Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold391
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: 290649
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
File 2 of 3
Found at i:111438 original size:24 final size:21
Alignment explanation
Indices: 111388--111428 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
111378 TTAATTTAAT
*
111388 TGTTATAATATTTAATCTCAC
1 TGTTATAATAATTAATCTCAC
*
111409 TATTATAATAATTAATCTCA
1 TGTTATAATAATTAATCTCA
111429 TCATCGTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.46
Consensus pattern (21 bp):
TGTTATAATAATTAATCTCAC
Found at i:115667 original size:16 final size:17
Alignment explanation
Indices: 115646--115681 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
115636 AGATGAACAC
115646 AAAGAA-CAAAACCCAG
1 AAAGAATCAAAACCCAG
*
115662 AAAGAATCAAGACCCAG
1 AAAGAATCAAAACCCAG
115679 AAA
1 AAA
115682 AAAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.61, C:0.22, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAGAATCAAAACCCAG
Found at i:118677 original size:18 final size:18
Alignment explanation
Indices: 118629--118685 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
118619 AATGTGTAAT
*
118629 TTTTTATTATTATAATTTA
1 TTTTTACTATTATAA-TTA
118648 TTTTT-C--TT-TAATTA
1 TTTTTACTATTATAATTA
*
118662 TTTTTACTATTATAATTG
1 TTTTTACTATTATAATTA
118680 TTTTTA
1 TTTTTA
118686 TAATTTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.25
15 4 0.12
16 2 0.06
17 2 0.06
18 11 0.34
19 5 0.16
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTTACTATTATAATTA
Found at i:119195 original size:55 final size:54
Alignment explanation
Indices: 119111--119221 Score: 159
Period size: 55 Copynumber: 2.0 Consensus size: 54
119101 GATAAAAAAA
*
119111 ATTCTAAGTATCATCAACCAACTGCTGTGAGCAAAGCACTGCGTAGCTGCAAATG
1 ATTCTAAGTATCATCAACCAACTGCTGTGAGC-AAGCACTGCGTACCTGCAAATG
* * * * *
119166 ATTCTGAGTATCATCAACCTATTGCTGTGAGCAAGCATTGCGTACCTGTAAATG
1 ATTCTAAGTATCATCAACCAACTGCTGTGAGCAAGCACTGCGTACCTGCAAATG
119220 AT
1 AT
119222 GATGTCACGA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
54 21 0.42
55 29 0.58
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.28
Consensus pattern (54 bp):
ATTCTAAGTATCATCAACCAACTGCTGTGAGCAAGCACTGCGTACCTGCAAATG
Found at i:119774 original size:26 final size:26
Alignment explanation
Indices: 119743--119795 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
119733 CAATTTATGA
* *
119743 AAACCTCTTATCTTAATTATTATTTT
1 AAACCTATTATCTTAATAATTATTTT
*
119769 AAACCTATTATTTTAATAATTATTTT
1 AAACCTATTATCTTAATAATTATTTT
119795 A
1 A
119796 GACTATGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (26 bp):
AAACCTATTATCTTAATAATTATTTT
Found at i:119808 original size:25 final size:26
Alignment explanation
Indices: 119755--119809 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
119745 ACCTCTTATC
* * *
119755 TTAATTATTATTTTAAACCTATTATT
1 TTAATAATTATTTTAAACCTATGAGT
*
119781 TTAATAATTATTTTAGA-CTATGAGT
1 TTAATAATTATTTTAAACCTATGAGT
119806 TTAA
1 TTAA
119810 ATTTTTTAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (26 bp):
TTAATAATTATTTTAAACCTATGAGT
Found at i:120282 original size:32 final size:32
Alignment explanation
Indices: 120246--120327 Score: 110
Period size: 32 Copynumber: 2.6 Consensus size: 32
120236 AGCACAATGT
* ** *
120246 AATATTAGACATAATTTTTTATAAATTTGATA
1 AATATTAAACATAATTACTAATAAATTTGATA
* *
120278 AATATTAAACAAAATTACTAATAAATTTGATG
1 AATATTAAACATAATTACTAATAAATTTGATA
120310 AATATTAAACATAATTAC
1 AATATTAAACATAATTAC
120328 ACATAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (32 bp):
AATATTAAACATAATTACTAATAAATTTGATA
Found at i:120349 original size:32 final size:32
Alignment explanation
Indices: 120278--120350 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
120268 AAATTTGATA
* *
120278 AATATTAAACAAAATTACTAATAAATTTGATG
1 AATATTAAACAAAATTACTAATAAAATTAATG
*
120310 AATATTAAACATAATTAC-ACATAAAATTAAT-
1 AATATTAAACAAAATTACTA-ATAAAATTAATG
120341 AATCATTAAA
1 AAT-ATTAAA
120351 AATTTTAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (32 bp):
AATATTAAACAAAATTACTAATAAAATTAATG
Found at i:122025 original size:12 final size:12
Alignment explanation
Indices: 122008--122034 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
121998 AAATAAATAT
122008 AAATTATATAAA
1 AAATTATATAAA
122020 AAATTATATAAA
1 AAATTATATAAA
122032 AAA
1 AAA
122035 ATAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTATATAAA
Found at i:122195 original size:55 final size:54
Alignment explanation
Indices: 122108--122218 Score: 150
Period size: 55 Copynumber: 2.0 Consensus size: 54
122098 GATAAAAAAA
* *
122108 ATTCTAAGTATCATCAACCAACTGCTGTGAGCAAAGCACTGCGTAGCTGCAAATG
1 ATTCTAAGTATCATCAACCAACTGCTGCGAGC-AAGCACTGCGTACCTGCAAATG
* * * * *
122163 ATTCTGAGTATCATCAACCTATTGCTGCGAGCAAGCATTGCGTACCTGTAAATG
1 ATTCTAAGTATCATCAACCAACTGCTGCGAGCAAGCACTGCGTACCTGCAAATG
122217 AT
1 AT
122219 GATGTCATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
54 21 0.43
55 28 0.57
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Consensus pattern (54 bp):
ATTCTAAGTATCATCAACCAACTGCTGCGAGCAAGCACTGCGTACCTGCAAATG
Found at i:122632 original size:35 final size:30
Alignment explanation
Indices: 122591--122660 Score: 77
Period size: 35 Copynumber: 2.2 Consensus size: 30
122581 TTAGATTAGT
122591 ATATTTTGATTAAAATTATTATTTAATTAATAAAA
1 ATATTTTGATTAAAA-TA-TA--TAATT-ATAAAA
* *
122626 ATATTTTTATTTAAATATATAATTATAAAA
1 ATATTTTGATTAAAATATATAATTATAAAA
122656 ATATT
1 ATATT
122661 AATATTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 11 0.33
31 5 0.15
33 2 0.06
34 2 0.06
35 13 0.39
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (30 bp):
ATATTTTGATTAAAATATATAATTATAAAA
Found at i:122642 original size:20 final size:20
Alignment explanation
Indices: 122601--122639 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
122591 ATATTTTGAT
*
122601 TAAAATTATTATTTAATTAA
1 TAAAAATATTATTTAATTAA
*
122621 TAAAAATATT-TTTATTTAA
1 TAAAAATATTATTTAATTAA
122640 ATATATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAAATATTATTTAATTAA
Found at i:122791 original size:12 final size:12
Alignment explanation
Indices: 122771--122817 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
122761 GAAAAACCTC
*
122771 TTATCTTAATTA
1 TTATTTTAATTA
122783 TTATTTTAAACTTA
1 TTATTTT-AA-TTA
*
122797 TTATTTTAATAA
1 TTATTTTAATTA
122809 TTATTTTAA
1 TTATTTTAA
122818 ACTATGAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 17 0.55
13 4 0.13
14 10 0.32
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATTTTAATTA
Found at i:122793 original size:26 final size:26
Alignment explanation
Indices: 122764--122819 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
122754 AATTTATGAA
* *
122764 AAACCTCTTATCTTAATTATTATTTT
1 AAACCTATTATCTTAATAATTATTTT
* *
122790 AAACTTATTATTTTAATAATTATTTT
1 AAACCTATTATCTTAATAATTATTTT
122816 AAAC
1 AAAC
122820 TATGAGTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.52
Consensus pattern (26 bp):
AAACCTATTATCTTAATAATTATTTT
Found at i:122799 original size:14 final size:14
Alignment explanation
Indices: 122780--122820 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
122770 CTTATCTTAA
122780 TTATTATTTTAAAC
1 TTATTATTTTAAAC
122794 TTATTATTTT-AA-
1 TTATTATTTTAAAC
*
122806 TAATTATTTTAAAC
1 TTATTATTTTAAAC
122820 T
1 T
122821 ATGAGTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 9 0.38
13 4 0.17
14 11 0.46
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTATTTTAAAC
Found at i:123226 original size:2 final size:2
Alignment explanation
Indices: 123219--123246 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
123209 TAAAATCTAC
123219 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
123247 AAAGTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:124646 original size:48 final size:44
Alignment explanation
Indices: 124530--124650 Score: 118
Period size: 45 Copynumber: 2.6 Consensus size: 44
124520 GTTATGCTTC
* * *
124530 GTTGCCGAAGTTCCCTTTGTTGTTGACGGTTCCCTTCCCCCCTTT
1 GTTGCCAAAGTTCCC-GTGTTGTTGACAGTTCCCTTCCCCCCTTT
* * *
124575 GTTGCCGAAA-TTCCCAGTATTGTTGATAGTTCCTTTCCCAGCCCCTTT
1 GTTGCC-AAAGTTCCC-GTGTTGTTGACAGTTCCCTT-CC--CCCCTTT
124623 GTTGCCAAAGTTCCCGTCGTTGTTGACA
1 GTTGCCAAAGTTCCCGT-GTTGTTGACA
124651 ACCGGCGTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
45 26 0.43
46 4 0.07
47 5 0.08
48 26 0.43
ACGTcount: A:0.13, C:0.30, G:0.20, T:0.37
Consensus pattern (44 bp):
GTTGCCAAAGTTCCCGTGTTGTTGACAGTTCCCTTCCCCCCTTT
Found at i:124780 original size:2 final size:2
Alignment explanation
