Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 123 of 163
Found at i:39591740 original size:18 final size:19
Alignment explanation
Indices: 39591719--39591759 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
39591709 AGATTATTAA
*
39591719 AATAATTAA-AATTAAAAT
1 AATAATTAATAAATAAAAT
*
39591737 AATAATTAATAAATAAACT
1 AATAATTAATAAATAAAAT
39591756 AATA
1 AATA
39591760 TTTGCATAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAATTAATAAATAAAAT
Found at i:39592754 original size:73 final size:73
Alignment explanation
Indices: 39592635--39592785 Score: 293
Period size: 73 Copynumber: 2.1 Consensus size: 73
39592625 TGAAAATTAA
39592635 CTCTTGCCGTTCAAACCAAAATTGCTTCTCTTTCATGGTATCAGATTTAGCCATCTTTTAGGATT
1 CTCTTGCCGTTCAAACCAAAATTGCTTCTCTTTCATGGTATCAGATTTAGCCATCTTTTAGGATT
39592700 CAACGCCG
66 CAACGCCG
*
39592708 CTCTTGCTGTTCAAACCAAAATTGCTTCTCTTTCATGGTATCAGATTTAGCCATCTTTTAGGATT
1 CTCTTGCCGTTCAAACCAAAATTGCTTCTCTTTCATGGTATCAGATTTAGCCATCTTTTAGGATT
39592773 CAACGCCG
66 CAACGCCG
39592781 CTCTT
1 CTCTT
39592786 TTTTTTTTCC
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.37
Consensus pattern (73 bp):
CTCTTGCCGTTCAAACCAAAATTGCTTCTCTTTCATGGTATCAGATTTAGCCATCTTTTAGGATT
CAACGCCG
Found at i:39597953 original size:115 final size:116
Alignment explanation
Indices: 39597749--39597981 Score: 432
Period size: 115 Copynumber: 2.0 Consensus size: 116
39597739 TTTGGTTCCG
39597749 TCCAGCTTTTTAAATTTTTGGAATAGTTGATTATAAGTCGGTTTTAGCTCGATTAGATTTTCGCT
1 TCCAGCTTTTT-AATTTTTGGAATAGTTGATTATAAGTCGGTTTTAGCTCGATTAGATTTTCGCT
39597814 TTTTTTTTATAATAATTTTTATTTTTTTAAATTTATTTTGATAAAATATATT
65 TTTTTTTTATAATAATTTTTATTTTTTTAAATTTATTTTGATAAAATATATT
39597866 TCCAGCTTTTT-ATTTTTGGAATAGTTGATTATAAGTCGGTTTTAGCTCGATTAGATTTTCGCTT
1 TCCAGCTTTTTAATTTTTGGAATAGTTGATTATAAGTCGGTTTTAGCTCGATTAGATTTTCGCTT
**
39597930 TTTTTTTATAATAATTTTTATTTTTTTTTATTTATTTTGATAAAATATATT
66 TTTTTTTATAATAATTTTTATTTTTTTAAATTTATTTTGATAAAATATATT
39597981 T
1 T
39597982 TGTTTTATAG
Statistics
Matches: 114, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
115 103 0.90
117 11 0.10
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (116 bp):
TCCAGCTTTTTAATTTTTGGAATAGTTGATTATAAGTCGGTTTTAGCTCGATTAGATTTTCGCTT
TTTTTTTATAATAATTTTTATTTTTTTAAATTTATTTTGATAAAATATATT
Found at i:39600707 original size:225 final size:225
Alignment explanation
Indices: 39600316--39600767 Score: 904
Period size: 225 Copynumber: 2.0 Consensus size: 225
39600306 NNNNNNNGTA
39600316 ATCACGAATTTTATACATACATTTTATAAGTCGTCCCTACAAATAATAATGAAACATATATTCAA
1 ATCACGAATTTTATACATACATTTTATAAGTCGTCCCTACAAATAATAATGAAACATATATTCAA
39600381 AAATCAAAAGCAAATATTTTAAACCAAAATATACATTGAATGGATGCTTACACAAATTCAACCAT
66 AAATCAAAAGCAAATATTTTAAACCAAAATATACATTGAATGGATGCTTACACAAATTCAACCAT
39600446 AATCAAACCTTCTGTATTCATGATTTCAAGATCAGTTTTCTTCCCCCAAAGAAATTTCACGTTAA
131 AATCAAACCTTCTGTATTCATGATTTCAAGATCAGTTTTCTTCCCCCAAAGAAATTTCACGTTAA
39600511 TTCTGTGAAATATATTATTCTCCTATTATT
196 TTCTGTGAAATATATTATTCTCCTATTATT
39600541 ATCACGAATTTTATACATACATTTTATAAGTCGTCCCTACAAATAATAATGAAACATATATTCAA
1 ATCACGAATTTTATACATACATTTTATAAGTCGTCCCTACAAATAATAATGAAACATATATTCAA
39600606 AAATCAAAAGCAAATATTTTAAACCAAAATATACATTGAATGGATGCTTACACAAATTCAACCAT
66 AAATCAAAAGCAAATATTTTAAACCAAAATATACATTGAATGGATGCTTACACAAATTCAACCAT
39600671 AATCAAACCTTCTGTATTCATGATTTCAAGATCAGTTTTCTTCCCCCAAAGAAATTTCACGTTAA
131 AATCAAACCTTCTGTATTCATGATTTCAAGATCAGTTTTCTTCCCCCAAAGAAATTTCACGTTAA
39600736 TTCTGTGAAATATATTATTCTCCTATTATT
196 TTCTGTGAAATATATTATTCTCCTATTATT
39600766 AT
1 AT
39600768 AATTATTAAA
Statistics
Matches: 227, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
225 227 1.00
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.35
Consensus pattern (225 bp):
ATCACGAATTTTATACATACATTTTATAAGTCGTCCCTACAAATAATAATGAAACATATATTCAA
AAATCAAAAGCAAATATTTTAAACCAAAATATACATTGAATGGATGCTTACACAAATTCAACCAT
AATCAAACCTTCTGTATTCATGATTTCAAGATCAGTTTTCTTCCCCCAAAGAAATTTCACGTTAA
TTCTGTGAAATATATTATTCTCCTATTATT
Found at i:39604387 original size:25 final size:25
Alignment explanation
Indices: 39604297--39604390 Score: 77
Period size: 25 Copynumber: 3.7 Consensus size: 25
39604287 CAACCCTAGT
* *
39604297 TTTTTCTCT-TTTCTTTCTCTTTTTC
1 TTTTTCTTTGTTTCTTT-TCTATTTC
* * *
39604322 -TATTCTTTCTTTCCTTATCTATTT-
1 TTTTTCTTTGTTT-CTTTTCTATTTC
39604346 TGTTTCTACTTTGTTTCTTTTCTATTTC
1 T-TTT-T-CTTTGTTTCTTTTCTATTTC
39604374 TTTTTCTTTGTTTCTTT
1 TTTTTCTTTGTTTCTTT
39604391 ATTTTATTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
24 6 0.11
25 21 0.38
26 6 0.11
27 14 0.25
28 8 0.15
ACGTcount: A:0.05, C:0.19, G:0.03, T:0.72
Consensus pattern (25 bp):
TTTTTCTTTGTTTCTTTTCTATTTC
Found at i:39607120 original size:19 final size:20
Alignment explanation
Indices: 39607098--39607136 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
39607088 ATTTTAATTA
*
39607098 ACTTGATT-AATTTAATTTT
1 ACTTGATTAAAATTAATTTT
39607117 ACTTGATTAAAATTAATTTT
1 ACTTGATTAAAATTAATTTT
39607137 CCCAAAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ACTTGATTAAAATTAATTTT
Found at i:39607657 original size:316 final size:316
Alignment explanation
Indices: 39607084--39607719 Score: 1191
Period size: 316 Copynumber: 2.0 Consensus size: 316
39607074 AAAACATCAT
*
39607084 ATTTATTTTAATTAACTTGATTAATTTAATTTTACTTGATTAAAATTAATTTTCCCAAAAATCAC
1 ATTTATTTTAATTAACTTGATTAATTTAATTTTACTTGATCAAAATTAATTTTCCCAAAAATCAC
*
39607149 TTAGATTTTCCAAATGAATTTTTCAAGAAAATTCTTGAATCAAATTCTCTAGTTGAACAATTCTC
66 TTAGATTTTCCAAATGAATTTTTCAAGAAAATTCTTAAATCAAATTCTCTAGTTGAACAATTCTC
* *
39607214 ACGACTGCCTAATTTAATTCCACATCGAATAAATCGACTCAATTAAATTATTTACAAAGTTATAG
131 ACGACTGCCTAATTTAATTCCACATCGAATAAATCGACTCAATTAAATTATTTACAAAGTCAAAG
* *
39607279 AATTTTCTTTTAATCCAAATGTAATCCGATTGAGTTTTTGTTGAGCTAGCGGAGAGACCAATCAA
196 AATTTTCTTCTAATCCAAATGTAATCCGATTGAGTTTTTGTTGAGCTAGCGAAGAGACCAATCAA
* *
39607344 ATATATAGAATTAGACTCGAGTAATTGCAATTATGTCCAGAAGGATCAGTCTGATA
261 ATATATAGAATTAGACTCGACTAATTGCAATTATGTCCAAAAGGATCAGTCTGATA
39607400 ATTTATTTTAATTAACTTGATTAATTTAATTTTACTTGATCAAAATTAATTTTCCCAAAAATCAC
1 ATTTATTTTAATTAACTTGATTAATTTAATTTTACTTGATCAAAATTAATTTTCCCAAAAATCAC
39607465 TTAGATTTTCCAAATGAATTTTTCAAGAAAATTCTTAAATCAAATTCTCTAGTTGAACAATTCTC
66 TTAGATTTTCCAAATGAATTTTTCAAGAAAATTCTTAAATCAAATTCTCTAGTTGAACAATTCTC
39607530 ACGACTGCCTAATTTAATTCCACATCGAATAAATCGACTCAATTAAATTATTTACAAAGTCAAAG
131 ACGACTGCCTAATTTAATTCCACATCGAATAAATCGACTCAATTAAATTATTTACAAAGTCAAAG
*
39607595 AATTTTCTTCTAATCCAAATGTAATCCGATTGAGTTTTTGTTGAGCTAGCGAAGGGACCAATCAA
196 AATTTTCTTCTAATCCAAATGTAATCCGATTGAGTTTTTGTTGAGCTAGCGAAGAGACCAATCAA
39607660 ATATATAGAATTAGACTCGACTAATTGCAATTATGTCCAAAAGGATCAGTCTGATA
261 ATATATAGAATTAGACTCGACTAATTGCAATTATGTCCAAAAGGATCAGTCTGATA
39607716 ATTT
1 ATTT
39607720 GCAATTTACT
Statistics
Matches: 311, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
316 311 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (316 bp):
ATTTATTTTAATTAACTTGATTAATTTAATTTTACTTGATCAAAATTAATTTTCCCAAAAATCAC
TTAGATTTTCCAAATGAATTTTTCAAGAAAATTCTTAAATCAAATTCTCTAGTTGAACAATTCTC
ACGACTGCCTAATTTAATTCCACATCGAATAAATCGACTCAATTAAATTATTTACAAAGTCAAAG
AATTTTCTTCTAATCCAAATGTAATCCGATTGAGTTTTTGTTGAGCTAGCGAAGAGACCAATCAA
ATATATAGAATTAGACTCGACTAATTGCAATTATGTCCAAAAGGATCAGTCTGATA
Found at i:39609648 original size:40 final size:41
Alignment explanation
Indices: 39609593--39609671 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 41
39609583 GGATTAATTC
* *
39609593 AAATATTGGTTAATAATAAAGATTATTGAAA-AATATTATT
1 AAATATTGATTAATAATAAAAATTATTGAAATAATATTATT
*
39609633 AAATATTTATTAATAATAAAAATTATTGAAATAATATTA
1 AAATATTGATTAATAATAAAAATTATTGAAATAATATTA
39609672 AAATATGTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 28 0.80
41 7 0.20
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (41 bp):
AAATATTGATTAATAATAAAAATTATTGAAATAATATTATT
Found at i:39609670 original size:27 final size:27
Alignment explanation
Indices: 39609622--39609676 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
39609612 AGATTATTGA
*
39609622 AAAATATTATTAAATATTTATTAATAAT
1 AAAATATTATTAAATATATATTAA-AAT
39609650 AAAA-ATTATTGAAATA-ATATTAAAAT
1 AAAATATTATT-AAATATATATTAAAAT
39609676 A
1 A
39609677 TGTTAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 4 0.16
27 12 0.48
28 9 0.36
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
AAAATATTATTAAATATATATTAAAAT
Found at i:39620722 original size:21 final size:21
Alignment explanation
Indices: 39620696--39620737 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
39620686 ATTTTCCCTT
39620696 TCTCCTTTCTCTTCTAAGCAA
1 TCTCCTTTCTCTTCTAAGCAA
39620717 TCTCCTTTCTCTTCTAAGCAA
1 TCTCCTTTCTCTTCTAAGCAA
39620738 ATTTTCTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.05, T:0.43
Consensus pattern (21 bp):
TCTCCTTTCTCTTCTAAGCAA
Found at i:39622836 original size:18 final size:18
Alignment explanation
Indices: 39622813--39622848 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39622803 CAATTAAACC
39622813 ATTTGATTGATATATTTA
1 ATTTGATTGATATATTTA
* *
39622831 ATTTGATTTATTTATTTA
1 ATTTGATTGATATATTTA
39622849 TAAATAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (18 bp):
ATTTGATTGATATATTTA
Found at i:39622911 original size:20 final size:20
Alignment explanation
Indices: 39622888--39622926 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39622878 CAATTTAAAA
39622888 TATAAAAAATTATTAATATG
1 TATAAAAAATTATTAATATG
* **
39622908 TATATAATTTTATTAATAT
1 TATAAAAAATTATTAATAT
39622927 ATGTAAAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAAATTATTAATATG
Found at i:39623055 original size:14 final size:14
Alignment explanation
Indices: 39623025--39623067 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
39623015 TATTTTTAGT
**
39623025 AAATCATTTTCCAG
1 AAATCATTTTCTGG
39623039 AAATCATTTTCTGG
1 AAATCATTTTCTGG
*
39623053 AAAACATTTTACTGG
1 AAATCATTTT-CTGG
39623068 CAAACAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (14 bp):
AAATCATTTTCTGG
Found at i:39632432 original size:13 final size:13
Alignment explanation
Indices: 39632399--39632432 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
39632389 AATTCTAATG
39632399 TCGATTTTCTTCT
1 TCGATTTTCTTCT
39632412 TC-AGTTTTCTTCT
1 TCGA-TTTTCTTCT
39632425 TCGATTTT
1 TCGATTTT
39632433 TCACCGCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.05
13 17 0.89
14 1 0.05
ACGTcount: A:0.09, C:0.21, G:0.09, T:0.62
Consensus pattern (13 bp):
TCGATTTTCTTCT
Found at i:39633521 original size:17 final size:18
Alignment explanation
Indices: 39633499--39633533 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39633489 ATCTGGGCCA
39633499 TGTGGG-CGACACGGGCG
1 TGTGGGCCGACACGGGCG
*
39633516 TGTGGGCCTACACGGGCG
1 TGTGGGCCGACACGGGCG
39633534 AACATCATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.11, C:0.26, G:0.49, T:0.14
Consensus pattern (18 bp):
TGTGGGCCGACACGGGCG
Found at i:39634734 original size:25 final size:25
Alignment explanation
Indices: 39634701--39634750 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
39634691 GATCAAAAAG
39634701 GGGTTGCTAAGTGCAGATTCCCCGA
1 GGGTTGCTAAGTGCAGATTCCCCGA
*
39634726 GGGTTGCTAAGTGCTGATTCCCCGA
1 GGGTTGCTAAGTGCAGATTCCCCGA
39634751 ATTATTGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.18, C:0.24, G:0.32, T:0.26
Consensus pattern (25 bp):
GGGTTGCTAAGTGCAGATTCCCCGA
