pattern (21 bp):
CTTTTTTCTCTATTTTCTTGG
Found at i:16401462 original size:4 final size:4
Alignment explanation
Indices: 16401453--16401505 Score: 58
Period size: 4 Copynumber: 13.8 Consensus size: 4
16401443 CACAATTGCA
* *
16401453 TTTG TTTG TTTG -TT- TTTG TTTG TTTG TTT- TTTGG TTTT TTTG TTTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT-G TTTG TTTG TTTG
16401499 TTTG TTT
1 TTTG TTT
16401506 TGTTCTATTG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
3 7 0.17
4 31 0.76
5 3 0.07
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (4 bp):
TTTG
Found at i:16401493 original size:9 final size:8
Alignment explanation
Indices: 16401453--16401506 Score: 67
Period size: 8 Copynumber: 7.0 Consensus size: 8
16401443 CACAATTGCA
*
16401453 TTTGTTTG
1 TTTGTTTT
16401461 TTTG--TT
1 TTTGTTTT
*
16401467 TTTGTTTG
1 TTTGTTTT
16401475 TTTGTTTT
1 TTTGTTTT
*
16401483 TTGGTTTT
1 TTTGTTTT
16401491 TTTGTTTT
1 TTTGTTTT
16401499 TTTGTTTT
1 TTTGTTTT
16401507 GTTCTATTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
6 5 0.13
8 34 0.87
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (8 bp):
TTTGTTTT
Found at i:16401506 original size:14 final size:14
Alignment explanation
Indices: 16401453--16401499 Score: 67
Period size: 14 Copynumber: 3.2 Consensus size: 14
16401443 CACAATTGCA
16401453 TTTGTTTGTTTGTT
1 TTTGTTTGTTTGTT
16401467 TTTGTTTGTTTGTTT
1 TTTGTTTGTTTG-TT
*
16401482 TTTGGTTTTTTTGTT
1 TTT-GTTTGTTTGTT
16401497 TTT
1 TTT
16401500 TTGTTTTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 12 0.40
15 10 0.33
16 8 0.27
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (14 bp):
TTTGTTTGTTTGTT
Found at i:16402708 original size:16 final size:16
Alignment explanation
Indices: 16402687--16402735 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
16402677 TTTTTATTTA
16402687 TATATATATATATATT
1 TATATATATATATATT
16402703 TATATA-ATTATATATT
1 TATATATA-TATATATT
* *
16402719 TAAATATTTATAT-TT
1 TATATATATATATATT
16402734 TA
1 TA
16402736 AAAAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 5 0.17
16 24 0.83
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATATATATATATT
Found at i:16402750 original size:22 final size:21
Alignment explanation
Indices: 16402721--16402772 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
16402711 TATATATTTA
16402721 AATA-TTTATATTTTAAAAAAT
1 AATATTTTATA-TTTAAAAAAT
16402742 AATATTTTATATTTAAAAAAT
1 AATATTTTATATTTAAAAAAT
16402763 AATATTTTAT
1 AATATTTTAT
16402773 TAATTTCGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 24 0.80
22 6 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATTTTATATTTAAAAAAT
Found at i:16404233 original size:2 final size:2
Alignment explanation
Indices: 16404228--16404261 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
16404218 ATAGAAAAAA
*
16404228 AT AT AT CT 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
16404262 TACATTCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16413301 original size:16 final size:17
Alignment explanation
Indices: 16413280--16413316 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
16413270 AATGATTTTA
16413280 AATTAAATAAG-AAAA-T
1 AATTAAA-AAGTAAAACT
16413296 AATTAAAAAGTAAAACT
1 AATTAAAAAGTAAAACT
16413313 AATT
1 AATT
16413317 TGAACAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.16
16 11 0.58
17 5 0.26
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (17 bp):
AATTAAAAAGTAAAACT
Found at i:16415867 original size:37 final size:37
Alignment explanation
Indices: 16415816--16415891 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
16415806 TATTCCTTAA
*
16415816 CATAGAATCATTGTTATTTCCATATCCAGCTAAAGAC
1 CATAGAATCATTGTTATTTCCATACCCAGCTAAAGAC
*
16415853 CATAGAATCGTTGTTATTTCCATACCCAGCTAAAGAC
1 CATAGAATCATTGTTATTTCCATACCCAGCTAAAGAC
16415890 CA
1 CA
16415892 CAACCCCTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (37 bp):
CATAGAATCATTGTTATTTCCATACCCAGCTAAAGAC
Found at i:16417208 original size:27 final size:27
Alignment explanation
Indices: 16417173--16417224 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
16417163 TACATTTTTT
**
16417173 AGAAATATTATGATTTCTCAAAAATAG
1 AGAAATATTACAATTTCTCAAAAATAG
*
16417200 AGAAATATTACAATTTTTCAAAAAT
1 AGAAATATTACAATTTCTCAAAAAT
16417225 TCATTTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (27 bp):
AGAAATATTACAATTTCTCAAAAATAG
Done.