Indices: 124767--124802 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
124757 CATGGTTTCA
*
124767 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
124803 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:125442 original size:13 final size:14
Alignment explanation
Indices: 125424--125456 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
125414 CACTCAAAGA
125424 AAATAAAAATA-TT
1 AAATAAAAATATTT
*
125437 AAATAAAATTATTT
1 AAATAAAAATATTT
125451 AAATAA
1 AAATAA
125457 TTATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATAAAAATATTT
Found at i:127616 original size:2 final size:2
Alignment explanation
Indices: 127609--127640 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
127599 AAAATTTTAA
127609 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
127641 TCCTAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:127926 original size:21 final size:20
Alignment explanation
Indices: 127894--127939 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
127884 TATTGGATTG
127894 ATATTTTTTAA-T--TAAAA
1 ATATTTTTTAATTAATAAAA
*
127911 TTATTTTTTAATTAATAAAA
1 ATATTTTTTAATTAATAAAA
127931 ATATTTTTT
1 ATATTTTTT
127940 TATTTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 10 0.42
18 1 0.04
20 13 0.54
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATTTTTTAATTAATAAAA
Found at i:127935 original size:20 final size:17
Alignment explanation
Indices: 127894--127952 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 17
127884 TATTGGATTG
127894 ATATTTTTTAATTAAAA
1 ATATTTTTTAATTAAAA
*
127911 TTATTTTTTAATTAATAAAA
1 ATATTTTTTAA-T--TAAAA
* *
127931 ATATTTTTTTATT-TAA
1 ATATTTTTTAATTAAAA
127947 ATATTT
1 ATATTT
127953 AATTATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 8 0.23
17 11 0.31
18 1 0.03
19 1 0.03
20 14 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATTTTTTAATTAAAA
Found at i:127941 original size:21 final size:21
Alignment explanation
Indices: 127901--127939 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
127891 TTGATATTTT
*
127901 TTAATTAAAATTATTTTTTAA
1 TTAATAAAAATTATTTTTTAA
127922 TTAATAAAAA-TATTTTTT
1 TTAATAAAAATTATTTTTT
127940 TATTTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAATAAAAATTATTTTTTAA
Found at i:127946 original size:21 final size:21
Alignment explanation
Indices: 127900--127946 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
127890 ATTGATATTT
*
127900 TTTAATTAAAATTATTTTTTA
1 TTTAATAAAAATTATTTTTTA
*
127921 ATTAATAAAAA-TATTTTTTTA
1 TTTAATAAAAATTA-TTTTTTA
127942 TTTAA
1 TTTAA
127947 ATATTTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAATAAAAATTATTTTTTA
Found at i:127964 original size:16 final size:16
Alignment explanation
Indices: 127917--127966 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
127907 AAAATTATTT
127917 TTTAATTAATAAAAATA
1 TTTAATT-ATAAAAATA
** **
127934 TTTTTTTATTTAAATA
1 TTTAATTATAAAAATA
127950 TTTAATTATAAAAATA
1 TTTAATTATAAAAATA
127966 T
1 T
127967 AAATTTTACT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAATTATAAAAATA
Found at i:128174 original size:16 final size:16
Alignment explanation
Indices: 128139--128187 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
128129 AAATTAATTT
*
128139 ATATAATTATTCTTAAAA
1 ATATAA-TATT-TAAAAA
128157 ATATAATATTTAAAAA
1 ATATAATATTTAAAAA
* *
128173 ATTTAAAATTTAAAA
1 ATATAATATTTAAAA
128188 TTTATAACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 4 0.14
18 6 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATAATATTTAAAAA
Found at i:128707 original size:3 final size:3
Alignment explanation
Indices: 128699--128740 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
128689 TTTGACTAGA
128699 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
128741 TTAAGATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:129402 original size:45 final size:44
Alignment explanation
Indices: 129346--129720 Score: 286
Period size: 45 Copynumber: 8.3 Consensus size: 44
129336 GTCATGCTTG
* * ** *
129346 GTTGCCGAAGTTTCCTTTGTTGTTGACAGTTCCCTTTCCTCCTTT
1 GTTGCCAAAGTTTCCATTGTTGTTGACAGTT-CCTCCCCTCCTTC
* * * *
129391 GTTGCCAAAGTTTCCGA-TGTTGTTGACAATTCCTTTCTCC-CATTT
1 GTTGCCAAAGTTTCC-ATTGTTGTTGACAGTTCC--TCCCCTCCTTC
* * * * *
129436 GTTGCCAAAGTTCCCAGTGTTGCTGACAGTGCCCACCCCTCCTTC
1 GTTGCCAAAGTTTCCATTGTTGTTGACAGT-TCCTCCCCTCCTTC
* *
129481 ATTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCTTG
1 GTTGCCAAAGTTTCCATTGTTGTTGACAGTTCCT-CCCCTCCTTC
* *** * * * ** *
129526 GTTGCCAAAGTTACCACCATTGTTGACAATTCCTTTCCTTATTTT
1 GTTGCCAAAGTTTCCATTGTTGTTGACAGTTCC-TCCCCTCCTTC
* * * ** *
129571 GTTGCCAAAGTTCCCAGTGTAGTTGACAGCACCCACCCCTCCTTC
1 GTTGCCAAAGTTTCCATTGTTGTTGACAG-TTCCTCCCCTCCTTC
* * *
129616 ATTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCCTG
1 GTTGCCAAAGTTTCCATTGTTGTTGACAGTTCCT-CCCCTCCTTC
* * ** *
129661 GTTGCCAAAGTTACCACTACTGTTGACAGTTCCTTGCCCTCCTTC
1 GTTGCCAAAGTTTCCATTGTTGTTGACAGTTCC-TCCCCTCCTTC
129706 GTTGCCAAAGTTTCC
1 GTTGCCAAAGTTTCC
129721 TGCGTTATCG
Statistics
Matches: 256, Mismatches: 63, Indels: 22
0.75 0.18 0.06
Matches are distributed among these distances:
44 10 0.04
45 236 0.92
46 10 0.04
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.36
Consensus pattern (44 bp):
GTTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTCCCCTCCTTC
Found at i:129589 original size:135 final size:135
Alignment explanation
Indices: 129347--129717 Score: 498
Period size: 135 Copynumber: 2.7 Consensus size: 135
129337 TCATGCTTGG
* * ** * * *
129347 TTGCCGAAGTTTCCTTTGTTGTTGACAGTTCCCT-TTCCTCCTTTGTTGCCAAAGTTTCCGA-TG
1 TTGCCAAAGTTTCCATTGTTGTTGACAGTT-CCTGCCCCTCCTTGGTTGCCAAAGTTACC-ACTA
* **
129410 TTGTTGACAATTCCTTTCTCCCATTTGTTGCCAAAGTTCCCAGTGTTGCTGACAGTGCCCACCCC
64 TTGTTGACAATTCCTTTCTCCCATTTGTTGCCAAAGTTCCCAGTGTAGCTGACAGCACCCACCCC
129475 TCCTTCA
129 TCCTTCA
*
129482 TTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCTTGGTTGCCAAAGTTACCACCATT
1 TTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCTTGGTTGCCAAAGTTACCACTATT
** *
129547 GTTGACAATTCCTTTC-CTTATTTTGTTGCCAAAGTTCCCAGTGTAGTTGACAGCACCCACCCCT
66 GTTGACAATTCCTTTCTCCCA-TTTGTTGCCAAAGTTCCCAGTGTAGCTGACAGCACCCACCCCT
129611 CCTTCA
130 CCTTCA
* *
129617 TTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCCTGGTTGCCAAAGTTACCACTACT
1 TTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCTTGGTTGCCAAAGTTACCACTATT
* * * *
129682 GTTGACAGTTCCTTGC-CCTCCTTCGTTGCCAAAGTT
66 GTTGACAATTCCTTTCTCC-CATTTGTTGCCAAAGTT
129718 TCCTGCGTTA
Statistics
Matches: 209, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
134 6 0.03
135 203 0.97
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.36
Consensus pattern (135 bp):
TTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCTTGGTTGCCAAAGTTACCACTATT
GTTGACAATTCCTTTCTCCCATTTGTTGCCAAAGTTCCCAGTGTAGCTGACAGCACCCACCCCTC
CTTCA
Found at i:130711 original size:27 final size:28
Alignment explanation
Indices: 130655--130733 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
130645 ATAATTTACG
*
130655 TAAATTAAAAATAAAATATAATAATTAAAT
1 TAAA-TAAATATAAAATATAATAA-TAAAT
130685 TAAATAAATATAAAATAT-ATAGA-AAAT
1 TAAATAAATATAAAATATAATA-ATAAAT
*
130712 TATATAAAAATATAAAAT-TAAT
1 TA-A-ATAAATATAAAATATAAT
130734 TAATTTTATA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
27 6 0.14
28 5 0.12
29 28 0.65
30 4 0.09
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (28 bp):
TAAATAAATATAAAATATAATAATAAAT
Found at i:131322 original size:20 final size:20
Alignment explanation
Indices: 131281--131319 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
131271 ATGCTTTGAT
*
131281 TAAAATTATTATTTAATTAA
1 TAAAAATATTATTTAATTAA
*
131301 TAAAAATATT-TTTATTTAA
1 TAAAAATATTATTTAATTAA
131320 ATATATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAAATATTATTTAATTAA
Found at i:131474 original size:26 final size:26
Alignment explanation
Indices: 131443--131498 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
131433 CAATTTATGA
* *
131443 AAACCTCTTATCTTAATTATTATTTT
1 AAACCTATTATCTTAATAATTATTTT
*
131469 AAACCTATTATTTTAATAATTATTTT
1 AAACCTATTATCTTAATAATTATTTT
131495 AAAC
1 AAAC
131499 AATGAGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (26 bp):
AAACCTATTATCTTAATAATTATTTT
Found at i:131986 original size:32 final size:32
Alignment explanation
Indices: 131945--132049 Score: 106
Period size: 32 Copynumber: 3.3 Consensus size: 32
131935 AGCACAATGC
** * *
131945 AATATTAAACATAATTTTTTATAAATTTGATA
1 AATATTAAACATAATTACTAATAAATTTAATA
* *
131977 AATATTAAACAAAATTACTAATAAATTTAATG
1 AATATTAAACATAATTACTAATAAATTTAATA
* *