Found at i:39634774 original size:42 final size:41
Alignment explanation
Indices: 39634727--39634876 Score: 165
Period size: 42 Copynumber: 3.6 Consensus size: 41
39634717 ATTCCCCGAG
39634727 GGTTGCTAAGTGCTGATTCCCCGAATTATTGATTCTAAATGT
1 GGTTGCTAAGTGCTGATTCCCCGAATTATTGATTCTAAA-GT
* * *
39634769 GGTTGCTAAGTGTTGATTCCCCCAATTATTGATTCTAAGGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATTATTGATTCTAA-AGT
* * * ** * *
39634811 GGTTTCTAAGTGTTGATTCCACCGTATCCTTGATTGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGAATTATTGATTCT-AAAGT
*
39634854 GGTTGCTATGTGCTGATTCCCCG
1 GGTTGCTAAGTGCTGATTCCCCG
39634877 TATCACTGAA
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
42 60 0.66
43 29 0.32
44 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCCCGAATTATTGATTCTAAAGT
Found at i:39637528 original size:18 final size:19
Alignment explanation
Indices: 39637483--39637531 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
39637473 AAATAAAACG
*
39637483 TTTTGAAATTGAATAATGA
1 TTTTGAAAATGAATAATGA
39637502 TTTCT--AAATGAATAAT-A
1 TTT-TGAAAATGAATAATGA
39637519 TTTTGAAAATGAA
1 TTTTGAAAATGAA
39637532 CGACATGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 1 0.04
17 4 0.15
18 17 0.65
19 3 0.12
20 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (19 bp):
TTTTGAAAATGAATAATGA
Found at i:39643090 original size:19 final size:19
Alignment explanation
Indices: 39643054--39643092 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
39643044 GTATGAGATC
*
39643054 AACATCCAAACAAGAAATG
1 AACATCCAAACAACAAATG
* *
39643073 AACATCCAAGCATCAAATG
1 AACATCCAAACAACAAATG
39643092 A
1 A
39643093 TGTGAAGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.23, G:0.10, T:0.13
Consensus pattern (19 bp):
AACATCCAAACAACAAATG
Found at i:39644764 original size:21 final size:22
Alignment explanation
Indices: 39644728--39644769 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
39644718 ATTGATTGCT
*
39644728 ACGCTTTTGAAATGTTTAGATC
1 ACGCTTTTGAAATGTTAAGATC
39644750 ACGCTTTTG-AATGTTAAGAT
1 ACGCTTTTGAAATGTTAAGAT
39644770 GTTTATGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (22 bp):
ACGCTTTTGAAATGTTAAGATC
Found at i:39647376 original size:25 final size:25
Alignment explanation
Indices: 39647346--39647415 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
39647336 GTTACCGGTT
*
39647346 TCAGCTCGTATGAGCTTACCGATAC
1 TCAGCTCGAATGAGCTTACCGATAC
* * *
39647371 TCAGCT-TACATGAGCTTACCGTTAT
1 TCAGCTCGA-ATGAGCTTACCGATAC
* *
39647396 TTAGCTCGAAGGAGCTTACC
1 TCAGCTCGAATGAGCTTACC
39647416 ATTTACAGCT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
25 35 0.97
26 1 0.03
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (25 bp):
TCAGCTCGAATGAGCTTACCGATAC
Found at i:39661391 original size:127 final size:127
Alignment explanation
Indices: 39661221--39661472 Score: 486
Period size: 127 Copynumber: 2.0 Consensus size: 127
39661211 TATTTAAAAC
39661221 GACACAATCCAATGTTGAAAATTAACTTCTCAAATGTAACAATAGGGAGCGCCTTAGTAAAAAGA
1 GACACAATCCAATGTTGAAAATTAACTTCTCAAATGTAACAATAGGGAGCGCCTTAGTAAAAAGA
39661286 TCTGTCAAATTCTCACTTGAACGAATTTGTTGAACATTTATATCTCTATTCTTTTGTAGAAT
66 TCTGTCAAATTCTCACTTGAACGAATTTGTTGAACATTTATATCTCTATTCTTTTGTAGAAT
* *
39661348 GACACAATCCAATGTTGAAAATTAACTTCTCAAATGTAGCAATAGTGAGCGCCTTAGTAAAAAGA
1 GACACAATCCAATGTTGAAAATTAACTTCTCAAATGTAACAATAGGGAGCGCCTTAGTAAAAAGA
39661413 TCTGTCAAATTCTCACTTGAACGAATTTGTTGAACATTTATATCTCTATTCTTTTGTAGA
66 TCTGTCAAATTCTCACTTGAACGAATTTGTTGAACATTTATATCTCTATTCTTTTGTAGA
39661473 TCACGAGTGA
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 123 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (127 bp):
GACACAATCCAATGTTGAAAATTAACTTCTCAAATGTAACAATAGGGAGCGCCTTAGTAAAAAGA
TCTGTCAAATTCTCACTTGAACGAATTTGTTGAACATTTATATCTCTATTCTTTTGTAGAAT
Found at i:39664658 original size:24 final size:24
Alignment explanation
Indices: 39664626--39664683 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
39664616 GTGTTTTGCA
39664626 ATTGAAATTGATTG-ATTTAGTATGTG
1 ATTG-AATTGATTGAATTTA-TAT-TG
*
39664652 A-TGAATTTATTGAATTTATATTG
1 ATTGAATTGATTGAATTTATATTG
39664675 ATTGAATTG
1 ATTGAATTG
39664684 GTATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 3 0.11
24 17 0.61
25 7 0.25
26 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (24 bp):
ATTGAATTGATTGAATTTATATTG
Found at i:39667394 original size:45 final size:45
Alignment explanation
Indices: 39667330--39667463 Score: 198
Period size: 45 Copynumber: 3.0 Consensus size: 45
39667320 TACGTGTACC
39667330 GGGTACCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACT
1 GGGTACCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACT
* *
39667375 GGGTATCATTGATTATAAAGGCGGTTGTTGTGTGCTGATTCCA-T
1 GGGTACCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACT
* * * *
39667419 CGGGTACCATTGATTATGAAGGTGGTTGCTATGTGCTAATTCCAC
1 -GGGTACCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCAC
39667464 CTAGTATCAT
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
44 1 0.01
45 78 0.99
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.37
Consensus pattern (45 bp):
GGGTACCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACT
Found at i:39667475 original size:45 final size:44
Alignment explanation
Indices: 39667331--39667482 Score: 187
Period size: 45 Copynumber: 3.4 Consensus size: 44
39667321 ACGTGTACCG
*
39667331 GGTACCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACT
1 GGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACT
* *
39667375 GGGTATCATTGATTATAAAGGCGGTTGTTGTGTGCTGATTCCATCG
1 -GGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCA-CT
* * * * *
39667421 GGTACCATTGATTATGAAGGTGGTTGCTATGTGCTAATTCCACCT
1 GGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCA-CT
* *
39667466 AGTATCATTGACTATAA
1 GGTATCATTGATTATAA
39667483 GTGTAATAGC
Statistics
Matches: 91, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
45 90 0.99
46 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (44 bp):
GGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACT
Found at i:39674375 original size:24 final size:23
Alignment explanation
Indices: 39674331--39674375 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
39674321 TTAAAGGTTA
** *
39674331 AAGAAGATGAAAGGTGGAAGGGC
1 AAGAAGATGAAAGACGAAAGGGC
39674354 AAGAGAGATGAAAGACGAAAGG
1 AAGA-AGATGAAAGACGAAAGG
39674376 TCCATTAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.49, C:0.04, G:0.40, T:0.07
Consensus pattern (23 bp):
AAGAAGATGAAAGACGAAAGGGC
Found at i:39678487 original size:54 final size:54
Alignment explanation
Indices: 39678405--39678515 Score: 222
Period size: 54 Copynumber: 2.1 Consensus size: 54
39678395 ACAAACTCTC
39678405 ATTGAAACAGACAATTCATTAATATTAACATTCATGCATAAAGATTCGTTTATT
1 ATTGAAACAGACAATTCATTAATATTAACATTCATGCATAAAGATTCGTTTATT
39678459 ATTGAAACAGACAATTCATTAATATTAACATTCATGCATAAAGATTCGTTTATT
1 ATTGAAACAGACAATTCATTAATATTAACATTCATGCATAAAGATTCGTTTATT
39678513 ATT
1 ATT
39678516 ATTATTATTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.38
Consensus pattern (54 bp):
ATTGAAACAGACAATTCATTAATATTAACATTCATGCATAAAGATTCGTTTATT
Found at i:39678516 original size:3 final size:3
Alignment explanation
Indices: 39678508--39678535 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
39678498 AAAGATTCGT
39678508 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
39678536 GGTACAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39684195 original size:25 final size:25
Alignment explanation
Indices: 39684117--39684367 Score: 122
Period size: 25 Copynumber: 10.2 Consensus size: 25
39684107 ACACACCATA
* *
39684117 GCTCTTATGAGCGTCCCAATACT-TG
1 GCTCTTATGAGCTTCCCGATA-TATG
* * * * * *
39684142 GCTCTCACGAGCTTTCCGTTATTTA
1 GCTCTTATGAGCTTCCCGATATATG
*
39684167 GCTCTTATGAGCATCCCGATATATG
1 GCTCTTATGAGCTTCCCGATATATG
**
39684192 GCTCACATGAGCTTCCCGAT-TAATG
1 GCTCTTATGAGCTTCCCGATAT-ATG
*
39684217 GCTCTT-CGAAGCTTCCCGATAT-TG
1 GCTCTTATG-AGCTTCCCGATATATG
* ** * * *
39684241 ACTCGCATAAGCTTCTCGA-ATTTG
1 GCTCTTATGAGCTTCCCGATATATG
* * * *
39684265 GTTCCCT-TGAGCTGCCCG-TTTATG
1 GCT-CTTATGAGCTTCCCGATATATG
*
39684289 GCTCGTATGAGCTTCCCGATA-ATTG
1 GCTCTTATGAGCTTCCCGATATA-TG
** * * *
39684314 GCTCGCAAGAGCTTCCCGTTACATG
1 GCTCTTATGAGCTTCCCGATATATG
** *
39684339 GCTCACATGAGCTTCCCGTTATATG
1 GCTCTTATGAGCTTCCCGATATATG
39684364 GCTC
1 GCTC
39684368 GAAAGAGCTT
Statistics
Matches: 169, Mismatches: 45, Indels: 24
0.71 0.19 0.10
Matches are distributed among these distances:
23 4 0.02
24 44 0.26
25 119 0.70
26 2 0.01
ACGTcount: A:0.19, C:0.28, G:0.21, T:0.32
Consensus pattern (25 bp):
GCTCTTATGAGCTTCCCGATATATG
Found at i:39684221 original size:50 final size:50
Alignment explanation
Indices: 39684117--39684367 Score: 153
Period size: 50 Copynumber: 5.1 Consensus size: 50
39684107 ACACACCATA
* * * * * * *
39684117 GCTCTTATGAGCGTCCCAATACT-TGGCTCTCACGAGCTTTCCG-TTATTTA
1 GCTCTTATGAGCTTCCCGATA-TATGGCTCACATGAGCTTCCCGATTA-ATG
*
39684167 GCTCTTATGAGCATCCCGATATATGGCTCACATGAGCTTCCCGATTAATG
1 GCTCTTATGAGCTTCCCGATATATGGCTCACATGAGCTTCCCGATTAATG
* * * * *
39684217 GCTCTT-CGAAGCTTCCCGATAT-TGACTCGCATAAGCTTCTCGAATT--TG
1 GCTCTTATG-AGCTTCCCGATATATGGCTCACATGAGCTTCCCG-ATTAATG
* * * * **
39684265 GTTCCCT-TGAGCTGCCCG-TTTATGGCTCGTATGAGCTTCCCGA-TAATTG
1 GCT-CTTATGAGCTTCCCGATATATGGCTCACATGAGCTTCCCGATTAA-TG
** * * *
39684314 GCTCGCAAGAGCTTCCCGTTACATGGCTCACATGAGCTTCCCG-TTATATG
1 GCTCTTATGAGCTTCCCGATATATGGCTCACATGAGCTTCCCGATTA-ATG
39684364 GCTC
1 GCTC
39684368 GAAAGAGCTT
Statistics
Matches: 157, Mismatches: 31, Indels: 26
0.73 0.14 0.12
Matches are distributed among these distances:
46 1 0.01
47 3 0.02
48 29 0.18
49 34 0.22
50 86 0.55
51 4 0.03
ACGTcount: A:0.19, C:0.28, G:0.21, T:0.32
Consensus pattern (50 bp):
GCTCTTATGAGCTTCCCGATATATGGCTCACATGAGCTTCCCGATTAATG
Found at i:39684368 original size:50 final size:50
Alignment explanation
Indices: 39684273--39684389 Score: 139
Period size: 50 Copynumber: 2.3 Consensus size: 50
39684263 TGGTTCCCTT
* * ** *
39684273 GAGCTGCCCGTT-TATGGCTCGTATGAGCTTCCCGATAATTGGCTCGCAA
1 GAGCTTCCCGTTACATGGCTCACATGAGCTTCCCGATAATTGGCTCGAAA
*
39684322 GAGCTTCCCGTTACATGGCTCACATGAGCTTCCCG-TTATATGGCTCGAAA
1 GAGCTTCCCGTTACATGGCTCACATGAGCTTCCCGATAAT-TGGCTCGAAA
*
39684372 GAGCTTCCTGATTACATG
1 GAGCTTCCCG-TTACATG
39684390 CTCGCACGGG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
49 14 0.24
50 37 0.64
51 7 0.12
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (50 bp):
GAGCTTCCCGTTACATGGCTCACATGAGCTTCCCGATAATTGGCTCGAAA
Found at i:39684375 original size:25 final size:25
Alignment explanation
Indices: 39684273--39684379 Score: 112
Period size: 25 Copynumber: 4.3 Consensus size: 25
39684263 TGGTTCCCTT
* * *
39684273 GAGCTGCCCGTT-TATGGCTCGTAT
1 GAGCTTCCCGTTATATGGCTCGAAA
* *
39684297 GAGCTTCCCGATA-ATTGGCTCGCAA
1 GAGCTTCCCGTTATA-TGGCTCGAAA
* *
39684322 GAGCTTCCCGTTACATGGCTC-ACAT
1 GAGCTTCCCGTTATATGGCTCGA-AA
39684347 GAGCTTCCCGTTATATGGCTCGAAA
1 GAGCTTCCCGTTATATGGCTCGAAA
39684372 GAGCTTCC
1 GAGCTTCC
39684380 TGATTACATG
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
24 11 0.16
25 56 0.81
26 2 0.03
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCGAAA
Found at i:39684392 original size:25 final size:25
Alignment explanation
Indices: 39684273--39684393 Score: 106
Period size: 25 Copynumber: 4.9 Consensus size: 25
39684263 TGGTTCCCTT
* * * *
39684273 GAGCTGCCCGTT-TATGGCTCGTAT
1 GAGCTTCCCGTTACATGGCTCGAAA
* *
39684297 GAGCTTCCCGATA-ATTGGCTCGCAA
1 GAGCTTCCCGTTACA-TGGCTCGAAA
*
39684322 GAGCTTCCCGTTACATGGCTC-ACAT
1 GAGCTTCCCGTTACATGGCTCGA-AA
*
39684347 GAGCTTCCCGTTATATGGCTCGAAA
1 GAGCTTCCCGTTACATGGCTCGAAA
*
39684372 GAGCTTCCTGATTACAT-GCTCG
1 GAGCTTCCCG-TTACATGGCTCG
39684394 CACGGGCATA
Statistics
Matches: 80, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
24 11 0.14
25 62 0.77
26 7 0.09
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (25 bp):
GAGCTTCCCGTTACATGGCTCGAAA
Found at i:39708639 original size:22 final size:21
Alignment explanation
Indices: 39708608--39708652 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
39708598 TTTAAAAAGT
39708608 AAGTTGAAGTC-AAATAGATTA
1 AAGTTGAAGTCAAAATA-ATTA
39708629 AAGTATGAAGTCAAAATAATTA
1 AAGT-TGAAGTCAAAATAATTA
39708651 AA
1 AA
39708653 TGGATATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.18
22 13 0.59
23 5 0.23
ACGTcount: A:0.53, C:0.04, G:0.16, T:0.27
Consensus pattern (21 bp):
AAGTTGAAGTCAAAATAATTA
Found at i:39715716 original size:29 final size:29
Alignment explanation
Indices: 39715662--39715719 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
39715652 TGAAAATTTC
*
39715662 TTTTTAAATACATTTAAACCATTTTTAAA
1 TTTTTAAATACATTTAAACAATTTTTAAA
39715691 TTTTTAAATA-ATTATAAA-AATATTTTAAA
1 TTTTTAAATACATT-TAAACAAT-TTTTAAA
39715720 ATTTACTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTTTAAATACATTTAAACAATTTTTAAA
Found at i:39719754 original size:28 final size:28
Alignment explanation
Indices: 39719723--39719777 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
39719713 ATAATTTTTT
39719723 TATAAAAAT-TATTAAATTTTAATAAAAA
1 TATAAAAATAT-TTAAATTTTAATAAAAA
*
39719751 TATAAAAATATTTAAATTTTATTAAAA
1 TATAAAAATATTTAAATTTTAATAAAA
39719778 GTTAGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TATAAAAATATTTAAATTTTAATAAAAA
Found at i:39719825 original size:30 final size:30
Alignment explanation
Indices: 39719789--39719846 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39719779 TTAGAAAAAA
* * *
39719789 TATAAAAATCTTTAAAAATTTATAAAATTT
1 TATAAAAATCATAAAAAAATTATAAAATTT
*
39719819 TATAAAAATCATAAAAAAATTATGAAAT
1 TATAAAAATCATAAAAAAATTATAAAAT
39719847 CCAGAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (30 bp):
TATAAAAATCATAAAAAAATTATAAAATTT
Found at i:39719826 original size:38 final size:38
Alignment explanation
Indices: 39719725--39719835 Score: 120
Period size: 38 Copynumber: 2.9 Consensus size: 38
39719715 AATTTTTTTA
*
39719725 TAAAAA-TTATTAAATTTTAATAAAAATATAAAAATATT
1 TAAAAATTTATAAAATTTT-ATAAAAATATAAAAATATT
* * * *
39719763 T-AAATTTTATTAAAA-GTTAGAAAAAATATAAAAATCTT
1 TAAAAATTTA-TAAAATTTTA-TAAAAATATAAAAATATT
39719801 TAAAAATTTATAAAATTTTATAAAAATCATAAAAA
1 TAAAAATTTATAAAATTTTATAAAAAT-ATAAAAA
39719836 AATTATGAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
37 4 0.07
38 34 0.58
39 21 0.36
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (38 bp):
TAAAAATTTATAAAATTTTATAAAAATATAAAAATATT
Found at i:39720821 original size:7 final size:7
Alignment explanation
Indices: 39720811--39720839 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
39720801 GTTCTTTGTT
39720811 CCTCTGC
1 CCTCTGC
39720818 CCTCTGC
1 CCTCTGC
39720825 CCTCTGC
1 CCTCTGC
39720832 CCTCTGC
1 CCTCTGC
39720839 C
1 C
39720840 AGTGAGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.59, G:0.14, T:0.28
Consensus pattern (7 bp):
CCTCTGC
Found at i:39720828 original size:33 final size:32
Alignment explanation
Indices: 39720741--39720831 Score: 105
Period size: 30 Copynumber: 2.9 Consensus size: 32
39720731 AGCCACAGAC
* * *
39720741 TCTTTGCTCTTTGCCCTCTGCTCTCTGCTGCT
1 TCTTTGCCCTCTGCCCTCTGCCCTCTGCTGCT
* *
39720773 TCTTTGCCCTC-G-TCTCTGCCCTCTGCTGGT
1 TCTTTGCCCTCTGCCCTCTGCCCTCTGCTGCT
*
39720803 TCTTTGTTCCTCTGCCCTCTGCCCTCTGC
1 TCTTTG-CCCTCTGCCCTCTGCCCTCTGC
39720832 CCTCTGCCAG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
30 21 0.43
31 5 0.10
32 10 0.20
33 13 0.27
ACGTcount: A:0.00, C:0.41, G:0.16, T:0.43
Consensus pattern (32 bp):
TCTTTGCCCTCTGCCCTCTGCCCTCTGCTGCT
Found at i:39724104 original size:66 final size:66
Alignment explanation
Indices: 39723998--39724306 Score: 609
Period size: 66 Copynumber: 4.7 Consensus size: 66
39723988 GTCTCGACTT
39723998 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAATCATTTATTGAATACAACCAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAATCATTTATTGAATACAACCAA
39724063 A
66 A
39724064 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAATCATTTATTGAATACAACCAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAATCATTTATTGAATACAACCAA
39724129 A
66 A
39724130 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAATCATTTATTGAATACAACCAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAATCATTTATTGAATACAACCAA
39724195 A
66 A
*
39724196 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAATCATTTATTGAATATAACCAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAATCATTTATTGAATACAACCAA
39724261 A
66 A
39724262 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAAT
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAAT
39724307 TTCATTTTCA
Statistics
Matches: 242, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 242 1.00
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.39
Consensus pattern (66 bp):
TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAATCATTTATTGAATACAACCAA
A
Found at i:39724257 original size:22 final size:21
Alignment explanation
Indices: 39724026--39724267 Score: 106
Period size: 22 Copynumber: 11.0 Consensus size: 21
39724016 CAAATATAAG
*
39724026 TATTGTATTAACCAAATCATT
1 TATTGAATTAACCAAATCATT
*
39724047 TATTGAATACAACCAAATCATTT
1 TATTGAAT-TAACCAAATCA-TT
* * *
39724070 TCATATG-CTT-ATCAAAT-ATAAG
1 T-AT-TGAATTAACCAAATCAT--T
*
39724092 TATTGTATTAACCAAATCATT
1 TATTGAATTAACCAAATCATT
*
39724113 TATTGAATACAACCAAATCATTT
1 TATTGAAT-TAACCAAATCA-TT
* * *
39724136 TCATATG-CTT-ATCAAAT-ATAAG
1 T-AT-TGAATTAACCAAATCAT--T
*
39724158 TATTGTATTAACCAAATCATT
1 TATTGAATTAACCAAATCATT
*
39724179 TATTGAATACAACCAAATCATTT
1 TATTGAAT-TAACCAAATCA-TT
* * *
39724202 TCATATG-CTT-ATCAAAT-ATAAG
1 T-AT-TGAATTAACCAAATCAT--T
*
39724224 TATTGTATTAACCAAATCATT
1 TATTGAATTAACCAAATCATT
39724245 TATTGAATATAACCAAATCATT
1 TATTGAAT-TAACCAAATCATT
39724267 T
1 T
39724268 TCATATGCTT
Statistics
Matches: 165, Mismatches: 28, Indels: 55
0.67 0.11 0.22
Matches are distributed among these distances:
20 9 0.05
21 43 0.26
22 83 0.50
23 15 0.09
24 9 0.05
25 6 0.04
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (21 bp):
TATTGAATTAACCAAATCATT
Found at i:39724321 original size:46 final size:46
Alignment explanation
Indices: 39724245--39724444 Score: 359
Period size: 46 Copynumber: 4.3 Consensus size: 46
39724235 CCAAATCATT
*
39724245 TATTGAATATAACCAAA--TCATTTTCATATGCTTATCAAATATAAG
1 TATTGTAT-TAACCAAATTTCATTTTCATATGCTTATCAAATATAAG
39724290 TATTGTATTAACCAAATTTCATTTTCATATGCTTATCAAATATAAG
1 TATTGTATTAACCAAATTTCATTTTCATATGCTTATCAAATATAAG
39724336 TATTGTATTAACCAAATTTCATTTTCATATGCTTATCAAATATAAG
1 TATTGTATTAACCAAATTTCATTTTCATATGCTTATCAAATATAAG
39724382 TATTGTATTAACCAAATTTCATTTTCATATGCTTATCAAATATAAG
1 TATTGTATTAACCAAATTTCATTTTCATATGCTTATCAAATATAAG
39724428 TATTGTATTAACTCAAA
1 TATTGTATTAAC-CAAA
39724445 AGCACTTCTC
Statistics
Matches: 151, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
44 8 0.05
45 7 0.05
46 132 0.87
47 4 0.03
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.42
Consensus pattern (46 bp):
TATTGTATTAACCAAATTTCATTTTCATATGCTTATCAAATATAAG
Found at i:39730281 original size:15 final size:15
Alignment explanation
Indices: 39730261--39730300 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
39730251 TTTCAAAGCT
39730261 TAATTTTTAAAAAAA
1 TAATTTTTAAAAAAA
39730276 TAA-TTTTAAAAAAA
1 TAATTTTTAAAAAAA
39730290 T-ATTTTATAAA
1 TAATTTT-TAAA
39730301 TTTATAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.04
14 15 0.65
15 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATTTTTAAAAAAA
Found at i:39730752 original size:20 final size:18
Alignment explanation
Indices: 39730716--39730755 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
39730706 TTGAACTTTA
39730716 TTTAATATTTTTATAAAT
1 TTTAATATTTTTATAAAT
*
39730734 TTTAATAATGTTTTGTAAAT
1 TTTAAT-AT-TTTTATAAAT
39730754 TT
1 TT
39730756 ATAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 11 0.58
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTAATATTTTTATAAAT
Found at i:39731300 original size:2 final size:2
Alignment explanation
Indices: 39731295--39731320 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39731285 ACTTTTTTAA
39731295 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
39731321 TGAGATAAAG
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:39732303 original size:14 final size:15
Alignment explanation
Indices: 39732277--39732305 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39732267 AAAGTTTAAA
39732277 CAAAAATATAAAATT
1 CAAAAATATAAAATT
39732292 CAAAAATA-AAAATT
1 CAAAAATATAAAATT
39732306 TGAACTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (15 bp):
CAAAAATATAAAATT
Found at i:39739623 original size:73 final size:72
Alignment explanation
Indices: 39739537--39739672 Score: 218
Period size: 73 Copynumber: 1.9 Consensus size: 72
39739527 TTAGAAAAGG
* * * *
39739537 GATCATGCCCAGTAAGTTAGGACACAATCTTTTTTTAATTCTCGAGATCGTTTAAAAACTTGAGG
1 GATCATGCACAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATCGTTT-AAAACTTGAGG
39739602 AAAAAATA
65 AAAAAATA
*
39739610 GATCATGCACAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAACTTGAG
1 GATCATGCACAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATCGTTTAAAACTTGAG
39739673 TTTGAAAAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
72 10 0.17
73 48 0.83
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (72 bp):
GATCATGCACAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATCGTTTAAAACTTGAGGA
AAAAATA
Found at i:39740137 original size:26 final size:26
Alignment explanation
Indices: 39740104--39740156 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
39740094 TATAACAAAT
*
39740104 ATATATGTATACATATAAATTATAAA
1 ATATATGTACACATATAAATTATAAA
* **
39740130 ATATATGTACATATATGTATTATAAA
1 ATATATGTACACATATAAATTATAAA
39740156 A
1 A
39740157 ATGTATAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.40
Consensus pattern (26 bp):
ATATATGTACACATATAAATTATAAA
Found at i:39740307 original size:3 final size:3
Alignment explanation
Indices: 39740299--39740330 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
39740289 ATAAATAGAT
39740299 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
39740331 GCAAAGCTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:39741944 original size:224 final size:225
Alignment explanation
Indices: 39741669--39742154 Score: 553
Period size: 224 Copynumber: 2.2 Consensus size: 225
39741659 TCGCTATGAC
* * * *
39741669 GCAACTTCAGAG--GTAAGATTTGCTATCTTC-AGTCTGCTCTACTGCAACTTCAAGAAGATAAG
1 GCAACTTCAGAGAAATAAGATTTGCTATCTTCTAATCTGCTCCACTGCAACTTCAAGAAGACAAG
* * * * * *
39741731 ACTTGTAT-CTTCAACT-T-GTCCCACTGCAACTTCATAGG-GATAATG-TTTGCTATTTCAACC