132009 AATATTAGACATAATTAC-ATATAAAATTAAT-
1 AATATTAAACATAATTACTA-ATAAATTTAATA
132040 AATCATTAAA
1 AAT-ATTAAA
132050 AATTTTAGCT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
31 4 0.07
32 57 0.93
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (32 bp):
AATATTAAACATAATTACTAATAAATTTAATA
Found at i:133283 original size:48 final size:44
Alignment explanation
Indices: 133190--133310 Score: 127
Period size: 45 Copynumber: 2.6 Consensus size: 44
133180 GTTATGCTTC
* * *
133190 GTTGCCGAAGTTCCCTTTGTTGTTGACGGTTCCCTTCCCCCCTTT
1 GTTGCCGAAATTCCC-GTGTTGTTGACAGTTCCCTTCCCCCCTTT
* *
133235 GTTGCCGAAATTCCCAGTATTGTTGACAGTTCCTTTCCCAGCCCCTTT
1 GTTGCCGAAATTCCC-GTGTTGTTGACAGTTCCCTT-CC--CCCCTTT
133283 GTTGCC-AAAGTTCCCGTCGTTGTTGACA
1 GTTGCCGAAA-TTCCCGT-GTTGTTGACA
133311 ACCGGCGTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
45 30 0.47
46 2 0.03
47 5 0.08
48 27 0.42
ACGTcount: A:0.13, C:0.31, G:0.20, T:0.36
Consensus pattern (44 bp):
GTTGCCGAAATTCCCGTGTTGTTGACAGTTCCCTTCCCCCCTTT
Found at i:134087 original size:13 final size:14
Alignment explanation
Indices: 134069--134101 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
134059 CACTCAAAGA
134069 AAATAAAAATA-TT
1 AAATAAAAATATTT
*
134082 AAATAAAATTATTT
1 AAATAAAAATATTT
134096 AAATAA
1 AAATAA
134102 TTATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATAAAAATATTT
Found at i:134400 original size:2 final size:2
Alignment explanation
Indices: 134393--134463 Score: 92
Period size: 2 Copynumber: 35.5 Consensus size: 2
134383 CAATTCCACA
* *
134393 AT AT AT AT AT AT AT AT AT AT AT AT AT A- ACT ACC AC A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T AT AT AT AT AT
134435 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
134464 CTTTTTTTAT
Statistics
Matches: 65, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
1 2 0.03
2 60 0.92
3 3 0.05
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:136083 original size:28 final size:28
Alignment explanation
Indices: 136052--136106 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
136042 AATTTATATG
136052 AATAAA-ATAAAATATAATAATTAAATTA
1 AATAAATATAAAATAT-ATAATTAAATTA
* *
136080 AATAAATATAAATTATATAATTTAATT
1 AATAAATATAAAATATATAATTAAATT
136107 TTATATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
AATAAATATAAAATATATAATTAAATTA
Found at i:136101 original size:23 final size:24
Alignment explanation
Indices: 136038--136104 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
136028 ATATATATAT
* * *
136038 ATATAATTTATATGAATAAAATAA
1 ATATAAATTATATAAATTAAATAA
*
136062 A-ATATAATAAT-TAAATTAAATAA
1 ATATA-AATTATATAAATTAAATAA
*
136085 ATATAAATTATATAATTTAA
1 ATATAAATTATATAAATTAA
136105 TTTTATATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
23 19 0.56
24 15 0.44
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (24 bp):
ATATAAATTATATAAATTAAATAA
Found at i:136649 original size:20 final size:22
Alignment explanation
Indices: 136612--136653 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
136602 TATTTTTATT
*
136612 TAAATATTTAATTGTAAAAATA
1 TAAATATTTAATTATAAAAATA
136634 TAAAT-TTT-ATTATAAAAATA
1 TAAATATTTAATTATAAAAATA
136654 AATTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 3 0.16
22 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAATATTTAATTATAAAAATA
Found at i:136828 original size:15 final size:15
Alignment explanation
Indices: 136808--136847 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
136798 TTATATAATT
136808 ATATTTAAAAACATA
1 ATATTTAAAAACATA
**
136823 ATATTTAAAAATTTA
1 ATATTTAAAAACATA
*
136838 AAATTTAAAA
1 ATATTTAAAA
136848 TTCAAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATTTAAAAACATA
Found at i:136842 original size:7 final size:7
Alignment explanation
Indices: 136825--136865 Score: 64
Period size: 7 Copynumber: 5.7 Consensus size: 7
136815 AAAACATAAT
136825 ATTTAAAA
1 ATTT-AAA
136833 ATTTAAA
1 ATTTAAA
136840 ATTTAAA
1 ATTTAAA
*
136847 ATTCAAA
1 ATTTAAA
136854 ATTTAAA
1 ATTTAAA
136861 ATTTA
1 ATTTA
136866 TAACAATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 27 0.87
8 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (7 bp):
ATTTAAA
Found at i:138183 original size:135 final size:135
Alignment explanation
Indices: 138007--138338 Score: 461
Period size: 135 Copynumber: 2.5 Consensus size: 135
137997 TCATGCTTGG
* ** * * **
138007 TTGCCGAAGTTTCCTATTGTTGTTGACAGTTCCCT-TTCCTCCTTTGTTGCCAAAGTTTCTGTTG
1 TTGCCAAAGTTTCC-ATTGTTGTTGACAGTT-CCTGCCCCTCCTTGGTTGCCAAAGTTACTGTCA
* * **
138071 TTGTTGACAATTCCTTTCCTCCA-TTTGTTGCCAAAGTTCCGAGTGTTGCTGACAGTGCCCAACC
64 TTGTTGACAATTCCTTTCC-CCATTTTGTTGCCAAAGTTCCCAGTGTAGCTGACAGCACCCAACC
138135 CTCCTTCA
128 CTCCTTCA
***
138143 TTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCTTGGTTGCCAAAGTTACCACCATT
1 TTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCTTGGTTGCCAAAGTTACTGTCATT
* * *
138208 GTTGACAATTCCTTTCCCTATTTTGTTGCCAAAGTTCCCAGTGTAGTTGACAGCACCCACCCCTC
66 GTTGACAATTCCTTTCCCCATTTTGTTGCCAAAGTTCCCAGTGTAGCTGACAGCACCCAACCCTC
138273 CTTCA
131 CTTCA
*
138278 TTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCCTGGTTGCCAAAGTTACTGT
1 TTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCTTGGTTGCCAAAGTTACTGT
138339 AGAGTAAAGA
Statistics
Matches: 173, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
134 5 0.03
135 155 0.90
136 13 0.08
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (135 bp):
TTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCTTGGTTGCCAAAGTTACTGTCATT
GTTGACAATTCCTTTCCCCATTTTGTTGCCAAAGTTCCCAGTGTAGCTGACAGCACCCAACCCTC
CTTCA
Found at i:138316 original size:45 final size:44
Alignment explanation
Indices: 138006--138333 Score: 264
Period size: 45 Copynumber: 7.3 Consensus size: 44
137996 GTCATGCTTG
* **
138006 GTTGCCGAAGTTTCCTATTGTTGTTGACAGTTCCCTTTCCTCCTTT
1 GTTGCCAAAGTTTCC-ATTGTTGTTGACAGTT-CCTCCCCTCCTTT
** * **
138052 GTTGCCAAAGTTTCTGTTGTTGTTGACAATTCCTTTCCTCCATTT
1 GTTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTCCCCTCC-TTT
* * * *
138097 GTTGCCAAAG-TTCCGAGTGTTGCTGACAGTGCC-CAACCCTCCTTC
1 GTTGCCAAAGTTTCC-ATTGTTGTTGACAGTTCCTC--CCCTCCTTT
* *
138142 ATTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCTTG
1 GTTGCCAAAGTTTCCATTGTTGTTGACAGTTCCT-CCCCTCCTTT
* *** * * **
138187 GTTGCCAAAGTTACCACCATTGTTGACAATTCCTTTCCCTATTTT
1 GTTGCCAAAGTTTCCATTGTTGTTGACAGTTCC-TCCCCTCCTTT
* * * ** * *
138232 GTTGCCAAAGTTCCCAGTGTAGTTGACAGCACCCACCCCTCCTTC
1 GTTGCCAAAGTTTCCATTGTTGTTGACAG-TTCCTCCCCTCCTTT
* * *
138277 ATTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCCTG
1 GTTGCCAAAGTTTCCATTGTTGTTGACAGTTCCT-CCCCTCCTTT
138322 GTTGCCAAAGTT
1 GTTGCCAAAGTT
138334 ACTGTAGAGT
Statistics
Matches: 221, Mismatches: 51, Indels: 21
0.75 0.17 0.07
Matches are distributed among these distances:
44 15 0.07
45 180 0.81
46 25 0.11
47 1 0.00
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (44 bp):
GTTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTCCCCTCCTTT
Found at i:138602 original size:34 final size:34
Alignment explanation
Indices: 138563--138790 Score: 243
Period size: 34 Copynumber: 7.4 Consensus size: 34
138553 ATATACATGT
*
138563 TAACACACCTAACATTCTCACCAAATAAATCACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
*
138597 TAACACACCTAACATTCTCACC-TA-ACA-CACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
*
138628 T---A-A-C--A--TTCTCACCAAACACATCACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
138653 TAACACACCTAACATTCTCACCAAATACATCACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
*
138687 TAACACACCTAACATTCTCACC-TA-ACA-CACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
*
138718 T---A-A-C--A--TTCTCACCAAACACATCACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
138743 TAACACACCTAACATTCTCACCAAATACATCACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
138777 TAACACACCTAACA
1 TAACACACCTAACA
138791 AAGAAATTAA
Statistics
Matches: 163, Mismatches: 7, Indels: 48
0.75 0.03 0.22
Matches are distributed among these distances:
22 16 0.10
23 2 0.01
24 8 0.05
25 10 0.06
26 2 0.01
27 2 0.01
28 4 0.02
29 2 0.01
30 2 0.01
31 10 0.06
32 7 0.04
33 2 0.01
34 96 0.59
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (34 bp):
TAACACACCTAACATTCTCACCAAATACATCACC
Found at i:138620 original size:22 final size:22
Alignment explanation
Indices: 138592--138737 Score: 151
Period size: 22 Copynumber: 6.5 Consensus size: 22
138582 ACCAAATAAA
138592 TCACCTAACACACCTAACATTC
1 TCACCTAACACACCTAACATTC
138614 TCACCTAACACACCTAACATTC
1 TCACCTAACACACCTAACATTC
*
138636 TCACCAAACACATCACCTAACA---
1 TCACC-TA-ACA-CACCTAACATTC