66 A-TTAT-TGCTTCAACTCTACT-CCACTACAACGTCA-AGGAGATAA-GACTTGCTACTTCAACC
* *
39741791 TGCTTTACTGCAACTTCAGAGAGATAAAGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGA
126 TGCTCTACTGCAACTTCAGAGAGATAAAGTTTGATATGATATGCTCTACTGCAACTTCAGAGAGA
* **
39741856 TGAGATCTGT-TATGGTAGATTTAATCTGTTCCACT
191 TGAGATCT-TCTATGGTAGATTTAACCTACTCCACT
* * * * * * ** *
39741891 GTAACTTGAGGGAAATAAGATTTGATAT-TTCTAATCTGCTCCACTGTAACTTCAGGGGGACGAG
1 GCAACTTCAGAGAAATAAGATTTGCTATCTTCTAATCTGCTCCACTGCAACTTCAAGAAGACAAG
* * * * * *
39741955 ATTATTGGTTCTAGTCTACTCCACTACAACGTCAGGGAGATAAGACTTGTTGCTTCAACCTGCTC
66 ATTATTGCTTCAACTCTACTCCACTACAACGTCAAGGAGATAAGACTTGCTACTTCAACCTGCTC
* *
39742020 TACTGCAACTTTAGAGAGATAAAGTTTGATATGATATGCTCTACTGTAACTTCAGAGAGATGAGA
131 TACTGCAACTTCAGAGAGATAAAGTTTGATATGATATGCTCTACTGCAACTTCAGAGAGATGAGA
39742085 TCTTCTATGGTAGATTTAACCTACTCCACT
196 TCTTCTATGGTAGATTTAACCTACTCCACT
39742115 GCAACTTCAGAGAAATAAGATTTGCTATCTT-TAATCTGCT
1 GCAACTTCAGAGAAATAAGATTTGCTATCTTCTAATCTGCT
39742155 TTGCTGCAAA
Statistics
Matches: 218, Mismatches: 36, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
222 10 0.05
223 15 0.07
224 190 0.87
225 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (225 bp):
GCAACTTCAGAGAAATAAGATTTGCTATCTTCTAATCTGCTCCACTGCAACTTCAAGAAGACAAG
ATTATTGCTTCAACTCTACTCCACTACAACGTCAAGGAGATAAGACTTGCTACTTCAACCTGCTC
TACTGCAACTTCAGAGAGATAAAGTTTGATATGATATGCTCTACTGCAACTTCAGAGAGATGAGA
TCTTCTATGGTAGATTTAACCTACTCCACT
Found at i:39742186 original size:31 final size:31
Alignment explanation
Indices: 39742148--39742218 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
39742138 GCTATCTTTA
* *
39742148 ATCTGCTTTGCTGCAAA-TCATGGTGTCTTCG
1 ATCTGCTTCGCTGCAAACT-ATGGTATCTTCG
39742179 ATCTGCTTCGCTGCAAACTATGGTATCTTCG
1 ATCTGCTTCGCTGCAAACTATGGTATCTTCG
39742210 ATCTGCTTC
1 ATCTGCTTC
39742219 ACTGTTAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 36 0.97
32 1 0.03
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (31 bp):
ATCTGCTTCGCTGCAAACTATGGTATCTTCG
Found at i:39742526 original size:177 final size:178
Alignment explanation
Indices: 39742204--39742641 Score: 501
Period size: 177 Copynumber: 2.5 Consensus size: 178
39742194 AACTATGGTA
* * * * *
39742204 TCTTCGATCTGCTTCACTGTTAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCTGCTG-
1 TCTTCGATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCCGCTGT
* * * * *
39742268 CAA-ACCCAGGGAGGCAAGACTGGTGTCTTCGATCTATTTCGCTGTCAGTATAGGAAGGCAATAT
66 CAATA--CAGGAAGGCAAGACTGGTGTCTTCGATCTACTTCGCTGTCAGTACAGAAAGGCAAAAT
* * * * *
39742332 ATGTTATCTTCAGTTTGCTCCGCT-GCA-AACCCAGGGAGGCAA-GACTGGTG
129 ATGATATCTTCAGTTTGCTCCACTAGCAGAA--CAGGAAGGCAATG-CCGGGG
* * * *
39742382 TCTTCGATCTACTTTG-TGTCAGTACAGGAAGGCAAGATCTATTATCTTCAGTCTACTCCGTTGT
1 TCTTCGATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCCGCTGT
* * * *
39742446 CAATACAGAAAGGCAAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGAAAGGTAAAATCT
66 CAATACAGGAAGGCAAGACTGGTGTCTTCGATCTACTTCGCTGTCAGTACAGAAAGGCAAAATAT
* * * *
39742511 GATATCTTTAGTTTGCTCTACTATCAGTACAGGAAGGCAATGCCGGGG
131 GATATCTTCAGTTTGCTCCACTAGCAGAACAGGAAGGCAATGCCGGGG
* * *
39742559 TCTTTGATCTGCTTCGCTGTCAGTACAGGAATGCAAGATCTACTATCTTCAGTCTGCTCCGCTGT
1 TCTTCGATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCCGCTGT
* *
39742624 CAGTACAGGAAGACAAGA
66 CAATACAGGAAGGCAAGA
39742642 TTTGCTATCT
Statistics
Matches: 217, Mismatches: 37, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
177 137 0.63
178 78 0.36
179 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (178 bp):
TCTTCGATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCCGCTGT
CAATACAGGAAGGCAAGACTGGTGTCTTCGATCTACTTCGCTGTCAGTACAGAAAGGCAAAATAT
GATATCTTCAGTTTGCTCCACTAGCAGAACAGGAAGGCAATGCCGGGG
Found at i:39742627 original size:89 final size:88
Alignment explanation
Indices: 39742199--39742819 Score: 490
Period size: 89 Copynumber: 7.0 Consensus size: 88
39742189 CTGCAAACTA
* * * * *
39742199 TGGTATCTTCGATCTGCTTCACTGTTAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCT
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCC
* *
39742264 GCTG-CAAACCCAGGGAGGCAAGAC
66 GCTGTCATA--CAGGAAGGCAAGAC
** * * * ** *
39742288 TGGTGTCTTCGATCTATTTCGCTGTCAGTATAGGAAGGCAATATATGTTATCTTCAGTTTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCC
* *
39742353 GCTG-CAAACCCAGGGAGGCAAGAC
66 GCTGTCATA--CAGGAAGGCAAGAC
* * * *
39742377 TGGTGTCTTCGATCTACTTTG-TGTCAGTACAGGAAGGCAAGATCTATTATCTTCAGTCTACTCC
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCC
* *
39742441 GTTGTCAATACAGAAAGGCAAGAC
66 GCTGTC-ATACAGGAAGGCAAGAC
* * * * *
39742465 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGAAAGGTAAAATCTGA-TATCTTTAGTTTGCTC
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCT-ACTATCTTCAGTCTGCTC
** *
39742529 TACTATCAGTACAGGAAGGCAATG-C
65 CGCTGTCA-TACAGGAAGGCAA-GAC
* * * *
39742554 CGGGGTCTTTGATCTGCTTCGCTGTCAGTACAGGAATGCAAGATCTACTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCC
* *
39742619 GCTGTCAGTACAGGAAGACAAGATT
66 GCTGTCA-TACAGGAAGGCAAGA-C
* * * * * * * * * *
39742644 TGCTATCTT-TAGTCTGTTTCGCTATCAGTACAGGAAGGTAAG-GCTAGTGTCTTC-GATCTGTT
1 TGGTGTCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAG-TCTGCT
* *
39742706 TCACTGTCAGTACAGGAAGGCAAGATC
64 CCGCTGTCA-TACAGGAAGGCAAGA-C
* * * * * * *
39742733 TGTTATCTTC-AGTCTGCTCCGCTGTCAGTACAGAAAGGCAAG-GCTAGTGTCTTC-GATCTGCT
1 TGGTGTCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAG-TCTGCT
* *
39742795 TCGCTGTCAGTGCAGGAAGGCAAGA
64 CCGCTGTCA-TACAGGAAGGCAAGA
39742820 TCTACTATCT
Statistics
Matches: 444, Mismatches: 76, Indels: 24
0.82 0.14 0.04
Matches are distributed among these distances:
88 75 0.17
89 334 0.75
90 35 0.08
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (88 bp):
TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCC
GCTGTCATACAGGAAGGCAAGAC
Found at i:39742795 original size:223 final size:223
Alignment explanation
Indices: 39742398--39742832 Score: 564
Period size: 223 Copynumber: 2.0 Consensus size: 223
39742388 ATCTACTTTG
* * * *
39742398 TGTCAGTACAGGAAGGCAAGATCTATTATCTTCAGTCTACTCCGTTGTCAATACAGAAAGGCAAG
1 TGTCAGTACAGGAAGACAAGATCTACTATCTTCAGTCTACTCCGCTATCAATACAGAAAGGCAAG
* * * * *
39742463 ACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGAAAGGTAAAATCTGATATCTTTAGTTTGCT
66 ACTAGTGTCTTCGATCTGCTTCACTGTCAGTACAGAAAGGCAAAATCTGATATCTTCAGTCTGCT
* * * * * *
39742528 CTACTATCAGTACAGGAAGGCAATGCCGGGGTCTTTGATCTGCTTCGCTGTCAGTACAGGAATGC
131 CCACTATCAGTACAGAAAGGCAAGGCCAGGGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGC
39742593 AAGATCTACTATCTTCAGTCTGCTCCGC
196 AAGATCTACTATCTTCAGTCTGCTCCGC
* * * ** * * * *
39742621 TGTCAGTACAGGAAGACAAGATTTGCTATCTTTAGTCTGTTTCGCTATCAGTACAGGAAGGTAAG
1 TGTCAGTACAGGAAGACAAGATCTACTATCTTCAGTCTACTCCGCTATCAATACAGAAAGGCAAG
* * * * *
39742686 GCTAGTGTCTTCGATCTGTTTCACTGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCTGCT
66 ACTAGTGTCTTCGATCTGCTTCACTGTCAGTACAGAAAGGCAAAATCTGATATCTTCAGTCTGCT
* * * * *
39742751 CCGCTGTCAGTACAGAAAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGC
131 CCACTATCAGTACAGAAAGGCAAGGCCAGGGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGC
39742816 AAGATCTACTATCTTCA
196 AAGATCTACTATCTTCA
39742833 CTGATCTGTT
Statistics
Matches: 178, Mismatches: 34, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
223 178 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (223 bp):
TGTCAGTACAGGAAGACAAGATCTACTATCTTCAGTCTACTCCGCTATCAATACAGAAAGGCAAG
ACTAGTGTCTTCGATCTGCTTCACTGTCAGTACAGAAAGGCAAAATCTGATATCTTCAGTCTGCT
CCACTATCAGTACAGAAAGGCAAGGCCAGGGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGC
AAGATCTACTATCTTCAGTCTGCTCCGC
Found at i:39742831 original size:134 final size:134
Alignment explanation
Indices: 39742274--39742831 Score: 424
Period size: 134 Copynumber: 4.2 Consensus size: 134
39742264 GCTGCAAACC
* * * * * * *
39742274 CAGGGAGGCAAGA-CTGGTGTCTTCGATCTATTTCGCTGTCAGTATAGGAAGGCAATATATGTTA
1 CAGGAAGGCAAGATCTAGTATCTTCGATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTA
* * ** * * * *
39742338 TCTTCAGTTTGCTCCGCTG-CA-AACCCAGGGAGGCAAGACTGGTGTCTTCGA-TCTACTTTG-T
66 TCTTCAGTCTGCTCCGCTGTCAGTA--CAGAAAGGCAAGACTGATATCTT-GAGTCTGCTTCGCT
*
39742399 GTCAGTA
128 ATCAGTA
* * * * * *
39742406 CAGGAAGGCAAGATCTATTATCTTC-AGTCTACTCCGTTGTCAATACAGAAAGGCAAGA-CTGGT
1 CAGGAAGGCAAGATCTAGTATCTTCGA-TCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTGTT
* * * * * * *
39742469 GTCTTC-GATCTGCTTCGCTGTCAGTACAGAAAGGTAAAATCTGATATCTTTAGTTTGC-TCTAC
65 ATCTTCAG-TCTGCTCCGCTGTCAGTACAGAAAGGCAAGA-CTGATATCTTGAGTCTGCTTC-GC
39742532 TATCAGTA
127 TATCAGTA
** ** * * * **
39742540 CAGGAAGGC-A-ATGCCGGGGTCTTTGATCTGCTTCGCTGTCAGTACAGGAATGCAAGATCTACT
1 CAGGAAGGCAAGAT-CTAGTATCTTCGATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTGTT
* * * * * *
39742603 ATCTTCAGTCTGCTCCGCTGTCAGTACAGGAAGACAAGATTTGCTATCTTTAGTCTGTTTCGCTA
65 ATCTTCAGTCTGCTCCGCTGTCAGTACAGAAAGGCAAGA-CTGATATCTTGAGTCTGCTTCGCTA
39742668 TCAGTA
129 TCAGTA
* * * ** *
39742674 CAGGAAGGTAAG-GCTAGTGTCTTCGATCTGTTTCACTGTCAGTACAGGAAGGCAAGATCTGTTA
1 CAGGAAGGCAAGATCTAGTATCTTCGATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTA
* * *
39742738 TCTTCAGTCTGCTCCGCTGTCAGTACAGAAAGGCAAGGCT-AGTGTCTTCGA-TCTGCTTCGCTG
66 TCTTCAGTCTGCTCCGCTGTCAGTACAGAAAGGCAAGACTGA-TATCTT-GAGTCTGCTTCGCTA
*
39742801 TCAGTG
129 TCAGTA
*
39742807 CAGGAAGGCAAGATCTACTATCTTC
1 CAGGAAGGCAAGATCTAGTATCTTC
39742832 ACTGATCTGT
Statistics
Matches: 328, Mismatches: 79, Indels: 36
0.74 0.18 0.08
Matches are distributed among these distances:
131 1 0.00
132 44 0.13
133 108 0.33
134 171 0.52
135 4 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (134 bp):
CAGGAAGGCAAGATCTAGTATCTTCGATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTA
TCTTCAGTCTGCTCCGCTGTCAGTACAGAAAGGCAAGACTGATATCTTGAGTCTGCTTCGCTATC
AGTA
Found at i:39744083 original size:5 final size:5
Alignment explanation
Indices: 39744073--39744123 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
39744063 GGCATCTCCT
* *
39744073 TTTTC TTTTC TTTT- TGTTC TTTTTC TTTTTG TTTTC TTTTC TTCTTC
1 TTTTC TTTTC TTTTC TTTTC -TTTTC -TTTTC TTTTC TTTTC TT-TTC
39744120 TTTT
1 TTTT
39744124 TCTAAACTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 3 0.08
5 22 0.56
6 14 0.36
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:39744087 original size:6 final size:6
Alignment explanation
Indices: 39744071--39744126 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
39744061 TTGGCATCTC
* * *
39744071 CTTTTT CTTTTCT TTTTGTT CTTTTT CTTTTT -GTTTT C-TTTT CTTCTT
1 CTTTTT CTTTT-T CTTT-TT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
39744119 CTTTTT CT
1 CTTTTT CT
39744127 AAACTCATAG
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
5 9 0.22
6 23 0.56
7 8 0.20
8 1 0.02
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:39744087 original size:11 final size:11
Alignment explanation
Indices: 39744071--39744123 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
39744061 TTGGCATCTC
39744071 CTTTTTCTTTT
1 CTTTTTCTTTT
*
39744082 C-TTTT-TGTT
1 CTTTTTCTTTT
39744091 CTTTTTCTTTT
1 CTTTTTCTTTT
39744102 -TGTTTTCTTTT
1 CT-TTTTCTTTT
*
39744113 CTTCTTCTTTT
1 CTTTTTCTTTT
39744124 TCTAAACTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
9 4 0.11
10 9 0.26
11 21 0.60
12 1 0.03