*
138658 -CACCTAACATTCTCACC-AA-ATAC
1 TCACCTAACA----CACCTAACATTC
138681 ATCACCTAACACACCTAACATTC
1 -TCACCTAACACACCTAACATTC
138704 TCACCTAACACACCTAACATTC
1 TCACCTAACACACCTAACATTC
*
138726 TCACCAAACACA
1 TCACCTAACACA
138738 TCACCTAACA
Statistics
Matches: 107, Mismatches: 4, Indels: 26
0.78 0.03 0.19
Matches are distributed among these distances:
19 3 0.03
20 2 0.02
21 10 0.09
22 67 0.63
23 4 0.04
24 3 0.03
25 18 0.17
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (22 bp):
TCACCTAACACACCTAACATTC
Found at i:138651 original size:56 final size:56
Alignment explanation
Indices: 138564--138737 Score: 232
Period size: 56 Copynumber: 3.1 Consensus size: 56
138554 TATACATGTT
* * *
138564 AACACACCTAACATTCTCACCAAATAAATCACCTAACACACCTAACATTCTCACCT
1 AACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACCA
138620 AACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACCAA
1 AACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC-A
*
138677 ATACATCACCTAACA----CACCTAACATTC-TCACCTAACACACCTAACATTCTCACCA
1 A-ACA-CACCTAACATTCTCACCAAACA--CATCACCTAACACACCTAACATTCTCACCA
138732 AACACA
1 AACACA
138738 TCACCTAACA
Statistics
Matches: 109, Mismatches: 4, Indels: 13
0.87 0.03 0.10
Matches are distributed among these distances:
53 2 0.02
54 3 0.03
55 10 0.09
56 80 0.73
57 2 0.02
58 3 0.03
59 9 0.08
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (56 bp):
AACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACCA
Found at i:138716 original size:90 final size:90
Alignment explanation
Indices: 138563--138790 Score: 447
Period size: 90 Copynumber: 2.5 Consensus size: 90
138553 ATATACATGT
*
138563 TAACACACCTAACATTCTCACCAAATAAATCACCTAACACACCTAACATTCTCACCTAACACACC
1 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACCTAACACACC
138628 TAACATTCTCACCAAACACATCACC
66 TAACATTCTCACCAAACACATCACC
138653 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACCTAACACACC
1 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACCTAACACACC
138718 TAACATTCTCACCAAACACATCACC
66 TAACATTCTCACCAAACACATCACC
138743 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACA
1 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACA
138791 AAGAAATTAA
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 137 1.00
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (90 bp):
TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACCTAACACACC
TAACATTCTCACCAAACACATCACC
Found at i:138739 original size:56 final size:55
Alignment explanation
Indices: 138592--138764 Score: 226
Period size: 56 Copynumber: 3.1 Consensus size: 55
138582 ACCAAATAAA
* * * **
138592 TCACCTAACACACCTAACATTCTCACC-TAACA-CACCTAACATTCTCACCAA-ACAC
1 TCACCTAACACACCTAACATTCTCACCAAAACATCACCTAACA--CAC-CTAACATTC
138647 ATCACCTAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTC
1 -TCACCTAACACACCTAACATTCTCACCAAA-ACATCACCTAACACACCTAACATTC
138704 TCACCTAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTC
1 TCACCTAACACACCTAACATTCTCACCAAA-ACATCACCTAACACACCTAACATTC
138760 TCACC
1 TCACC
138765 AAATACATCA
Statistics
Matches: 107, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
56 90 0.84
57 5 0.05
58 3 0.03
59 9 0.08
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (55 bp):
TCACCTAACACACCTAACATTCTCACCAAAACATCACCTAACACACCTAACATTC
Found at i:143519 original size:22 final size:22
Alignment explanation
Indices: 143488--143633 Score: 136
Period size: 22 Copynumber: 6.5 Consensus size: 22
143478 ACCAAATACA
*
143488 TCACCTAACACACCTAACATTC
1 TCACCAAACACACCTAACATTC
143510 TCACCAAACACACCTAACATTC
1 TCACCAAACACACCTAACATTC
**
143532 TCACCAAACACATCACCTAACACAC
1 TCACC-AA-ACA-CACCTAACATTC
* ** * *
143557 -CTAACATTCTCACC-AA-ATAC
1 TC-ACCAAACACACCTAACATTC
*
143577 ATCACCTAACACACCTAACATTC
1 -TCACCAAACACACCTAACATTC
*
143600 TCACCTAACACACCTAACATTC
1 TCACCAAACACACCTAACATTC
143622 TCACCAAACACA
1 TCACCAAACACA
143634 TCACCTAACA
Statistics
Matches: 101, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
20 3 0.03
21 9 0.09
22 66 0.65
23 6 0.06
24 5 0.05
25 12 0.12
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.19
Consensus pattern (22 bp):
TCACCAAACACACCTAACATTC
Found at i:143546 original size:56 final size:56
Alignment explanation
Indices: 143460--143633 Score: 250
Period size: 56 Copynumber: 3.1 Consensus size: 56
143450 TATACATGTT
*
143460 AACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACCA
1 AACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACCA
143516 AACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACCAA
1 AACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC-A
*
143573 ATACATCACCTAACA----CACCTAACATTC-TCACCTAACACACCTAACATTCTCACCA
1 A-ACA-CACCTAACATTCTCACCAAACA--CATCACCTAACACACCTAACATTCTCACCA
143628 AACACA
1 AACACA
143634 TCACCTAACA
Statistics
Matches: 111, Mismatches: 2, Indels: 13
0.88 0.02 0.10
Matches are distributed among these distances:
53 2 0.02
54 3 0.03
55 10 0.09
56 81 0.73
57 3 0.03
58 3 0.03
59 9 0.08
ACGTcount: A:0.41, C:0.40, G:0.00, T:0.19
Consensus pattern (56 bp):
AACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACCA
Found at i:143548 original size:34 final size:34
Alignment explanation
Indices: 143510--143611 Score: 177
Period size: 34 Copynumber: 3.0 Consensus size: 34
143500 CCTAACATTC
*
143510 TCACCAAACACACCTAACATTCTCACCAAACACA
1 TCACCTAACACACCTAACATTCTCACCAAACACA
*
143544 TCACCTAACACACCTAACATTCTCACCAAATACA
1 TCACCTAACACACCTAACATTCTCACCAAACACA
*
143578 TCACCTAACACACCTAACATTCTCACCTAACACA
1 TCACCTAACACACCTAACATTCTCACCAAACACA
143612 CCTAACATTC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.41, C:0.40, G:0.00, T:0.19
Consensus pattern (34 bp):
TCACCTAACACACCTAACATTCTCACCAAACACA
Found at i:143612 original size:90 final size:90
Alignment explanation
Indices: 143459--143686 Score: 438
Period size: 90 Copynumber: 2.5 Consensus size: 90
143449 ATATACATGT
143459 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACCAAACACACC
1 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACCAAACACACC
143524 TAACATTCTCACCAAACACATCACC
66 TAACATTCTCACCAAACACATCACC
*
143549 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACCTAACACACC
1 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACCAAACACACC
143614 TAACATTCTCACCAAACACATCACC
66 TAACATTCTCACCAAACACATCACC
*
143639 TAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACA
1 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACA
143687 AAGAAATTAA
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 136 1.00
ACGTcount: A:0.41, C:0.40, G:0.00, T:0.19
Consensus pattern (90 bp):
TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACCAAACACACC
TAACATTCTCACCAAACACATCACC
Found at i:143635 original size:56 final size:55
Alignment explanation
Indices: 143488--143667 Score: 251
Period size: 56 Copynumber: 3.2 Consensus size: 55
143478 ACCAAATACA
*
143488 TCACCTAACACACCTAACATTCTCACC-AAACA-CACCTAACATTCTCACCAAACA--C
1 TCACCTAACACACCTAACATTCTCACCAAAACATCACCTAACA----CACCTAACATTC
143543 ATCACCTAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTC
1 -TCACCTAACACACCTAACATTCTCACCAAA-ACATCACCTAACACACCTAACATTC
143600 TCACCTAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTC
1 TCACCTAACACACCTAACATTCTCACCAAA-ACATCACCTAACACACCTAACATTC
*
143656 TCACCAAACACA
1 TCACCTAACACA
143668 TCACCTAACA
Statistics
Matches: 116, Mismatches: 3, Indels: 10
0.90 0.02 0.08
Matches are distributed among these distances:
55 8 0.07
56 93 0.80
57 3 0.03
58 3 0.03
59 9 0.08
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.19
Consensus pattern (55 bp):
TCACCTAACACACCTAACATTCTCACCAAAACATCACCTAACACACCTAACATTC
Found at i:143642 original size:34 final size:34
Alignment explanation
Indices: 143600--143686 Score: 174
Period size: 34 Copynumber: 2.6 Consensus size: 34
143590 CCTAACATTC
143600 TCACCTAACACACCTAACATTCTCACCAAACACA
1 TCACCTAACACACCTAACATTCTCACCAAACACA
143634 TCACCTAACACACCTAACATTCTCACCAAACACA
1 TCACCTAACACACCTAACATTCTCACCAAACACA
143668 TCACCTAACACACCTAACA
1 TCACCTAACACACCTAACA
143687 AAGAAATTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.17
Consensus pattern (34 bp):
TCACCTAACACACCTAACATTCTCACCAAACACA
Found at i:144710 original size:18 final size:16
Alignment explanation
Indices: 144687--144725 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 16
144677 AGGTAAATCA
144687 AAAATTAAATATAATAAT
1 AAAATTAAATA-AAT-AT
144705 AAAATTAAATAAATAT
1 AAAATTAAATAAATAT
144721 AAAAT
1 AAAAT
144726 ATATAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.33
17 3 0.14
18 11 0.52