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (11 bp):
CTTTTTCTTTT
Found at i:39744098 original size:15 final size:16
Alignment explanation
Indices: 39744076--39744115 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
39744066 ATCTCCTTTT
39744076 TCTTTTCTTTTTGTTC
1 TCTTTTCTTTTTGTTC
*
39744092 T-TTTTCTTTTTGTTT
1 TCTTTTCTTTTTGTTC
39744107 TCTTTTCTT
1 TCTTTTCTT
39744116 CTTCTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (16 bp):
TCTTTTCTTTTTGTTC
Found at i:39748543 original size:19 final size:20
Alignment explanation
Indices: 39748516--39748566 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
39748506 GTATATAGAT
*
39748516 ATATATAGA-TATGTAAACAA
1 ATATATAGAGTATATAAA-AA
39748536 AT-TATAGAGTATATAAAAA
1 ATATATAGAGTATATAAAAA
39748555 ATATATA-AGTAT
1 ATATATAGAGTAT
39748567 GTATATGTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (20 bp):
ATATATAGAGTATATAAAAA
Found at i:39748800 original size:15 final size:15
Alignment explanation
Indices: 39748780--39748814 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
39748770 TGGTAATAGT
*
39748780 AATAACAATATTAAA
1 AATAACAATAGTAAA
39748795 AATAACAATAGTAAA
1 AATAACAATAGTAAA
39748810 AATAA
1 AATAA
39748815 TGATAACATT
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:0.69, C:0.06, G:0.03, T:0.23
Consensus pattern (15 bp):
AATAACAATAGTAAA
Found at i:39755955 original size:25 final size:25
Alignment explanation
Indices: 39755927--39755980 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
39755917 ATAGGCTGTT
39755927 AATTACAAAGGGAAAGTCCTAATAG
1 AATTACAAAGGGAAAGTCCTAATAG
* * ***
39755952 AATTCCTAATTTAAAGTCCTAATAG
1 AATTACAAAGGGAAAGTCCTAATAG
39755977 AATT
1 AATT
39755981 CCTAGTAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (25 bp):
AATTACAAAGGGAAAGTCCTAATAG
Found at i:39755960 original size:12 final size:12
Alignment explanation
Indices: 39755943--39755984 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
39755933 AAAGGGAAAG
39755943 TCCTAATAGAAT
1 TCCTAATAGAAT
*
39755955 TCCTAATTTA-AAG
1 TCCTAA--TAGAAT
39755968 TCCTAATAGAAT
1 TCCTAATAGAAT
39755980 TCCTA
1 TCCTA
39755985 GTAAAGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 2 0.08
12 13 0.52
13 8 0.32
14 2 0.08
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (12 bp):
TCCTAATAGAAT
Found at i:39760821 original size:27 final size:29
Alignment explanation
Indices: 39760790--39760849 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
39760780 AAATAAAAAA
*
39760790 CCTAATA-AAA-TAAGTAAAACTAAAACT
1 CCTAATAGAAATTAAATAAAACTAAAACT
*
39760817 CCTAA-AGAAATTAAATAAATCTAAAACT
1 CCTAATAGAAATTAAATAAAACTAAAACT
39760845 -CTAAT
1 CCTAAT
39760850 TCATATTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 1 0.04
27 12 0.43
28 15 0.54
ACGTcount: A:0.57, C:0.15, G:0.03, T:0.25
Consensus pattern (29 bp):
CCTAATAGAAATTAAATAAAACTAAAACT
Found at i:39766091 original size:238 final size:238
Alignment explanation
Indices: 39765406--39766118 Score: 740
Period size: 237 Copynumber: 3.0 Consensus size: 238
39765396 CCTAAGGTAA
39765406 GCAAAAGTGACCATGGGTGTAGTTTACCCTTAAATCTAATACCCAAATACAATTTGTAAAAGTTT
1 GCAAAAGTGACCATGGGTGTAGTTTACCCTTAAATCTAATACCCAAATACAATTTGTAAAAGTTT
39765471 AAGCACAATTCAAAATTTATTTAATAAAAATAATATTTTATTAAGATATTAAATTTTTAATAATA
66 AAGCACAATTCAAAATTTATTTAATAAAAATAATATTTTATTAAGATATTAAATTTTTAATAATA
39765536 TTTTATGTATTGCTAGTTATAATTATATATGTGCATCAATGATTAAACATTATAATAACATGTAA
131 TTTTATGTATTGCTAGTTATAATTATATATGTGCATCAATGATTAAACATTATAATAACATGTAA
39765601 TACTATATATTTTATTATAATCTATAATATAATAATAGTTATT
196 TACTATATATTTTATTATAATCTATAATATAATAATAGTTATT
* * *** ***
39765644 -TATAATAGTAGTA-CAT---TATA-TATTATTGTTTATAAT-T-ATACTGCGTCAAATATGTTT
1 GCA-AA-AGT-G-ACCATGGGTGTAGT-TTA-CCCTTA-AATCTAATAC--C--CAAATACAATT
* * * ** * ** * **** *** * * *
39765701 TAAGTCTCTATATTTTTCGTAC-ATTTGAAAGTTA-GCCCTCCTACT-ATACTATA-T-A-ATAT
55 T--G--T-AAAAGTTTAAGCACAATTCAAAATTTATTTAATAAAAATAATATTTTATTAAGATAT
* * ** * * * * ** ** * * * *
39765760 CATA-TCAT-AGAGTATATGACATATTAATGGTT-TATTTATATATATGCATTAATGATTAAACA
115 TAAATTTTTAATAATATTTTATGTATTGCTAGTTATAATTATATATGTGCATCAATGATTAAACA
* * * *
39765822 TTACAATATCATGTAATGCTATATCTTTTATTATAATCTATAATATAATAATAGTTATT
180 TTATAATAACATGTAATACTATATATTTTATTATAATCTATAATATAATAATAGTTATT
39765881 GCAAAAGTGACCATGGGTGTAGTTTACCCTTAAATCTAATACCCAAATACAATTTGTAAAAGTTT
1 GCAAAAGTGACCATGGGTGTAGTTTACCCTTAAATCTAATACCCAAATACAATTTGTAAAAGTTT
39765946 AAGCACAATTCAAAATTTATTTAATAAAAATAATATTTTATTAAGATATTAAATTTTTAATAATA
66 AAGCACAATTCAAAATTTATTTAATAAAAATAATATTTTATTAAGATATTAAATTTTTAATAATA
39766011 TTTTATGTATTGCTAGTTATAATTATATATGTGCATCAATGATTAAACATTATAATAACATGTAA
131 TTTTATGTATTGCTAGTTATAATTATATATGTGCATCAATGATTAAACATTATAATAACATGTAA
39766076 TACTATATATTTTATTATAATCTATAATATAATAATAGTTATT
196 TACTATATATTTTATTATAATCTATAATATAATAATAGTTATT
39766119 TATAATAGTA
Statistics
Matches: 348, Mismatches: 94, Indels: 66
0.69 0.19 0.13
Matches are distributed among these distances:
229 8 0.02
230 10 0.03
231 3 0.01
232 7 0.02
233 1 0.00
234 11 0.03
235 10 0.03
236 10 0.03
237 114 0.33
238 114 0.33
239 10 0.03
240 10 0.03
241 11 0.03
242 1 0.00
243 7 0.02
244 3 0.01
245 10 0.03
246 8 0.02
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (238 bp):
GCAAAAGTGACCATGGGTGTAGTTTACCCTTAAATCTAATACCCAAATACAATTTGTAAAAGTTT
AAGCACAATTCAAAATTTATTTAATAAAAATAATATTTTATTAAGATATTAAATTTTTAATAATA
TTTTATGTATTGCTAGTTATAATTATATATGTGCATCAATGATTAAACATTATAATAACATGTAA
TACTATATATTTTATTATAATCTATAATATAATAATAGTTATT
Found at i:39766296 original size:475 final size:475
Alignment explanation
Indices: 39765406--39766354 Score: 1898
Period size: 475 Copynumber: 2.0 Consensus size: 475
39765396 CCTAAGGTAA
39765406 GCAAAAGTGACCATGGGTGTAGTTTACCCTTAAATCTAATACCCAAATACAATTTGTAAAAGTTT
1 GCAAAAGTGACCATGGGTGTAGTTTACCCTTAAATCTAATACCCAAATACAATTTGTAAAAGTTT
39765471 AAGCACAATTCAAAATTTATTTAATAAAAATAATATTTTATTAAGATATTAAATTTTTAATAATA
66 AAGCACAATTCAAAATTTATTTAATAAAAATAATATTTTATTAAGATATTAAATTTTTAATAATA
39765536 TTTTATGTATTGCTAGTTATAATTATATATGTGCATCAATGATTAAACATTATAATAACATGTAA
131 TTTTATGTATTGCTAGTTATAATTATATATGTGCATCAATGATTAAACATTATAATAACATGTAA
39765601 TACTATATATTTTATTATAATCTATAATATAATAATAGTTATTTATAATAGTAGTACATTATATA
196 TACTATATATTTTATTATAATCTATAATATAATAATAGTTATTTATAATAGTAGTACATTATATA
39765666 TTATTGTTTATAATTATACTGCGTCAAATATGTTTTAAGTCTCTATATTTTTCGTACATTTGAAA
261 TTATTGTTTATAATTATACTGCGTCAAATATGTTTTAAGTCTCTATATTTTTCGTACATTTGAAA
39765731 GTTAGCCCTCCTACTATACTATATAATATCATATCATAGAGTATATGACATATTAATGGTTTATT
326 GTTAGCCCTCCTACTATACTATATAATATCATATCATAGAGTATATGACATATTAATGGTTTATT
39765796 TATATATATGCATTAATGATTAAACATTACAATATCATGTAATGCTATATCTTTTATTATAATCT
391 TATATATATGCATTAATGATTAAACATTACAATATCATGTAATGCTATATCTTTTATTATAATCT
39765861 ATAATATAATAATAGTTATT
456 ATAATATAATAATAGTTATT
39765881 GCAAAAGTGACCATGGGTGTAGTTTACCCTTAAATCTAATACCCAAATACAATTTGTAAAAGTTT
1 GCAAAAGTGACCATGGGTGTAGTTTACCCTTAAATCTAATACCCAAATACAATTTGTAAAAGTTT
39765946 AAGCACAATTCAAAATTTATTTAATAAAAATAATATTTTATTAAGATATTAAATTTTTAATAATA
66 AAGCACAATTCAAAATTTATTTAATAAAAATAATATTTTATTAAGATATTAAATTTTTAATAATA
39766011 TTTTATGTATTGCTAGTTATAATTATATATGTGCATCAATGATTAAACATTATAATAACATGTAA
131 TTTTATGTATTGCTAGTTATAATTATATATGTGCATCAATGATTAAACATTATAATAACATGTAA
39766076 TACTATATATTTTATTATAATCTATAATATAATAATAGTTATTTATAATAGTAGTACATTATATA
196 TACTATATATTTTATTATAATCTATAATATAATAATAGTTATTTATAATAGTAGTACATTATATA
39766141 TTATTGTTTATAATTATACTGCGTCAAATATGTTTTAAGTCTCTATATTTTTCGTACATTTGAAA
261 TTATTGTTTATAATTATACTGCGTCAAATATGTTTTAAGTCTCTATATTTTTCGTACATTTGAAA
39766206 GTTAGCCCTCCTACTATACTATATAATATCATATCATAGAGTATATGACATATTAATGGTTTATT
326 GTTAGCCCTCCTACTATACTATATAATATCATATCATAGAGTATATGACATATTAATGGTTTATT
39766271 TATATATATGCATTAATGATTAAACATTACAATATCATGTAATGCTATATCTTTTATTATAATCT
391 TATATATATGCATTAATGATTAAACATTACAATATCATGTAATGCTATATCTTTTATTATAATCT
39766336 ATAATATAATAATAGTTAT
456 ATAATATAATAATAGTTAT
39766355 ATATAATTGT
Statistics
Matches: 474, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
475 474 1.00
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (475 bp):
GCAAAAGTGACCATGGGTGTAGTTTACCCTTAAATCTAATACCCAAATACAATTTGTAAAAGTTT
AAGCACAATTCAAAATTTATTTAATAAAAATAATATTTTATTAAGATATTAAATTTTTAATAATA
TTTTATGTATTGCTAGTTATAATTATATATGTGCATCAATGATTAAACATTATAATAACATGTAA
TACTATATATTTTATTATAATCTATAATATAATAATAGTTATTTATAATAGTAGTACATTATATA
TTATTGTTTATAATTATACTGCGTCAAATATGTTTTAAGTCTCTATATTTTTCGTACATTTGAAA
GTTAGCCCTCCTACTATACTATATAATATCATATCATAGAGTATATGACATATTAATGGTTTATT
TATATATATGCATTAATGATTAAACATTACAATATCATGTAATGCTATATCTTTTATTATAATCT
ATAATATAATAATAGTTATT
Found at i:39766328 original size:237 final size:236
Alignment explanation
Indices: 39765549--39766559 Score: 1010
Period size: 237 Copynumber: 4.3 Consensus size: 236
39765539 TATGTATTGC
* * * *
39765549 TAGTTATAATTATATATGTGCATCAATGATTAAACATTATAATAACATGTAATACTATATATTTT
1 TAGTT-TATTTATATATATGCATCAATGATTAAACATTATAATATCATGTAATACTATATCTTTT
39765614 ATTATAATCTATAATATAATAATAGTTATTTATAATAGTAGTACATTATATATTATTGTTTATAA
65 ATTATAATCTATAATATAATAATAGTTATTTATAATAGTAGTACATTATATATTATTGTTTATAA
*
39765679 TTATACTGCGTCAAATATGTTTTAAGTCTCTATATTTTTCGTACATTTGAAAGTTAGCCCTCCTA
130 TTATACTGCGTCAAATATATTTT-AGTCTCTATATTTTTCGTACATTTGAAAGTTAGCCCTCCTA
39765744 CTATACTATATAATATCATATCATAGAGTATATGACATATTAA
194 CTATACTATATAATATCATATCATAGAGTATATGACATATTAA
* * * *
39765787 TGGTTTATTTATATATATGCATTAATGATTAAACATTACAATATCATGTAATGCTATATCTTTTA
1 TAGTTTATTTATATATATGCATCAATGATTAAACATTATAATATCATGTAATACTATATCTTTTA
* * ***
39765852 TTATAATCTATAATATAATAATAGTTATTGCA-AA-AGT-G-ACCATGGGTGTAGT-TTA-CCCT
66 TTATAATCTATAATATAATAATAGTTATT-TATAATAGTAGTA-CAT---TATA-TATTATTGTT
* * * * * ** * ** * *
39765911 TA-AATCTAATAC--C--CAAATACAATTT-G--T-AAAAGTTTAAGCACAATTCAAAATTTATT
125 TATAAT-T-ATACTGCGTCAAATATATTTTAGTCTCTATATTTTTCGTAC-ATTTGAAAGTTA-G
*** *** * * * * * ** * * * * ** **
39765967 TAATAAAAATAATATTTTATTAAGATATTAAATTTTTAATAATATTTTATGTATTGC
186 CCCTCCTACT-ATACTATA-T-A-ATATCATA-TCAT-AGAGTATATGACATATTAA
* * * *
39766024 TAGTTATAATTATATATGTGCATCAATGATTAAACATTATAATAACATGTAATACTATATATTTT
1 TAGTT-TATTTATATATATGCATCAATGATTAAACATTATAATATCATGTAATACTATATCTTTT
39766089 ATTATAATCTATAATATAATAATAGTTATTTATAATAGTAGTACATTATATATTATTGTTTATAA
65 ATTATAATCTATAATATAATAATAGTTATTTATAATAGTAGTACATTATATATTATTGTTTATAA
*
39766154 TTATACTGCGTCAAATATGTTTTAAGTCTCTATATTTTTCGTACATTTGAAAGTTAGCCCTCCTA
130 TTATACTGCGTCAAATATATTTT-AGTCTCTATATTTTTCGTACATTTGAAAGTTAGCCCTCCTA
39766219 CTATACTATATAATATCATATCATAGAGTATATGACATATTAA
194 CTATACTATATAATATCATATCATAGAGTATATGACATATTAA
* * * *
39766262 TGGTTTATTTATATATATGCATTAATGATTAAACATTACAATATCATGTAATGCTATATCTTTTA
1 TAGTTTATTTATATATATGCATCAATGATTAAACATTATAATATCATGTAATACTATATCTTTTA
* * * *
39766327 TTATAATCTATAATATAATAATAGTTATATATAATTGTAGTATATTATATATTATTGTTTATTAT
66 TTATAATCTATAATATAATAATAGTTATTTATAATAGTAGTACATTATATATTATTGTTTATAAT
*** * * * *
39766392 TATACTATTTGAAATATACTTTAGATCCCTATACTTTTCGTACATTTGAAAGTTAGCCCTCCTAC
131 TATACTGCGTCAAATATATTTTAG-TCTCTATATTTTTCGTACATTTGAAAGTTAGCCCTCCTAC
* *
39766457 --TA-TAT-T-ATATCATATCATATG-GTATATAATATATTAA
195 TATACTATATAATATCATATCATA-GAGTATATGACATATTAA
* *
39766494 TAG----TTTATATATATGCATCAATGATTAAACATTATAATATCATGTAATATTGTATCTTTTA
1 TAGTTTATTTATATATATGCATCAATGATTAAACATTATAATATCATGTAATACTATATCTTTTA
39766555 TTATA
66 TTATA
39766560 NNNNNNNNNN
Statistics
Matches: 616, Mismatches: 122, Indels: 80
0.75 0.15 0.10
Matches are distributed among these distances:
228 58 0.09
229 8 0.01
230 10 0.02
231 3 0.00
232 36 0.06
233 3 0.00
234 14 0.02
235 12 0.02
236 12 0.02
237 282 0.46
238 118 0.19
239 10 0.02
240 10 0.02
241 11 0.02
242 1 0.00
243 7 0.01
244 3 0.00
245 10 0.02
246 8 0.01
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (236 bp):
TAGTTTATTTATATATATGCATCAATGATTAAACATTATAATATCATGTAATACTATATCTTTTA
TTATAATCTATAATATAATAATAGTTATTTATAATAGTAGTACATTATATATTATTGTTTATAAT
TATACTGCGTCAAATATATTTTAGTCTCTATATTTTTCGTACATTTGAAAGTTAGCCCTCCTACT
ATACTATATAATATCATATCATAGAGTATATGACATATTAA
Found at i:39770238 original size:129 final size:129
Alignment explanation
Indices: 39770008--39770507 Score: 621
Period size: 129 Copynumber: 3.9 Consensus size: 129
39769998 TACCAAGATT
* * * * *
39770008 TGATAACATGTAAGACCATGTTTGGGACATTGGCATT-ATACTGTGATTACGTATAAGACCATGT
1 TGATAACATATAAGACCATGTCTGGGACATTGGCATTGTTA-TATGATTACGTATAAGACCCTGT
* * ** * * * * *
39770072 CTGGGACATTGGCATC-ATTATATGATTTCGTATAAGACCCTGTCTGGGACAGTGGCATCGATA-
65 CTGGGACAGTGGCATCGA-TATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTG-TAC
39770135 TG
128 TG
* * * * *
39770137 TGATAACATGTAAGACCATGTTTGAGACATTAGCATTG-TACTGTGATTACGTATAAGACCCTGT
1 TGATAACATATAAGACCATGTCTGGGACATTGGCATTGTTA-TATGATTACGTATAAGACCCTGT
*
39770201 CTGGGACAGTGGCACCGATATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTGTACTG
65 CTGGGACAGTGGCATCGATATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTGTACTG
* * * * *
39770266 TGATTACGTATAAGACCATGCCTGGGGCATTGGCATTGTTATATGATTTCGTATAAGACCCTGTC
1 TGATAACATATAAGACCATGTCTGGGACATTGGCATTGTTATATGATTACGTATAAGACCCTGTC
* *
39770331 TGGGACAGTGGCATCAATATGTGATAACATGTAAGACCATGTCTGGGACATTAGCATTGTACTG
66 TGGGACAGTGGCATCGATATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTGTACTG
* * * * *
39770395 TGATTACGTATAAGACCATGTCTGGGACATTGACATCGTTATATGATTTCGTATAAGACCCTGTC
1 TGATAACATATAAGACCATGTCTGGGACATTGGCATTGTTATATGATTACGTATAAGACCCTGTC
* * *
39770460 TGGGACAGTGGCATCGATATGTAATAACATGTAAGAACATATCTGGGA
66 TGGGACAGTGGCATCGATATGTGATAACATGTAAGACCATGTCTGGGA
39770508 TATGACATTA
Statistics
Matches: 333, Mismatches: 34, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
128 2 0.01
129 328 0.98
130 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (129 bp):
TGATAACATATAAGACCATGTCTGGGACATTGGCATTGTTATATGATTACGTATAAGACCCTGTC
TGGGACAGTGGCATCGATATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTGTACTG
Found at i:39770507 original size:43 final size:43
Alignment explanation
Indices: 39770018--39770481 Score: 488
Period size: 43 Copynumber: 10.8 Consensus size: 43
39770008 TGATAACATG
* *
39770018 TAAGACCATGTTTGGGACATTGGCAT-TATACTGTGATTACGTA
1 TAAGACCATGTCTGGGACATTGGCATCGATA-TGTGATTACGTA
* *
39770061 TAAGACCATGTCTGGGACATTGGCATC-ATTATATGATTTCGTA
1 TAAGACCATGTCTGGGACATTGGCATCGA-TATGTGATTACGTA
* * * * *
39770104 TAAGACCCTGTCTGGGACAGTGGCATCGATATGTGATAACATG
1 TAAGACCATGTCTGGGACATTGGCATCGATATGTGATTACGTA
* * * *
39770147 TAAGACCATGTTTGAGACATTAGCATTG-TACTGTGATTACGTA
1 TAAGACCATGTCTGGGACATTGGCATCGATA-TGTGATTACGTA
* * * * * *
39770190 TAAGACCCTGTCTGGGACAGTGGCACCGATATGTGATAACATG
1 TAAGACCATGTCTGGGACATTGGCATCGATATGTGATTACGTA
*
39770233 TAAGACCATGTCTGGGACATTGGCATTG-TACTGTGATTACGTA
1 TAAGACCATGTCTGGGACATTGGCATCGATA-TGTGATTACGTA
* * * * * *
39770276 TAAGACCATGCCTGGGGCATTGGCATTGTTATATGATTTCGTA
1 TAAGACCATGTCTGGGACATTGGCATCGATATGTGATTACGTA
* * * * * *
39770319 TAAGACCCTGTCTGGGACAGTGGCATCAATATGTGATAACATG
1 TAAGACCATGTCTGGGACATTGGCATCGATATGTGATTACGTA
* *
39770362 TAAGACCATGTCTGGGACATTAGCATTG-TACTGTGATTACGTA
1 TAAGACCATGTCTGGGACATTGGCATCGATA-TGTGATTACGTA
* * * *
39770405 TAAGACCATGTCTGGGACATTGACATCGTTATATGATTTCGTA
1 TAAGACCATGTCTGGGACATTGGCATCGATATGTGATTACGTA
* *
39770448 TAAGACCCTGTCTGGGACAGTGGCATCGATATGT
1 TAAGACCATGTCTGGGACATTGGCATCGATATGT
39770482 AATAACATGT
Statistics
Matches: 342, Mismatches: 70, Indels: 18
0.80 0.16 0.04
Matches are distributed among these distances:
42 6 0.02
43 327 0.96
44 9 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (43 bp):
TAAGACCATGTCTGGGACATTGGCATCGATATGTGATTACGTA
Found at i:39773519 original size:31 final size:31
Alignment explanation
Indices: 39773481--39773543 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
39773471 TTCGTTTCAA
39773481 TATATGGCAAGTACTTGGGTTGTGAATCGGT
1 TATATGGCAAGTACTTGGGTTGTGAATCGGT
39773512 TATATGGCAAGTACTTGGGTTGTGAATCGGT
1 TATATGGCAAGTACTTGGGTTGTGAATCGGT
39773543 T
1 T
39773544 TTGTATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.22, C:0.10, G:0.32, T:0.37
Consensus pattern (31 bp):
TATATGGCAAGTACTTGGGTTGTGAATCGGT
Found at i:39775138 original size:30 final size:29
Alignment explanation
Indices: 39775104--39775206 Score: 97
Period size: 25 Copynumber: 3.4 Consensus size: 29
39775094 AATATCTTGC
39775104 AATACTATATCTTTTAATAATTATTTTTAA
1 AATACTATATCTTTTAAT-ATTATTTTTAA
* *
39775134 AATACTATATC-ATT-ATAGTA--TTTAA
1 AATACTATATCTTTTAATATTATTTTTAA
39775159 AATACTATATCATTATAGTATATCATTATTTTTAA
1 AATACTATATC-TT-T--TA-AT-ATTATTTTTAA
39775194 AATACTATATCTT
1 AATACTATATCTT
39775207 GCAATACTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
25 16 0.27
27 3 0.05
28 3 0.05
29 2 0.03
30 12 0.20
32 2 0.03
33 3 0.05
34 2 0.03
35 16 0.27
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.49
Consensus pattern (29 bp):
AATACTATATCTTTTAATATTATTTTTAA
Found at i:39775158 original size:25 final size:25
Alignment explanation
Indices: 39775129--39775179 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
39775119 AATAATTATT
39775129 TTTAAAATACTATATCATTATAGTA
1 TTTAAAATACTATATCATTATAGTA
39775154 TTTAAAATACTATATCATTATAGTA
1 TTTAAAATACTATATCATTATAGTA
39775179 T
1 T
39775180 ATCATTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (25 bp):
TTTAAAATACTATATCATTATAGTA
Found at i:39775182 original size:13 final size:13
Alignment explanation
Indices: 39775139--39775187 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
39775129 TTTAAAATAC
39775139 TATATCATTATAG
1 TATATCATTATAG
* ** *
39775152 TAT-TTAAAATAC
1 TATATCATTATAG
39775164 TATATCATTATAG
1 TATATCATTATAG
39775177 TATATCATTAT
1 TATATCATTAT
39775188 TTTTAAAATA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
12 8 0.30
13 19 0.70
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (13 bp):
TATATCATTATAG
Found at i:39780476 original size:23 final size:24
Alignment explanation
Indices: 39780450--39780499 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
39780440 CTTGATAAAC
* *
39780450 AAATTATGACAC-AATAAATTTTA
1 AAATTATGAAACAAATAAATTTCA
*
39780473 AAA-TATTAAACAAATAAATTTCA
1 AAATTATGAAACAAATAAATTTCA
39780496 AAAT
1 AAAT
39780500 ATTTATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATTATGAAACAAATAAATTTCA
Found at i:39781382 original size:8 final size:8
Alignment explanation
Indices: 39781352--39781408 Score: 62
Period size: 8 Copynumber: 6.9 Consensus size: 8
39781342 AATTGGAAAG
39781352 TAAAATAA
1 TAAAATAA
*
39781360 T-AAATGA
1 TAAAATAA
*
39781367 TGATAAATGA
1 T-A-AAATAA
39781377 TAAAATAA
1 TAAAATAA
39781385 TAAAATAA
1 TAAAATAA
39781393 TAAAATAA
1 TAAAATAA
39781401 TGAAAATA
1 T-AAAATA
39781409 TAATCATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
7 6 0.14
8 23 0.53
9 7 0.16
10 7 0.16
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (8 bp):
TAAAATAA
Found at i:39781411 original size:16 final size:17
Alignment explanation
Indices: 39781353--39781408 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 17
39781343 ATTGGAAAGT
*
39781353 AAAATAAT-AAATGATG
1 AAAATAATAAAATAATG
*
39781369 ATAAATGATAAAATAAT-
1 A-AAATAATAAAATAATG
39781386 AAAATAATAAAATAATG
1 AAAATAATAAAATAATG
39781403 AAAATA
1 AAAATA
39781409 TAATCATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 15 0.44
17 13 0.38
18 6 0.18
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (17 bp):
AAAATAATAAAATAATG
Found at i:39782447 original size:46 final size:46
Alignment explanation
Indices: 39782392--39782483 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
39782382 CCTGTTATAT
* * *
39782392 GGCTTTTTGTGAGCTTCTCAATA-GGCTCTTCTTGAGCTTCCCGATA
1 GGCTCTTTGTGAGCTTCTCAATATGGCTC-GCTTGAACTTCCCGATA
* *
39782438 GGCTCTTTGTGAGCTTCTCGATATTGCTCGCTTGAACTTCCCGATA
1 GGCTCTTTGTGAGCTTCTCAATATGGCTCGCTTGAACTTCCCGATA
39782484 TATGGCTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 36 0.90
47 4 0.10
ACGTcount: A:0.15, C:0.25, G:0.22, T:0.38
Consensus pattern (46 bp):
GGCTCTTTGTGAGCTTCTCAATATGGCTCGCTTGAACTTCCCGATA
Found at i:39782459 original size:23 final size:23
Alignment explanation
Indices: 39782392--39782460 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
39782382 CCTGTTATAT
* *
39782392 GGCTTTTTGTGAGCTTCTCAATA
1 GGCTCTTTGTGAGCTTCTCGATA
*
39782415 GGCTCTTCT-TGAGCTTCCCGATA
1 GGCTCTT-TGTGAGCTTCTCGATA
39782438 GGCTCTTTGTGAGCTTCTCGATA
1 GGCTCTTTGTGAGCTTCTCGATA
39782461 TTGCTCGCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 38 0.95
24 1 0.03
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.39
Consensus pattern (23 bp):
GGCTCTTTGTGAGCTTCTCGATA
Found at i:39787434 original size:36 final size:37
Alignment explanation
Indices: 39787365--39787435 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
39787355 CAACGAAAAT
*
39787365 ATCCACAGGTATTTCCACGGATTTCTACTTTCTCCAA
1 ATCCACAGGTATTTCCACAGATTTCTACTTTCTCCAA
39787402 ATCCACAGGTATTTCCACAGA-TTCTACTTTCTCC
1 ATCCACAGGTATTTCCACAGATTTCTACTTTCTCC
39787436 TAATAATCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 13 0.39
37 20 0.61
ACGTcount: A:0.24, C:0.31, G:0.10, T:0.35
Consensus pattern (37 bp):
ATCCACAGGTATTTCCACAGATTTCTACTTTCTCCAA
Found at i:39802062 original size:7 final size:7
Alignment explanation
Indices: 39802050--39802076 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
39802040 CACCAAGAAA
39802050 AAAAAAG
1 AAAAAAG
39802057 AAAAAAG
1 AAAAAAG
39802064 AAAAAAG
1 AAAAAAG
39802071 AAAAAA
1 AAAAAA
39802077 ACAATTGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:39802534 original size:18 final size:18
Alignment explanation
Indices: 39802511--39802545 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39802501 GGTAATGAAT
*
39802511 TATAGTTTAGGTACCATA
1 TATAGTTTAAGTACCATA
39802529 TATAGTTTAAGTACCAT
1 TATAGTTTAAGTACCAT
39802546 TTGTAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (18 bp):
TATAGTTTAAGTACCATA
Found at i:39807655 original size:27 final size:26
Alignment explanation
Indices: 39807623--39807674 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
39807613 ATATAAGTTA
39807623 AAAATTAAAAATTTATTTTATTTATAC
1 AAAATTAAAAATTTATTTT-TTTATAC
***
39807650 AAAATTAAGGGTTTATTTTTTTATA
1 AAAATTAAAAATTTATTTTTTTATA
39807675 ATCTAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (26 bp):
AAAATTAAAAATTTATTTTTTTATAC
Found at i:39826703 original size:12 final size:12
Alignment explanation
Indices: 39826688--39826717 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39826678 AATAATTAAA
39826688 TAAATTAGAAAT
1 TAAATTAGAAAT
*
39826700 TAAATTGGAAAT
1 TAAATTAGAAAT
39826712 TAAATT
1 TAAATT
39826718 TGGATTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (12 bp):
TAAATTAGAAAT
Found at i:39827749 original size:18 final size:18
Alignment explanation