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATTAAATAAATAT
Found at i:145347 original size:20 final size:20
Alignment explanation
Indices: 145306--145344 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
145296 ATGCTTTGAT
*
145306 TAAAATTATTATTTAATTAA
1 TAAAAATATTATTTAATTAA
*
145326 TAAAAATATT-TTTATTTAA
1 TAAAAATATTATTTAATTAA
145345 ATATATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAAATATTATTTAATTAA
Found at i:145499 original size:26 final size:26
Alignment explanation
Indices: 145468--145523 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
145458 CAATTTATGA
* *
145468 AAACCTCTTATCTTAATTATTATTTT
1 AAACCTATTATCTTAATAATTATTTT
*
145494 AAACCTATTATTTTAATAATTATTTT
1 AAACCTATTATCTTAATAATTATTTT
145520 AAAC
1 AAAC
145524 AATGAGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (26 bp):
AAACCTATTATCTTAATAATTATTTT
Found at i:146011 original size:32 final size:32
Alignment explanation
Indices: 145970--146074 Score: 106
Period size: 32 Copynumber: 3.3 Consensus size: 32
145960 AGCACAATGC
** * *
145970 AATATTAAACATAATTTTTTATAAATTTGATA
1 AATATTAAACATAATTACTAATAAATTTAATA
* *
146002 AATATTAAACAAAATTACTAATAAATTTAATG
1 AATATTAAACATAATTACTAATAAATTTAATA
* *
146034 AATATTAGACATAATTAC-ATATAAAATTAAT-
1 AATATTAAACATAATTACTA-ATAAATTTAATA
146065 AATCATTAAA
1 AAT-ATTAAA
146075 AATTTTAGCT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
31 4 0.07
32 57 0.93
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (32 bp):
AATATTAAACATAATTACTAATAAATTTAATA
Found at i:147301 original size:48 final size:44
Alignment explanation
Indices: 147208--147328 Score: 127
Period size: 45 Copynumber: 2.6 Consensus size: 44
147198 GTTATGCTTC
* * *
147208 GTTGCCGAAGTTCCCTTTGTTGTTGACGGTTCCCTTCCCCCCTTT
1 GTTGCCGAAATTCCC-GTGTTGTTGACAGTTCCCTTCCCCCCTTT
* *
147253 GTTGCCGAAATTCCCAGTATTGTTGACAGTTCCTTTCCCAGCCCCTTT
1 GTTGCCGAAATTCCC-GTGTTGTTGACAGTTCCCTT-CC--CCCCTTT
147301 GTTGCC-AAAGTTCCCGTTGTTGTTGACA
1 GTTGCCGAAA-TTCCCG-TGTTGTTGACA
147329 ACCGGCGTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
45 30 0.47
46 2 0.03
47 4 0.06
48 28 0.44
ACGTcount: A:0.13, C:0.30, G:0.20, T:0.37
Consensus pattern (44 bp):
GTTGCCGAAATTCCCGTGTTGTTGACAGTTCCCTTCCCCCCTTT
Found at i:148116 original size:13 final size:14
Alignment explanation
Indices: 148098--148130 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
148088 CACTCAAAGA
148098 AAATAAAAATA-TT
1 AAATAAAAATATTT
*
148111 AAATAAAATTATTT
1 AAATAAAAATATTT
148125 AAATAA
1 AAATAA
148131 TTATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATAAAAATATTT
Found at i:150101 original size:28 final size:30
Alignment explanation
Indices: 150048--150106 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
150038 ATAATTTACA
150048 TAAATAAAAAATAAAATATTATAATTAAAT
1 TAAATAAAAAATAAAATATTATAATTAAAT
* * *
150078 TAAAT-AAATATAAATTA-TATAATTTAAT
1 TAAATAAAAAATAAAATATTATAATTAAAT
150106 T
1 T
150107 TCATATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 11 0.42
29 10 0.38
30 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
TAAATAAAAAATAAAATATTATAATTAAAT
Found at i:150330 original size:2 final size:2
Alignment explanation
Indices: 150323--150348 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
150313 AAAATTTTAA
150323 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
150349 TCTCAATAAT
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:150652 original size:20 final size:20
Alignment explanation
Indices: 150611--150662 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
150601 TATTCGATTG
150611 ATATTTTTTAA-T--TAAAA
1 ATATTTTTTAATTAATAAAA
*
150628 TTATTTTTTAATTAATAAAA
1 ATATTTTTTAATTAATAAAA
*
150648 ATATTTTTTATTTAA
1 ATATTTTTTAATTAA
150663 ATATTTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 10 0.34
18 1 0.03
20 18 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTTTTTAATTAATAAAA
Found at i:150680 original size:16 final size:16
Alignment explanation
Indices: 150634--150682 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
150624 AAAATTATTT
150634 TTTAATTAATAAAAATA
1 TTTAATT-ATAAAAATA
* **
150651 TTT-TTTATTTAAATA
1 TTTAATTATAAAAATA
150666 TTTAATTATAAAAATA
1 TTTAATTATAAAAATA
150682 T
1 T
150683 AAATTTTACT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
15 10 0.40
16 12 0.48
17 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTAATTATAAAAATA
Found at i:150892 original size:16 final size:16
Alignment explanation
Indices: 150857--150905 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
150847 AAATTAATTT
*
150857 ATATAATTATTCTTAAAA
1 ATATAA-TATT-TAAAAA
150875 ATATAATATTTAAAAA
1 ATATAATATTTAAAAA
* *
150891 ATTTAAAATTTAAAA
1 ATATAATATTTAAAA
150906 TTTATAACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 4 0.14
18 6 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATAATATTTAAAAA
Found at i:151426 original size:3 final size:3
Alignment explanation
Indices: 151418--151459 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
151408 TTTGACTAGA
151418 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
151460 TTGAGATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:152121 original size:45 final size:44
Alignment explanation
Indices: 152065--152439 Score: 277
Period size: 45 Copynumber: 8.3 Consensus size: 44
152055 GTCATGCTTG
* * ** *
152065 GTTGCCGAAGTTTCCTTTGTTGTTGACAGTTCCCTTTCCTCCTTT
1 GTTGCCAAAGTTTCCATTGTTGTTGACAGTT-CCTCCCCTCCTTC
* * * *
152110 GTTGCCAAAGTTTCCGA-TGTTGTTGACAATTCCTTTCTCC-CATTT
1 GTTGCCAAAGTTTCC-ATTGTTGTTGACAGTTCC--TCCCCTCCTTC
* * * * *
152155 GTTGCCAAAGTTCCCAGTGTTGCTGACAGTGCCCACCCCTCCTTC
1 GTTGCCAAAGTTTCCATTGTTGTTGACAGT-TCCTCCCCTCCTTC
* *
152200 ATTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCTTG
1 GTTGCCAAAGTTTCCATTGTTGTTGACAGTTCCT-CCCCTCCTTC
* *** * * * ** *
152245 GTTGCCAAAGTTACCACCATTGTTGACAATTCCTTTCCTTATTTT
1 GTTGCCAAAGTTTCCATTGTTGTTGACAGTTCC-TCCCCTCCTTC
* * * ** *
152290 GTTGCCAAAGTTCCCAGTGTAGTTGACAGCACCCACCCCTCCTTC
1 GTTGCCAAAGTTTCCATTGTTGTTGACAG-TTCCTCCCCTCCTTC
* * *
152335 ATTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCCTG
1 GTTGCCAAAGTTTCCATTGTTGTTGACAGTTCCT-CCCCTCCTTC
* * ** * *
152380 GTTGCCAAAGTTACCACTACTGTTGATAGTTCCTTGCCCTCCTTC
1 GTTGCCAAAGTTTCCATTGTTGTTGACAGTTCC-TCCCCTCCTTC
152425 GTTGCCAAAGTTTCC
1 GTTGCCAAAGTTTCC
152440 TGCGTTATCG
Statistics
Matches: 255, Mismatches: 64, Indels: 22
0.75 0.19 0.06
Matches are distributed among these distances:
44 10 0.04
45 235 0.92
46 10 0.04
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.36
Consensus pattern (44 bp):
GTTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTCCCCTCCTTC
Found at i:152308 original size:135 final size:135
Alignment explanation
Indices: 152066--152436 Score: 489
Period size: 135 Copynumber: 2.7 Consensus size: 135
152056 TCATGCTTGG
* * ** * * *
152066 TTGCCGAAGTTTCCTTTGTTGTTGACAGTTCCCT-TTCCTCCTTTGTTGCCAAAGTTTCCGA-TG
1 TTGCCAAAGTTTCCATTGTTGTTGACAGTT-CCTGCCCCTCCTTGGTTGCCAAAGTTACC-ACTA
* **
152129 TTGTTGACAATTCCTTTCTCCCATTTGTTGCCAAAGTTCCCAGTGTTGCTGACAGTGCCCACCCC
64 TTGTTGACAATTCCTTTCTCCCATTTGTTGCCAAAGTTCCCAGTGTAGCTGACAGCACCCACCCC
152194 TCCTTCA
129 TCCTTCA
*
152201 TTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCTTGGTTGCCAAAGTTACCACCATT
1 TTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCTTGGTTGCCAAAGTTACCACTATT
** *
152266 GTTGACAATTCCTTTC-CTTATTTTGTTGCCAAAGTTCCCAGTGTAGTTGACAGCACCCACCCCT
66 GTTGACAATTCCTTTCTCCCA-TTTGTTGCCAAAGTTCCCAGTGTAGCTGACAGCACCCACCCCT
152330 CCTTCA
130 CCTTCA
* *
152336 TTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCCTGGTTGCCAAAGTTACCACTACT
1 TTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCTTGGTTGCCAAAGTTACCACTATT
* * * * *
152401 GTTGATAGTTCCTTGC-CCTCCTTCGTTGCCAAAGTT
66 GTTGACAATTCCTTTCTCC-CATTTGTTGCCAAAGTT
152437 TCCTGCGTTA
Statistics
Matches: 208, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
134 6 0.03
135 202 0.97
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.36
Consensus pattern (135 bp):
TTGCCAAAGTTTCCATTGTTGTTGACAGTTCCTGCCCCTCCTTGGTTGCCAAAGTTACCACTATT
GTTGACAATTCCTTTCTCCCATTTGTTGCCAAAGTTCCCAGTGTAGCTGACAGCACCCACCCCTC
CTTCA
Found at i:153430 original size:27 final size:28
Alignment explanation
Indices: 153374--153452 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
153364 ATAATTTACG
*
153374 TAAATTAAAAATAAAATATAATAATTAAAT
1 TAAA-TAAATATAAAATATAATAA-TAAAT
153404 TAAATAAATATAAAATAT-ATAGA-AAAT
1 TAAATAAATATAAAATATAATA-ATAAAT
*
153431 TATATAAAAATATAAAAT-TAAT
1 TA-A-ATAAATATAAAATATAAT
153453 TAATTTTATA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
27 6 0.14
28 5 0.12
29 28 0.65
30 4 0.09
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (28 bp):
TAAATAAATATAAAATATAATAATAAAT
Found at i:154041 original size:20 final size:20
Alignment explanation
Indices: 154000--154038 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
153990 ATGCTTTGAT
*
154000 TAAAATTATTATTTAATTAA
1 TAAAAATATTATTTAATTAA
*
154020 TAAAAATATT-TTTATTTAA
1 TAAAAATATTATTTAATTAA
154039 ATATATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAAATATTATTTAATTAA
Found at i:154193 original size:26 final size:26
Alignment explanation
Indices: 154162--154217 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
154152 CAATTTATGA
* *
154162 AAACCTCTTATCTTAATTATTATTTT
1 AAACCTATTATCTTAATAATTATTTT
*
154188 AAACCTATTATTTTAATAATTATTTT
1 AAACCTATTATCTTAATAATTATTTT
154214 AAAC
1 AAAC
154218 AATGAGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (26 bp):
AAACCTATTATCTTAATAATTATTTT
Found at i:154705 original size:32 final size:32
Alignment explanation
Indices: 154664--154768 Score: 106
Period size: 32 Copynumber: 3.3 Consensus size: 32
154654 AGCACAATGC
** * *
154664 AATATTAAACATAATTTTTTATAAATTTGATA
1 AATATTAAACATAATTACTAATAAATTTAATA
* *
154696 AATATTAAACAAAATTACTAATAAATTTAATG
1 AATATTAAACATAATTACTAATAAATTTAATA
* *
154728 AATATTAGACATAATTAC-ATATAAAATTAAT-
1 AATATTAAACATAATTACTA-ATAAATTTAATA
154759 AATCATTAAA
1 AAT-ATTAAA
154769 AATTTTAGCT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
31 4 0.07
32 57 0.93
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (32 bp):
AATATTAAACATAATTACTAATAAATTTAATA
Found at i:156002 original size:48 final size:44
Alignment explanation
Indices: 155909--156029 Score: 127
Period size: 45 Copynumber: 2.6 Consensus size: 44
155899 GTTATGCTTC
* * *
155909 GTTGCCGAAGTTCCCTTTGTTGTTGACGGTTCCCTTCCCCCCTTT
1 GTTGCCGAAATTCCC-GTGTTGTTGACAGTTCCCTTCCCCCCTTT
* *
155954 GTTGCCGAAATTCCCAGTATTGTTGACAGTTCCTTTCCCAGCCCCTTT
1 GTTGCCGAAATTCCC-GTGTTGTTGACAGTTCCCTT-CC--CCCCTTT
156002 GTTGCC-AAAGTTCCCGTCGTTGTTGACA
1 GTTGCCGAAA-TTCCCGT-GTTGTTGACA
156030 ACCGGCGTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
45 30 0.47
46 2 0.03
47 5 0.08
48 27 0.42
ACGTcount: A:0.13, C:0.31, G:0.20, T:0.36
Consensus pattern (44 bp):
GTTGCCGAAATTCCCGTGTTGTTGACAGTTCCCTTCCCCCCTTT
Found at i:156806 original size:13 final size:14
Alignment explanation
Indices: 156788--156820 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
156778 CACTCAAAGA
156788 AAATAAAAATA-TT
1 AAATAAAAATATTT
*
156801 AAATAAAATTATTT
1 AAATAAAAATATTT
156815 AAATAA
1 AAATAA
156821 TTATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATAAAAATATTT
Found at i:158544 original size:20 final size:20
Alignment explanation
Indices: 158516--158555 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
158506 CATTTATGAG
*
158516 ATTTGATAATATAATTGTAT
1 ATTTAATAATATAATTGTAT
158536 ATTTAATAATATAATTGTAT
1 ATTTAATAATATAATTGTAT
158556 TGATCATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
ATTTAATAATATAATTGTAT
Found at i:158765 original size:24 final size:23
Alignment explanation
Indices: 158722--158770 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
158712 AATGAATAAA
*
158722 AAATAAAATATAACAAATAAATT
1 AAATAAAATAAAACAAATAAATT
* *
158745 AAATAAATATAAAACATATAATTT
1 AAATAAA-ATAAAACAAATAAATT
158769 AA
1 AA
158771 TTTTATACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATAAAATAAAACAAATAAATT
Found at i:158823 original size:14 final size:14
Alignment explanation
Indices: 158804--158831 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
158794 ATCTTTTTAA
158804 AAAAATTAAAATTC
1 AAAAATTAAAATTC
158818 AAAAATTAAAATTC
1 AAAAATTAAAATTC
158832 TAACTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAAATTAAAATTC
Found at i:159313 original size:32 final size:34
Alignment explanation
Indices: 159274--159337 Score: 89
Period size: 32 Copynumber: 1.9 Consensus size: 34
159264 AAAATTATTT
*
159274 TTTAATTAATAAAAA-AT-ATTTTTATT-TAAATA
1 TTTAATT-ATAAAAATATAAATTTTATTATAAATA
159306 TTTAATTATAAAAATATAAATTTTATTATAAA
1 TTTAATTATAAAAATATAAATTTTATTATAAA
159338 AATAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 7 0.25
32 9 0.32
33 8 0.29
34 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (34 bp):
TTTAATTATAAAAATATAAATTTTATTATAAATA
Found at i:159333 original size:20 final size:22
Alignment explanation
Indices: 159300--159341 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
159290 TATTTTTATT
159300 TAAATATTTAATTATAAAAATA
1 TAAATATTTAATTATAAAAATA
159322 TAAAT-TTT-ATTATAAAAATA
1 TAAATATTTAATTATAAAAATA
159342 ATTTTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.60
21 3 0.15
22 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATATTTAATTATAAAAATA
Found at i:159529 original size:16 final size:16
Alignment explanation
Indices: 159494--159542 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
159484 AAATTAATTT
*
159494 ATATAATTATTTTTAAAA
1 ATATAA-TA-TTTAAAAA
159512 ATATAATATTTAAAAA
1 ATATAATATTTAAAAA
* *
159528 ATTTAAAATTTAAAA
1 ATATAATATTTAAAA
159543 TTTATAACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 20 0.71
17 2 0.07
18 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATAATATTTAAAAA
Found at i:160064 original size:3 final size:3
Alignment explanation
Indices: 160056--160091 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
160046 TTTGACTAGA
*
160056 AAT AAT AAT AAT AAT CAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
160092 TTGAGATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:160529 original size:2 final size:2
Alignment explanation
Indices: 160522--160567 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
160512 GTTCCACTCT
160522 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
160564 TA TA
1 TA TA
160568 ACAATTGCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:161073 original size:24 final size:26
Alignment explanation
Indices: 161046--161100 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 26
161036 AATAGTAAAC
161046 AAATAATAAGTT-AATTTAAA-TTTT
1 AAATAATAAGTTAAATTTAAATTTTT
*
161070 AAAT-A-AATTTAAATTTAAATTTTT
1 AAATAATAAGTTAAATTTAAATTTTT
161094 AAATAAT
1 AAATAAT
161101 TTTAAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 4 0.15
23 9 0.35
24 12 0.46
25 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
AAATAATAAGTTAAATTTAAATTTTT
Found at i:161078 original size:17 final size:16
Alignment explanation
Indices: 161058--161089 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
161048 ATAATAAGTT
161058 AATTTAAATTTTAAATA
1 AATTTAAA-TTTAAATA
161075 AATTTAAATTTAAAT
1 AATTTAAATTTAAAT
161090 TTTTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Found at i:161086 original size:23 final size:24
Alignment explanation
Indices: 161058--161107 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
161048 ATAATAAGTT
161058 AATTTAAA-TTTTAAATAAATTTA
1 AATTTAAATTTTTAAATAAATTTA
*
161081 AATTTAAATTTTTAAATAATTTTA
1 AATTTAAATTTTTAAATAAATTTA
161105 AAT
1 AAT
161108 ATTCAAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AATTTAAATTTTTAAATAAATTTA
Found at i:161265 original size:5 final size:5
Alignment explanation
Indices: 161255--161280 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
161245 ATAATTTTTT
161255 ATTTA ATTTA ATTTA ATTTA ATTTA A
1 ATTTA ATTTA ATTTA ATTTA ATTTA A
161281 AATATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTTA
Found at i:161331 original size:49 final size:48
Alignment explanation
Indices: 161239--161357 Score: 125
Period size: 50 Copynumber: 2.4 Consensus size: 48
161229 TCTTCGAATC
* * * *
161239 TTAAATATAATTTTTTATTTAATTTAATTTAATTTAAT-TTAAAATATTTT
1 TTAAAAATAA-TTTTTATTTAATTTAATTTAA-TAAATATAAAAATA-TTA
161289 TTAAAAATAATTTTTATTTAAATTTAATTATAA-AAATATAAAAATATTA
1 TTAAAAATAATTTTTATTT-AATTTAATT-TAATAAATATAAAAATATTA
*
161338 ATATAAAATAATTTTTATTT
1 TTA-AAAATAATTTTTATTT
161358 TTATTATTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
49 16 0.27
50 41 0.68
51 3 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (48 bp):
TTAAAAATAATTTTTATTTAATTTAATTTAATAAATATAAAAATATTA
Found at i:168204 original size:25 final size:25
Alignment explanation
Indices: 168152--168204 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
168142 AATATTTTAT
* *
168152 TTATGAAAAATTATTTGATTTATTA
1 TTATGAAAAATTATTTAAATTATTA
*
168177 TTATTAAAAATT-TTTAAATTATTCA
1 TTATGAAAAATTATTTAAATTATT-A
168202 TTA
1 TTA
168205 AGTTATATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (25 bp):
TTATGAAAAATTATTTAAATTATTA