Indices: 39827726--39827765 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
39827716 GAAATATTTA
*
39827726 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
39827744 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
39827762 TTTT
1 TTTT
39827766 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:39827788 original size:12 final size:12
Alignment explanation
Indices: 39827767--39827800 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39827757 TATATTTTTT
*
39827767 AAAATTATATAA
1 AAAATAATATAA
39827779 AAAATAATATAA
1 AAAATAATATAA
*
39827791 AAAGTAATAT
1 AAAATAATAT
39827801 GGGCGGGTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:39829376 original size:2 final size:2
Alignment explanation
Indices: 39829369--39829393 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39829359 NNNNNNNNNN
39829369 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
39829394 GTTTTGGTAA
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:39830219 original size:21 final size:23
Alignment explanation
Indices: 39830193--39830238 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39830183 AGTTACACTC
39830193 AAGTATTA-TT-TTTGAT-AAATA
1 AAGTATTACTTGTTT-ATCAAATA
39830214 AAGTATTACTTGTTTATCAAATA
1 AAGTATTACTTGTTTATCAAATA
39830237 AA
1 AA
39830239 AGTGTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 8 0.36
22 4 0.18
23 10 0.45
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (23 bp):
AAGTATTACTTGTTTATCAAATA
Found at i:39831051 original size:21 final size:21
Alignment explanation
Indices: 39831025--39831072 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
39831015 GCATCTAATT
39831025 ATTTTTTTATAAAAATTTTA-A
1 ATTTTTTTA-AAAAATTTTATA
* *
39831046 ATTTTTTTAATAATTTTTATA
1 ATTTTTTTAAAAAATTTTATA
39831067 ATTTTT
1 ATTTTT
39831073 AAATAATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTTTTTAAAAAATTTTATA
Found at i:39841669 original size:7 final size:6
Alignment explanation
Indices: 39841656--39841716 Score: 61
Period size: 6 Copynumber: 9.8 Consensus size: 6
39841646 TTTCACTTTC
* * *
39841656 TTTCTT TTTCCTT TTTCTT TTTCTT TTT-TT TTTGTT TTGTCCT TCTCTT
1 TTTCTT TTT-CTT TTTCTT TTTCTT TTTCTT TTTCTT TT-TCTT TTTCTT
39841705 CTTTCTT TTTCT
1 -TTTCTT TTTCT
39841717 CTTTATTGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
5 5 0.11
6 27 0.59
7 14 0.30
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (6 bp):
TTTCTT
Found at i:39843674 original size:46 final size:46
Alignment explanation
Indices: 39843621--39843714 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
39843611 CCATGGAAAA
*
39843621 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAGCCATACTAAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTAAG
*
39843667 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTAAG
39843713 TT
1 TT
39843715 ATAACATTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.30
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTAAG
Found at i:39843937 original size:86 final size:86
Alignment explanation
Indices: 39843791--39843951 Score: 286
Period size: 86 Copynumber: 1.9 Consensus size: 86
39843781 GATCCTTAAA
39843791 TTGACAAGTATTTGTAAGTGCAATTGAAGCTAAATGTTGGAATAAAAGTTGATATCTGATATTGA
1 TTGACAAGTATTTGTAAGTGCAATTGAAGCTAAATGTTGGAATAAAAGTTGATATCTGATATTGA
*
39843856 GCTCGATTGAACGATTCTTAT
66 GCTCAATTGAACGATTCTTAT
** *
39843877 TTGACAAGTATTTGTAAGTGCAATTGAAGCTAAATGTTGGAATATCAGTTGATATTTGATATTGA
1 TTGACAAGTATTTGTAAGTGCAATTGAAGCTAAATGTTGGAATAAAAGTTGATATCTGATATTGA
39843942 GCTCAATTGA
66 GCTCAATTGA
39843952 GTAAATTCAT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 71 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.37
Consensus pattern (86 bp):
TTGACAAGTATTTGTAAGTGCAATTGAAGCTAAATGTTGGAATAAAAGTTGATATCTGATATTGA
GCTCAATTGAACGATTCTTAT
Found at i:39852798 original size:14 final size:14
Alignment explanation
Indices: 39852779--39852835 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
39852769 AAATAATCTA
39852779 TTATGTTAATTTTT
1 TTATGTTAATTTTT
39852793 TTATGTTAATTTTT
1 TTATGTTAATTTTT
*
39852807 TT-T-TTACTTTTT
1 TTATGTTAATTTTT
* *
39852819 TT-TGTCAATTTTA
1 TTATGTTAATTTTT
39852832 TTAT
1 TTAT
39852836 TTATATTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.30
13 9 0.24
14 17 0.46
ACGTcount: A:0.19, C:0.04, G:0.05, T:0.72
Consensus pattern (14 bp):
TTATGTTAATTTTT
Found at i:39856819 original size:18 final size:17
Alignment explanation
Indices: 39856798--39856840 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
39856788 TCAAAAAATT
39856798 TTAATTTTTATATATTTC
1 TTAATTTTTATAT-TTTC
* *
39856816 TTAAATTTTTATGTTTTG
1 TT-AATTTTTATATTTTC
39856834 TTAATTT
1 TTAATTT
39856841 GAAAATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 7 0.32
19 10 0.45
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (17 bp):
TTAATTTTTATATTTTC
Found at i:39856894 original size:27 final size:27
Alignment explanation
Indices: 39856864--39856915 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
39856854 GTTTTAAATA
39856864 ATTTTTTTAT-TTTTATAAAACTTTTGC
1 ATTTTTTTATATTTT-TAAAACTTTTGC
*
39856891 ATTTTTTTATATTTTTATAACTTTT
1 ATTTTTTTATATTTTTAAAACTTTT
39856916 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (27 bp):
ATTTTTTTATATTTTTAAAACTTTTGC
Found at i:39859087 original size:16 final size:18
Alignment explanation
Indices: 39859052--39859089 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
39859042 ATCCTTATTT
*
39859052 AAATAAAATACAGTAGTA
1 AAATAAAATACAGAAGTA
39859070 AAATAAAATA-A-AAGTA
1 AAATAAAATACAGAAGTA
39859086 AAAT
1 AAAT
39859090 CCATATAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (18 bp):
AAATAAAATACAGAAGTA
Found at i:39859954 original size:18 final size:19
Alignment explanation
Indices: 39859909--39859962 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
39859899 CAAGTTTACT
39859909 TTTATATATATATATATAC
1 TTTATATATATATATATAC
* *
39859928 TTAGATATATATTATTTATAC
1 TT-TATATATA-TATATATAC
*
39859949 TTTATATACATATA
1 TTTATATATATATA
39859963 CACATATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 5 0.18
20 13 0.46
21 10 0.36
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTATATATATATATATAC
Found at i:39863423 original size:21 final size:23
Alignment explanation
Indices: 39863381--39863423 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
39863371 TTATCATTGT
**
39863381 TATAAAAAATATTTAATTATAAC
1 TATAAAAAATATTTAAAAATAAC
39863404 TATAAAAAA-A-TTAAAAATAA
1 TATAAAAAATATTTAAAAATAA
39863424 TTATCATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
22 1 0.06
23 9 0.50
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
TATAAAAAATATTTAAAAATAAC
Found at i:39863689 original size:21 final size:21
Alignment explanation
Indices: 39863665--39863717 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
39863655 CATTGTTTCT
*
39863665 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAGTAACC
*
39863686 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
39863707 AATCTCACCGC
1 AATCTCACCGC
39863718 CACCGCTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.40, G:0.09, T:0.21
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:39868667 original size:33 final size:33
Alignment explanation
Indices: 39868630--39868710 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 33
39868620 AAATTTAAAT
39868630 TTTTTTATATTTTCAAAATATTT-AA-A-TTTTCTA
1 TTTTTTATATTTT-AAAAT-TTTAAAGAGTTTT-TA
39868663 -TTTTT-TATTTTAAAATTTTAAAGAGTTTTTA
1 TTTTTTATATTTTAAAATTTTAAAGAGTTTTTA
*
39868694 TTTTTTATAATTTAAAA
1 TTTTTTATATTTTAAAA
39868711 AAAATATATC
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
29 3 0.07
30 7 0.17
31 9 0.21
32 14 0.33
33 9 0.21
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (33 bp):
TTTTTTATATTTTAAAATTTTAAAGAGTTTTTA
Found at i:39868696 original size:31 final size:30
Alignment explanation
Indices: 39868631--39868710 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 30
39868621 AATTTAAATT
39868631 TTTTTATATTTTCAAAATATTTAAATTTTCTA
1 TTTTT-TATTTT-AAAATATTTAAATTTTCTA
39868663 TTTTTTATTTTAAAAT-TTTAAAGAGTTTT-TA
1 TTTTTTATTTTAAAATATTT-AA-A-TTTTCTA
39868694 TTTTTTATAATTTAAAA
1 TTTTTTAT--TTTAAAA
39868711 AAAATATATC
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
29 3 0.07
30 7 0.16
31 17 0.40
32 9 0.21
33 7 0.16
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (30 bp):
TTTTTTATTTTAAAATATTTAAATTTTCTA
Found at i:39871820 original size:33 final size:33
Alignment explanation
Indices: 39871783--39871863 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 33
39871773 AAATTTAAAT
39871783 TTTTTTATATTTTCAAAATATTT-AA-A-TTTTCTA
1 TTTTTTATATTTT-AAAAT-TTTAAAGAGTTTT-TA
39871816 -TTTTT-TATTTTAAAATTTTAAAGAGTTTTTA
1 TTTTTTATATTTTAAAATTTTAAAGAGTTTTTA
*
39871847 TTTTTTATAATTTAAAA
1 TTTTTTATATTTTAAAA
39871864 AAAATATATC
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
29 3 0.07
30 7 0.17
31 9 0.21
32 14 0.33
33 9 0.21
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (33 bp):
TTTTTTATATTTTAAAATTTTAAAGAGTTTTTA
Found at i:39871849 original size:31 final size:30
Alignment explanation
Indices: 39871784--39871863 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 30
39871774 AATTTAAATT
39871784 TTTTTATATTTTCAAAATATTTAAATTTTCTA
1 TTTTT-TATTTT-AAAATATTTAAATTTTCTA
39871816 TTTTTTATTTTAAAAT-TTTAAAGAGTTTT-TA
1 TTTTTTATTTTAAAATATTT-AA-A-TTTTCTA
39871847 TTTTTTATAATTTAAAA
1 TTTTTTAT--TTTAAAA
39871864 AAAATATATC
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
29 3 0.07
30 7 0.16
31 17 0.40
32 9 0.21
33 7 0.16
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (30 bp):
TTTTTTATTTTAAAATATTTAAATTTTCTA
Found at i:39872443 original size:19 final size:19
Alignment explanation
Indices: 39872430--39872467 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
39872420 AAAAAAACCT
39872430 GAAAAATGAAAAAAAAAAA
1 GAAAAATGAAAAAAAAAAA
*
39872449 GAGAAATGAAAAAAAAAAA
1 GAAAAATGAAAAAAAAAAA
39872468 CTAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (19 bp):
GAAAAATGAAAAAAAAAAA
Found at i:39872465 original size:24 final size:25
Alignment explanation
Indices: 39872429--39872478 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
39872419 AAAAAAAACC
39872429 TGAAAAATGAAAAAAAAAAAGAGAAA
1 TGAAAAA-GAAAAAAAAAAAGAGAAA
**
39872455 TGAAAAA-AAAAAACTAAAGAGAAA
1 TGAAAAAGAAAAAAAAAAAGAGAAA
39872479 AAAAAGTCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.68
26 7 0.32
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.08
Consensus pattern (25 bp):
TGAAAAAGAAAAAAAAAAAGAGAAA
Found at i:39872792 original size:21 final size:21
Alignment explanation
Indices: 39872768--39872807 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39872758 TTTATCAGTA
* *
39872768 ATTCCATTTCATTTATATTAT
1 ATTCCATATCATATATATTAT
*
39872789 ATTCTATATCATATATATT
1 ATTCCATATCATATATATT
39872808 TTAAAATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTCCATATCATATATATTAT
Found at i:39883759 original size:14 final size:15
Alignment explanation
Indices: 39883730--39883761 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
39883720 AAAAACATCA
39883730 TAATTTTATCTATTT
1 TAATTTTATCTATTT
39883745 TAATTTTAT-TATTT
1 TAATTTTATCTATTT
39883759 TAA
1 TAA
39883762 CTATAACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTATCTATTT
Found at i:39885591 original size:124 final size:124
Alignment explanation
Indices: 39885370--39885745 Score: 538
Period size: 124 Copynumber: 3.0 Consensus size: 124
39885360 TTAGGGTTTT
* * *
39885370 TAGGTCTTGGAAGAAAT-AATTTTGAGTTGACGTTTCTGATCAAATAGTATAAAATCGCTTCTAG
1 TAGGTCATGGAAGAAATAAATTTT--TTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
* * * * *
39885434 CAGGATGCTATTTGAGAAGAATTTGTGAAATCGCACCCTTGTGGACGCGCATTTGCTACAG
64 CAAGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
*
39885495 TAGGTCATGGAAGAAATAAATTTTTTTGACGTTTTTGAGCAAATAGTATAAAATCGCTTCTAGCA
1 TAGGTCATGGAAGAAATAAATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
* ** *
39885560 TGATGCTATTTGAGATCAATTTGTAAAATCGCGCCCTCGTGGTCGCGCTTTTGCTACAG
66 AGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* * * *
39885619 TCGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCTCTTCTAACA
1 TAGGTCATGGAAGAAATAAATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
* * *
39885684 AGATGCTATTTGAAAAGAATTTTTGAAAATCGCGCCCTCGTGGACGCGTTTTTGCTACAG
66 AGATGCTATTTGAGAAGAATTTGT-AAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
39885744 TA
1 TA
39885746 ACATGTTTGG
Statistics
Matches: 224, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
124 168 0.75
125 50 0.22
126 6 0.03
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.34
Consensus pattern (124 bp):
TAGGTCATGGAAGAAATAAATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
AGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:39888919 original size:22 final size:22
Alignment explanation
Indices: 39888893--39889253 Score: 351
Period size: 22 Copynumber: 16.3 Consensus size: 22
39888883 GTTAGTAAAA
*
39888893 AAGTTAAGGGTTTAGTGTTTTT
1 AAGTTAAGGGTTTAGGGTTTTT
*
39888915 AAGTTAAGGGTTTAGTGTTTTT
1 AAGTTAAGGGTTTAGGGTTTTT
*
39888937 AAGTTAAGGGTTTAGTGTTTTT
1 AAGTTAAGGGTTTAGGGTTTTT
*
39888959 AAGTTAAGGGTTTAGTGTTTTT
1 AAGTTAAGGGTTTAGGGTTTTT
*
39888981 AAGTTAAGGGTTTAGTGTTTTT
1 AAGTTAAGGGTTTAGGGTTTTT
*
39889003 AAGTTAAGGGTTTAGTGTTTTT
1 AAGTTAAGGGTTTAGGGTTTTT
39889025 AAGTTAAGGG-TTA-GGTTTTT
1 AAGTTAAGGGTTTAGGGTTTTT
** *
39889045 AA-TTAATTAGATTAGGGTTTTT
1 AAGTTAA-GGGTTTAGGGTTTTT
* *
39889067 AAGTTTAGGGTTTAGAGTTTTT
1 AAGTTAAGGGTTTAGGGTTTTT
* * *
39889089 AATTTAATTAGG-TTAGAGTTTTT
1 AAGTTAA--GGGTTTAGGGTTTTT
* *
39889112 AAGTTAATTAGG-CTAGGGTTTTT
1 AAGTTAA--GGGTTTAGGGTTTTT
*
39889135 AAGTTAAGGGGGTTAGGGTTTTT
1 AAGTTAA-GGGTTTAGGGTTTTT
* * *
39889158 AAATTTAGAGTTTAGGGTTTTT
1 AAGTTAAGGGTTTAGGGTTTTT
* **
39889180 AATTTAATTAGTTTAGGGTTTTT
1 AAGTTAA-GGGTTTAGGGTTTTT
* *
39889203 AATTTAATTAGG-TTAGGGTTTTT
1 AAGTTAA--GGGTTTAGGGTTTTT
39889226 AAGATT-AGGGTTTAGGGTTTTT
1 AAG-TTAAGGGTTTAGGGTTTTT
39889248 AA-TTAA
1 AAGTTAA
39889254 ATTAGGTTAG
Statistics
Matches: 299, Mismatches: 28, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
19 4 0.01
20 11 0.04
21 9 0.03
22 178 0.60
23 91 0.30
24 6 0.02
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (22 bp):
AAGTTAAGGGTTTAGGGTTTTT
Found at i:39889104 original size:23 final size:23
Alignment explanation
Indices: 39889033--39889267 Score: 220
Period size: 23 Copynumber: 10.4 Consensus size: 23
39889023 TTAAGTTAAG
39889033 GGTTA-GGTTTTTAA-TTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
* *
39889054 GATTAGGGTTTTTAAGTTT-A--G
1 GGTTAGGGTTTTTAA-TTTAATTA
*
39889075 GGTTTAGAGTTTTTAATTTAATTA
1 GG-TTAGGGTTTTTAATTTAATTA
* *
39889099 GGTTAGAGTTTTTAAGTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
* * ***
39889122 GGCTAGGGTTTTTAAGTTAAGGG
1 GGTTAGGGTTTTTAATTTAATTA
*
39889145 GGTTAGGGTTTTTAAATTT-A-GA
1 GGTTAGGGTTTTT-AATTTAATTA
*
39889167 GTTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
*
39889190 GTTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
*
39889213 GGTTAGGGTTTTTAA---GATTA
1 GGTTAGGGTTTTTAATTTAATTA
*
39889233 GGGTTTAGGGTTTTTAATTAAATTA
1 -GG-TTAGGGTTTTTAATTTAATTA
39889258 GGTTAGGGTT
1 GGTTAGGGTT
39889268 AGGGTTAGGG
Statistics
Matches: 180, Mismatches: 19, Indels: 28
0.79 0.08 0.12
Matches are distributed among these distances:
20 4 0.02
21 15 0.08
22 49 0.27
23 98 0.54
24 10 0.06
25 4 0.02
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (23 bp):
GGTTAGGGTTTTTAATTTAATTA
Found at i:39889217 original size:68 final size:67
Alignment explanation
Indices: 39888902--39889267 Score: 331
Period size: 68 Copynumber: 5.5 Consensus size: 67
39888892 AAAGTTAAGG
* * * * * *
39888902 GTTTAGTGTTTTTAAGTTAA--GGGTTTAGTGTTTTTAAGTTAAGGGTTTAGTGTTTTTAAGTTA
1 GTTTAGGGTTTTTAAGTTAATTAGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAATTT
*
39888965 AGG
65 AGA
* * * * * *
39888968 GTTTAGTGTTTTTAAGTTAA--GGGTTTAGTGTTTTTAAGTTAAGGGTTTAGTGTTTTTAAGTTA
1 GTTTAGGGTTTTTAAGTTAATTAGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAATTT
39889031 AG-
65 AGA
* * * *
39889033 GGTTA-GGTTTTTAA-TTAATTAGATTAGGGTTTTTAAGTTTAGGGTTTAGAGTTTTT-AATTTA
1 GTTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAATTT-
*
39889095 ATTA
65 A-GA
* * * *
39889099 GGTTAGAGTTTTTAAGTTAATTAGGCTAGGGTTTTTAAGTTAAGGGGGTTAGGGTTTTTAAATTT
1 GTTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAA-GGGTTTAGGGTTTTTAAATTT
39889164 AGA
65 AGA
* * * *
39889167 GTTTAGGGTTTTTAATTTAATTAGTTTAGGGTTTTTAATTTAATTAGG-TTAGGGTTTTTAAGA-
1 GTTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTTAGGGTTTTTAA-AT
*
39889230 TTAGG
63 TTAGA
39889235 GTTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTT
1 GTTTAGGGTTTTTAAGTT-AATTAGGTTAGGGTT
39889268 AGGGTTAGGG
Statistics
Matches: 261, Mismatches: 27, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
63 7 0.03
64 39 0.15
65 5 0.02
66 70 0.27
67 10 0.04
68 108 0.41
69 17 0.07
70 5 0.02
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (67 bp):
GTTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAATTTA
GA
Found at i:39889267 original size:91 final size:91
Alignment explanation
Indices: 39888953--39889249 Score: 281
Period size: 91 Copynumber: 3.3 Consensus size: 91
39888943 AGGGTTTAGT
* * * * * * *
39888953 GTTTTTAAGTTAA-GGGTTTAGTGTTTTT-AAGTTAAGGGTTTAGTGTTTTTAAGTTAA--GGGT
1 GTTTTTAAGTTAAGGGGGTTAGGGTTTTTAAAATT-AGAGTTTAGGGTTTTTAATTTAATTAGG-
* * *
39889014 TTAGTGTTTTTAAGTTAA--GGGTTA-G
64 TTAGAGTTTTTAAGTTAATTAGGCTAGG
*** * ** * *
39889039 GTTTTTAA-TTAATTAGATTAGGGTTTTTAAGTTTAGGGTTTAGAGTTTTTAATTTAATTAGGTT
1 GTTTTTAAGTTAAGGGGGTTAGGGTTTTTAAAATTAGAGTTTAGGGTTTTTAATTTAATTAGGTT
39889103 AGAGTTTTTAAGTTAATTAGGCTAGG
66 AGAGTTTTTAAGTTAATTAGGCTAGG
* *
39889129 GTTTTTAAGTTAAGGGGGTTAGGGTTTTTAAATTTAGAGTTTAGGGTTTTTAATTTAATTAGTTT
1 GTTTTTAAGTTAAGGGGGTTAGGGTTTTTAAAATTAGAGTTTAGGGTTTTTAATTTAATTAGGTT
* * *
39889194 AGGGTTTTTAATTTAATTAGGTTAGG
66 AGAGTTTTTAAGTTAATTAGGCTAGG
*
39889220 GTTTTTAAGATT-A-GGGTTTAGGGTTTTTAA
1 GTTTTTAAG-TTAAGGGGGTTAGGGTTTTTAA
39889250 TTAAATTAGG
Statistics
Matches: 178, Mismatches: 24, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
85 4 0.02
86 40 0.22
87 20 0.11
88 2 0.01
89 4 0.02
90 25 0.14
91 81 0.46
92 2 0.01
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (91 bp):
GTTTTTAAGTTAAGGGGGTTAGGGTTTTTAAAATTAGAGTTTAGGGTTTTTAATTTAATTAGGTT
AGAGTTTTTAAGTTAATTAGGCTAGG
Found at i:39889568 original size:35 final size:35
Alignment explanation
Indices: 39889230--39889560 Score: 653
Period size: 35 Copynumber: 9.4 Consensus size: 35
39889220 GTTTTTAAGA
39889230 TTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGG
39889266 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
39889301 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
39889336 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
39889371 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
39889406 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
39889441 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
39889476 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
39889511 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
39889546 TTAGGGTTAGGGTTT
1 TTAGGGTTAGGGTTT
39889561 GCAATTAATG
Statistics
Matches: 295, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
35 289 0.98
36 6 0.02
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.43
Consensus pattern (35 bp):
TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
Found at i:39889688 original size:21 final size:20
Alignment explanation
Indices: 39889642--39889689 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
39889632 ATTTCTCTAG
* *
39889642 CTTCCGGCGGGGTTGTTGTT
1 CTTCCGGCGGGGTTCTGGTT
*
39889662 CCTCCGGCGGGGATTCTGGTT
1 CTTCCGGCGGGG-TTCTGGTT
39889683 CTTCCGG
1 CTTCCGG
39889690 TACGACATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.02, C:0.27, G:0.38, T:0.33
Consensus pattern (20 bp):
CTTCCGGCGGGGTTCTGGTT
Found at i:39889972 original size:18 final size:18
Alignment explanation
Indices: 39889949--39889984 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
39889939 CGAAAAAGGG
*
39889949 TACATATAAGGGTTAGGA
1 TACATATAAGGGCTAGGA
39889967 TACATATAAGGGCTAGGA
1 TACATATAAGGGCTAGGA
39889985 AACGCACCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25
Consensus pattern (18 bp):
TACATATAAGGGCTAGGA
Found at i:39890644 original size:7 final size:7
Alignment explanation
Indices: 39890634--39890658 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39890624 TTATATACAT
39890634 AATACTA
1 AATACTA
39890641 AATACTA
1 AATACTA
39890648 AATACTA
1 AATACTA
39890655 AATA
1 AATA
39890659 TCAATCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:39900668 original size:1 final size:1
Alignment explanation
Indices: 39900664--39900697 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
39900654 CAATATGTAG
**
39900664 AAAAAAAAAAAAAAAAAAGGAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
39900698 GCCAATAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:39900669 original size:54 final size:54
Alignment explanation
Indices: 39900610--39900736 Score: 191
Period size: 54 Copynumber: 2.4 Consensus size: 54
39900600 AAATTAAGCA
* **
39900610 AAAAAAAAAAAAAAAAAAGGAGATCAAAAAAAAAGCCAAAAAACCAATATGTAG
1 AAAAAAAAAAAAAAAAAAGGAAAAAAAAAAAAAAGCCAAAAAACCAATATGTAG
*
39900664 AAAAAAAAAAAAAAAAAAGGAAAAAAAAAAAAAAGCCAATAAACCAATATGTAG
1 AAAAAAAAAAAAAAAAAAGGAAAAAAAAAAAAAAGCCAAAAAACCAATATGTAG
* * *
39900718 TAACAAATAAAAAAAAAAG
1 AAAAAAAAAAAAAAAAAAG
39900737 TGAATCTAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.75, C:0.08, G:0.09, T:0.08
Consensus pattern (54 bp):
AAAAAAAAAAAAAAAAAAGGAAAAAAAAAAAAAAGCCAAAAAACCAATATGTAG
Found at i:39900687 original size:16 final size:16
Alignment explanation
Indices: 39900668--39900698 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
39900658 ATGTAGAAAA
39900668 AAAAAAAAAAAAAAGG
1 AAAAAAAAAAAAAAGG
39900684 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
39900699 CCAATAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGG
Found at i:39904964 original size:22 final size:21
Alignment explanation
Indices: 39904929--39904986 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
39904919 AAAGGGTATC
* * *
39904929 TACAAATTAAATCTCTGAGAT
1 TACAAATCATATCTCTAAGAT
39904950 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
*
39904973 TACATATCATATCT
1 TACAAATCATATCT
39904987 AAGATTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.55
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Done.