Found at i:168396 original size:22 final size:22
Alignment explanation
Indices: 168369--168419 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
168359 GTATTTAAAA
168369 AATATTAAAATATTTT-TAAATT
1 AATATTAAAATATTTTAT-AATT
* *
168391 AATATTTATATATTTTATAATT
1 AATATTAAAATATTTTATAATT
*
168413 AAAATTA
1 AATATTA
168420 TATAAAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATTAAAATATTTTATAATT
Found at i:168698 original size:21 final size:19
Alignment explanation
Indices: 168647--168703 Score: 53
Period size: 21 Copynumber: 2.9 Consensus size: 19
168637 TTGTAAAAAC
168647 TTTTAATAT-AAATAATTT
1 TTTTAATATAAAATAATTT
** *
168665 TTTTGTTAAAAAATGTAATTT
1 TTTTAATATAAAA--TAATTT
*
168686 TTTTAATATAAAAAAATT
1 TTTTAATATAAAATAATT
168704 ACATTTTAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
18 6 0.21
19 7 0.24
21 16 0.55
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
TTTTAATATAAAATAATTT
Found at i:169277 original size:24 final size:24
Alignment explanation
Indices: 169250--169321 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
169240 TTATTTTATT
* *
169250 TTATTAATTTTTA-ATATATGTAAA
1 TTATTAATTTATATATAAAT-TAAA
*
169274 TTATT-ATTTATATATAAATTTAA
1 TTATTAATTTATATATAAATTAAA
169297 TTATTAATTTATATA-AAA-TAAA
1 TTATTAATTTATATATAAATTAAA
169319 TTA
1 TTA
169322 CTAACGTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
22 6 0.14
23 17 0.40
24 19 0.45
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (24 bp):
TTATTAATTTATATATAAATTAAA
Found at i:169298 original size:23 final size:23
Alignment explanation
Indices: 169272--169315 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
169262 AATATATGTA
169272 AATTATT-ATTTATATATAAATTT
1 AATTATTAATTTATATA-AAATTT
169295 AATTATTAATTTATATAAAAT
1 AATTATTAATTTATATAAAAT
169316 AAATTACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATTATTAATTTATATAAAATTT
Found at i:176138 original size:20 final size:19
Alignment explanation
Indices: 176110--176154 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
176100 TCTATTTAAA
* *
176110 ATATTTATATTTATTATATT
1 ATATATATATTTA-AATATT
176130 ATATATATATTTAAATATT
1 ATATATATATTTAAATATT
176149 A-ATATA
1 ATATATA
176155 AAAATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 5 0.22
19 6 0.26
20 12 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATATATATTTAAATATT
Found at i:176479 original size:5 final size:5
Alignment explanation
Indices: 176469--176494 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
176459 TATATATAGG
176469 TATTA TATTA TATTA TATTA TATTA T
1 TATTA TATTA TATTA TATTA TATTA T
176495 GTGTTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:176985 original size:17 final size:18
Alignment explanation
Indices: 176965--176999 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
176955 ATCATATTAG
*
176965 TTTAATTATAA-AGAAAA
1 TTTAAATATAACAGAAAA
176982 TTTAAATATAACAGAAAA
1 TTTAAATATAACAGAAAA
177000 AATTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (18 bp):
TTTAAATATAACAGAAAA
Found at i:179605 original size:30 final size:30
Alignment explanation
Indices: 179571--179631 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
179561 GTTTTCAATC
179571 ACTTGATCTGCAGCCTGATAATCCATATCA
1 ACTTGATCTGCAGCCTGATAATCCATATCA
*
179601 ACTTGATCTGCAGCTTGATAATCCATATCA
1 ACTTGATCTGCAGCCTGATAATCCATATCA
179631 A
1 A
179632 GTAGAAAGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (30 bp):
ACTTGATCTGCAGCCTGATAATCCATATCA
Found at i:179871 original size:16 final size:15
Alignment explanation
Indices: 179829--179876 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
179819 TAAACATGAA
179829 AATATTTTAAAATTT
1 AATATTTTAAAATTT
* * *
179844 ATATAATATAAATTATT
1 A-ATATTTTAAAAT-TT
179861 AATATTTTAAAATTT
1 AATATTTTAAAATTT
179876 A
1 A
179877 TATAAATATG
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
15 4 0.16
16 18 0.72
17 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATTTTAAAATTT
Found at i:181556 original size:4 final size:4
Alignment explanation
Indices: 181539--181581 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
181529 ATTCTAACCC
**
181539 TTTA TTTA CCTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
181582 TAATTCACCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:184055 original size:22 final size:22
Alignment explanation
Indices: 184027--184069 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
184017 AAAATCAACT
*
184027 AACCAAATTAAACTAATTAACC
1 AACCAAATTAAACCAATTAACC
*
184049 AACCAAATTGAACCAATTAAC
1 AACCAAATTAAACCAATTAAC
184070 TTCGATTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.23, G:0.02, T:0.21
Consensus pattern (22 bp):
AACCAAATTAAACCAATTAACC
Found at i:191373 original size:234 final size:232
Alignment explanation
Indices: 190958--191791 Score: 1197
Period size: 234 Copynumber: 3.6 Consensus size: 232
190948 AGGTTATCAA
* * * * *
190958 CAACACCTACAACATAATTCACAGAAGATGCTATGCATTGATACATCACCTAACAATACAAAAAA
1 CAACAACTACAACATGATTCACAGAAGATGATATTCATTGATACATCACCTACCAATAC-AAAAA
* *
191023 TGTCCTAATGACCATTATAGAACCATGCTTCCAATCTGCTGTCATAACAACATTCTAAAGGAAAC
65 TGCCCTAATGACCATTATAGAACCATGCTTCCAATCTGCAGTCATAACAACATTCTAAAGGAAAC
191088 ATGCAACCATTCGAAAACAAAAACACGAATTGAAAACTTATTACATAAGCAAAGCCATGAACAAA
130 ATGCAACCATTCGAAAACAAAAACACGAATTGAAAACTTATTACATAAGCAAAGCCATGAACAAA
*
191153 TCTTGCATATTTCCAAGTCATATAACAATATTAAATCGT
195 TCTTGCATATTTCCAAGTCATA-AACAACATTAAATCGT
191192 CAACAACTACAACATGATTCACAGAAGATGATATTCATTGATACATCACCTACCAATACAAAAAA
1 CAACAACTACAACATGATTCACAGAAGATGATATTCATTGATACATCACCTACCAATAC-AAAAA
* *
191257 TGTCCTAATGACCATTATAGAACCATGCTTCCAATCTGCAGTCATAACAACATTCCAAAGGAAAC
65 TGCCCTAATGACCATTATAGAACCATGCTTCCAATCTGCAGTCATAACAACATTCTAAAGGAAAC
191322 ATGCAACCATTCGAAAACAAAAACACGAATTGAAAACTTATTACATAAGCAAAGCCATGAACAAA
130 ATGCAACCATTCGAAAACAAAAACACGAATTGAAAACTTATTACATAAGCAAAGCCATGAACAAA
191387 TCTTGCATATTTCCAAGTCATAAAACAACATTAAATCGT
195 TCTTGCATATTTCCAAGTCAT-AAACAACATTAAATCGT
*
191426 CAAAAACTACAACATGATTCACAGAAGATGATATTCATTGATACATCACCTACCAATAC-AAAAT
1 CAACAACTACAACATGATTCACAGAAGATGATATTCATTGATACATCACCTACCAATACAAAAAT
* * * * * * * *
191490 GCCCTAATGTCCATTATCGAAAC-TGTACTTCCAGTCTGCAGTCACAACGACATTCTGGACGGAA
66 GCCCTAATGACCATTATAGAACCATG--CTTCCAATCTGCAGTCATAACAACATTCT-AAAGGAA
** * * * *
191554 ACGGGCAACCATTCG-AAACAAACACAAGAATTGAAAAACTTAATACATGAGCAAAGCCATGAAC
128 ACATGCAACCATTCGAAAACAAAAACACGAATTG-AAAACTTATTACATAAGCAAAGCCATGAAC
* * * *
191618 GAATTTTGCATATTCCCAATTCATAAAGCAACATTAAATCGT
192 AAATCTTGCATATTTCCAAGTCATAAA-CAACATTAAATCGT
* * **
191660 CAACAACTACAACGTGATTCACAGAAGATGATATTCATTGATACATCACCTGCTGATACAAAAAT
1 CAACAACTACAACATGATTCACAGAAGATGATATTCATTGATACATCACCTACCAATACAAAAAT
* * * * * * *
191725 GCCCTAATGTCCACTATAGAAACCTTACTTCAAATCTGCAGTTATAACAACATTCTAAAGCAAAC
66 GCCCTAATGACCATTATAG-AACCATGCTTCCAATCTGCAGTCATAACAACATTCTAAAGGAAAC
191790 AT
130 AT
191792 AAAGGAAACA
Statistics
Matches: 543, Mismatches: 48, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
231 2 0.00
232 24 0.04
233 44 0.08
234 422 0.78
235 47 0.09
236 3 0.01
237 1 0.00
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.24
Consensus pattern (232 bp):
CAACAACTACAACATGATTCACAGAAGATGATATTCATTGATACATCACCTACCAATACAAAAAT
GCCCTAATGACCATTATAGAACCATGCTTCCAATCTGCAGTCATAACAACATTCTAAAGGAAACA
TGCAACCATTCGAAAACAAAAACACGAATTGAAAACTTATTACATAAGCAAAGCCATGAACAAAT
CTTGCATATTTCCAAGTCATAAACAACATTAAATCGT
Found at i:193333 original size:15 final size:14
Alignment explanation
Indices: 193299--193331 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
193289 GAAAGAGAAA
193299 GGGGGTGGGAAAAT
1 GGGGGTGGGAAAAT
193313 GGGGGTGGGAAAAT
1 GGGGGTGGGAAAAT
193327 GGGGG
1 GGGGG
193332 GTTTGGTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.64, T:0.12
Consensus pattern (14 bp):
GGGGGTGGGAAAAT
Found at i:194169 original size:26 final size:29
Alignment explanation
Indices: 194127--194190 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 29
194117 AAAAAAAAGA
194127 AAAAAT-ATTATAATTA-TT-TGGA-TTT
1 AAAAATAATTATAATTATTTCTGGAGTTT
* *
194152 AAAAATAATTTTACTTATTTCTGGAGTTT
1 AAAAATAATTATAATTATTTCTGGAGTTT
194181 AAATAATAAT
1 AAA-AATAAT
194191 CTTTTTTCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 6 0.19
26 8 0.25
27 2 0.06
28 4 0.12
29 6 0.19
30 6 0.19
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (29 bp):
AAAAATAATTATAATTATTTCTGGAGTTT
Found at i:194744 original size:23 final size:24
Alignment explanation
Indices: 194708--194758 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
194698 CATTAAATTT
*
194708 TTTAAATAATAATA-ATTAATTAA
1 TTTAAATAATAATATATTAATAAA
*
194731 TTTAAAT-ATAAATATTTTAATAAA
1 TTTAAATAAT-AATATATTAATAAA
194755 TTTA
1 TTTA
194759 TTTTAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.08
23 11 0.46
24 11 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTAAATAATAATATATTAATAAA
Found at i:194782 original size:28 final size:27
Alignment explanation
Indices: 194699--194785 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 27
194689 TTTTATTATC
194699 ATTAAATT-TTTT-AAA-TAATA-ATA
1 ATTAAATTATTTTAAAATTAATATATA
* * *
194722 ATT-AATTAATTTAAATATAAATATTTTA
1 ATTAAATTATTTTAAA-ATTAATA-TATA
194750 A-TAAATTTATTTTAAAATTAATATATA
1 ATTAAA-TTATTTTAAAATTAATATATA
194777 ATTAAATTA
1 ATTAAATTA
194786 AAAATAAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
22 4 0.08
23 6 0.12
24 2 0.04
25 1 0.02
26 4 0.08
27 8 0.16
28 15 0.31
29 9 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTAAATTATTTTAAAATTAATATATA
Found at i:196554 original size:22 final size:23
Alignment explanation
Indices: 196495--196555 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
196485 ATACATGTAA
* * *
196495 ATATATGTAAATTTAAAATTCAT
1 ATATATATAAATTTCAAATACAT
* **
196518 ATTTATATACCTTTCAAATACAT
1 ATATATATAAATTTCAAATACAT
196541 A-ATATATAAATTTCA
1 ATATATATAAATTTCA
196556 TGCTTACAAT
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATATATAAATTTCAAATACAT
Found at i:203414 original size:23 final size:24
Alignment explanation
Indices: 203378--203428 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
203368 CATTAAATTT
*
203378 TTTAAATAATAATA-ATTAATTAA
1 TTTAAATAATAATATATTAATAAA
*
203401 TTTAAAT-ATAAATATTTTAATAAA
1 TTTAAATAAT-AATATATTAATAAA
203425 TTTA
1 TTTA
203429 TTTTAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.08
23 11 0.46
24 11 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTAAATAATAATATATTAATAAA
Found at i:203452 original size:28 final size:27
Alignment explanation
Indices: 203369--203455 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 27
203359 TTTTATTATC
203369 ATTAAATT-TTTT-AAA-TAATA-ATA
1 ATTAAATTATTTTAAAATTAATATATA
* * *
203392 ATT-AATTAATTTAAATATAAATATTTTA
1 ATTAAATTATTTTAAA-ATTAATA-TATA
203420 A-TAAATTTATTTTAAAATTAATATATA
1 ATTAAA-TTATTTTAAAATTAATATATA
203447 ATTAAATTA
1 ATTAAATTA
203456 AAAATAAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
22 4 0.08
23 6 0.12
24 2 0.04
25 1 0.02
26 4 0.08
27 8 0.16
28 15 0.31
29 9 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTAAATTATTTTAAAATTAATATATA
Found at i:205227 original size:22 final size:23
Alignment explanation
Indices: 205168--205228 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
205158 ATACATGTAA
* * *
205168 ATATATGTAAATTTAAAATTCAT
1 ATATATATAAATTTCAAATACAT
* **
205191 ATTTATATACCTTTCAAATACAT
1 ATATATATAAATTTCAAATACAT
205214 A-ATATATAAATTTCA
1 ATATATATAAATTTCA
205229 TGCTTACAAT
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATATATAAATTTCAAATACAT
Found at i:212086 original size:23 final size:24
Alignment explanation
Indices: 212050--212100 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
212040 CATTAAATTT
*
212050 TTTAAATAATAATA-ATTAATTAA
1 TTTAAATAATAATATATTAATAAA
*
212073 TTTAAAT-ATAAATATTTTAATAAA
1 TTTAAATAAT-AATATATTAATAAA
212097 TTTA
1 TTTA
212101 TTTTAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.08
23 11 0.46
24 11 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTAAATAATAATATATTAATAAA
Found at i:212124 original size:28 final size:27
Alignment explanation
Indices: 212041--212127 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 27
212031 TTTTATTATC
212041 ATTAAATT-TTTT-AAA-TAATA-ATA
1 ATTAAATTATTTTAAAATTAATATATA
* * *
212064 ATT-AATTAATTTAAATATAAATATTTTA
1 ATTAAATTATTTTAAA-ATTAATA-TATA
212092 A-TAAATTTATTTTAAAATTAATATATA
1 ATTAAA-TTATTTTAAAATTAATATATA
212119 ATTAAATTA
1 ATTAAATTA
212128 AAAATAAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
22 4 0.08
23 6 0.12
24 2 0.04
25 1 0.02
26 4 0.08
27 8 0.16
28 15 0.31
29 9 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTAAATTATTTTAAAATTAATATATA
Found at i:213901 original size:22 final size:23
Alignment explanation
Indices: 213842--213902 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
213832 ATACATGTAA
* * *
213842 ATATATGTAAATTTAAAATTCAT
1 ATATATATAAATTTCAAATACAT
* **
213865 ATTTATATACCTTTCAAATACAT
1 ATATATATAAATTTCAAATACAT
213888 A-ATATATAAATTTCA
1 ATATATATAAATTTCA
213903 TGCTTACAAT
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATATATAAATTTCAAATACAT
Found at i:221324 original size:2 final size:2
Alignment explanation
Indices: 221266--221307 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
221256 GCCAAATCTT
221266 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
221308 AAATTGTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:221539 original size:13 final size:14
Alignment explanation
Indices: 221521--221557 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
221511 TAGAAAAATT
221521 TATATATTTT-TTA
1 TATATATTTTATTA
221534 TATATATTTTATTA
1 TATATATTTTATTA
*
221548 T-TATAATTTA
1 TATATATTTTA
221558 AATTTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATATATTTTATTA
Found at i:221580 original size:24 final size:22
Alignment explanation
Indices: 221519--221580 Score: 52
Period size: 24 Copynumber: 2.6 Consensus size: 22
221509 ATTAGAAAAA
* *
221519 TTTATATATTTTTTATATATAT
1 TTTATATATTATTTAAATATAT
* *
221541 TTTATTATTATAATTTAAATTTATT
1 TTTA-TA-TATTATTTAAATATA-T
221566 TTTATATAATTATTT
1 TTTATAT-ATTATTT
221581 TGATTGAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
22 4 0.13
23 3 0.10
24 19 0.61
25 5 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTATATATTATTTAAATATAT
Found at i:221718 original size:27 final size:27
Alignment explanation
Indices: 221688--221745 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
221678 TTTAATCTAA
**
221688 ATAAATATT-TAAATTATTTATTTATTT
1 ATAAA-ATTATAAATTACATATTTATTT
* *
221715 ATAAAATTATAACTTGCATATTTATTT
1 ATAAAATTATAAATTACATATTTATTT
221742 ATAA
1 ATAA
221746 TTAAAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (27 bp):
ATAAAATTATAAATTACATATTTATTT
Found at i:222547 original size:30 final size:31
Alignment explanation
Indices: 222479--222550 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
222469 TTTAAAAAAA
* *
222479 TATTTATTT-TTATATTTTAATATCATATTT
1 TATTTATTTATAATATTTTAATATCAAATTT
222509 TA-TTATTTATAATAATTTT-ATAT-AAATTT
1 TATTTATTTATAAT-ATTTTAATATCAAATTT
222538 TATTTATTTATAA
1 TATTTATTTATAA
222551 AAAATAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
29 13 0.35
30 19 0.51
31 5 0.14
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (31 bp):
TATTTATTTATAATATTTTAATATCAAATTT
Found at i:222766 original size:2 final size:2
Alignment explanation
Indices: 222761--222795 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
222751 GTTCAGAAAC
222761 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
222796 CACACGCGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:226599 original size:13 final size:14
Alignment explanation
Indices: 226575--226614 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
226565 ATAAATATTT
226575 TAAAATT-TATATA
1 TAAAATTATATATA
226588 TATAAATTATATAT-
1 TA-AAATTATATATA
226602 TAAAATT-TATATA
1 TAAAATTATATATA
226615 AATATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.21
13 7 0.29
14 7 0.29
15 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAAATTATATATA
Found at i:226614 original size:14 final size:14
Alignment explanation
Indices: 226569--226614 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
226559 GAATTCATAA
*
226569 ATATTTTAAAATTT
1 ATATATTAAAATTT
226583 ATATA-TATAAA-TT
1 ATATATTA-AAATTT
226596 ATATATTAAAATTT
1 ATATATTAAAATTT
226610 ATATA
1 ATATA
226615 AATATAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 12 0.43
14 16 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATTAAAATTT
Found at i:227416 original size:16 final size:17
Alignment explanation
Indices: 227357--227453 Score: 69
Period size: 17 Copynumber: 5.7 Consensus size: 17
227347 AATTTTATAT
*
227357 TTTTAT-TTTTTA-AAA
1 TTTTATATTTATATAAA
*
227372 TTATT-TATTTATAATTAA
1 TT-TTATATTTAT-ATAAA
227390 TATTTATATTTATATAAA
1 T-TTTATATTTATATAAA
227408 TTTTA-ATTTATATTAAA
1 TTTTATATTTATA-TAAA
* *
227425 TTTT-TATAATATATAAT
1 TTTTATAT-TTATATAAA
*
227442 TTTTATTTTTAT
1 TTTTATATTTAT
227454 TCATATTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
15 3 0.05
16 13 0.20
17 25 0.38
18 16 0.25
19 8 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTATATTTATATAAA
Done.