Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 11 of 32
Found at i:1535685 original size:13 final size:14
Alignment explanation
Indices: 1535667--1535695 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1535657 TAACTTTAGC
1535667 TTAATTATAAT-TT
1 TTAATTATAATATT
1535680 TTAATTATAATATT
1 TTAATTATAATATT
1535694 TT
1 TT
1535696 TTATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTAATTATAATATT
Found at i:1536014 original size:21 final size:21
Alignment explanation
Indices: 1535988--1536027 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1535978 TATATATATA
1535988 TATTTTTTAAA-ATTATTTTTT
1 TATTTTTTAAATA-TATTTTTT
1536009 TATTTTTTAAATATATTTT
1 TATTTTTTAAATATATTTT
1536028 AATAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TATTTTTTAAATATATTTTTT
Found at i:1536683 original size:16 final size:16
Alignment explanation
Indices: 1536664--1536697 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1536654 AAATATTTTA
*
1536664 AATATAATTATAATAT
1 AATATAAATATAATAT
*
1536680 AATATAAATATGATAT
1 AATATAAATATAATAT
1536696 AA
1 AA
1536698 AAAGTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AATATAAATATAATAT
Found at i:1537966 original size:2 final size:2
Alignment explanation
Indices: 1537961--1537993 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1537951 TTTACATGTC
*
1537961 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1537994 GCATCCATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1537976 original size:12 final size:12
Alignment explanation
Indices: 1537947--1537990 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
1537937 GATCTTTTTT
* *
1537947 TATATTTACATG
1 TATATATACATA
*
1537959 TCTATATACATA
1 TATATATACATA
*
1537971 TATATATATATA
1 TATATATACATA
1537983 TATATATA
1 TATATATA
1537991 TATGCATCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (12 bp):
TATATATACATA
Found at i:1538622 original size:14 final size:14
Alignment explanation
Indices: 1538605--1538681 Score: 81
Period size: 14 Copynumber: 5.6 Consensus size: 14
1538595 TTTTTTATTA
1538605 AATAAAATTTAATT
1 AATAAAATTTAATT
1538619 AATAAAATTT-ATT
1 AATAAAATTTAATT
* *
1538632 AAAAAATATTTAATA
1 AATAAA-ATTTAATT
1538647 AAT-AAATTTAAATT
1 AATAAAATTT-AATT
1538661 --TAAAATTTAATT
1 AATAAAATTTAATT
1538673 ATATAAAAT
1 A-ATAAAAT
1538682 ATAAAATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
12 5 0.10
13 18 0.35
14 19 0.37
15 10 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATAAAATTTAATT
Found at i:1538633 original size:17 final size:17
Alignment explanation
Indices: 1538589--1538633 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1538579 TTTAATATTT
*
1538589 ATAAAATTTTTTATTAA
1 ATAAAATTTTTAATTAA
1538606 ATAAAA--TTTAATT-A
1 ATAAAATTTTTAATTAA
1538620 ATAAAATTTATTAA
1 ATAAAATTT-TTAA
1538634 AAAATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
14 7 0.29
15 6 0.25
16 1 0.04
17 10 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAAATTTTTAATTAA
Found at i:1538634 original size:28 final size:28
Alignment explanation
Indices: 1538598--1538681 Score: 95
Period size: 28 Copynumber: 3.0 Consensus size: 28
1538588 TATAAAATTT
1538598 TTTATTAAATAAAATTTAATTAATAAAA
1 TTTATTAAATAAAATTTAATTAATAAAA
*
1538626 TTTATTAAA-AAATATTTAATAAAT-AAA
1 TTTATTAAATAAA-ATTTAATTAATAAAA
*
1538653 TTTA--AATTTAAAATTTAATTATATAAAA
1 TTTATTAA-ATAAAATTTAATTA-ATAAAA
1538681 T
1 T
1538682 ATAAAATAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
25 2 0.04
26 8 0.17
27 15 0.31
28 23 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TTTATTAAATAAAATTTAATTAATAAAA
Found at i:1538705 original size:54 final size:54
Alignment explanation
Indices: 1538607--1538729 Score: 128
Period size: 54 Copynumber: 2.3 Consensus size: 54
1538597 TTTTATTAAA
* **
1538607 TAAAATTTAATTAATAAAATTTATTAAAAAATATTTAATAAATAAATTTA-AATT
1 TAAAATTTAATTAATAAAA-TTATTAAAAAATATTAAATAAATAAAAATATAATT
1538661 TAAAATTTAATTATATAAAA-TA-TAAAATAA-ATTAAGATATAATAAAAATATAATT
1 TAAAATTTAATTA-ATAAAATTATTAAAA-AATATTAA-ATA-AATAAAAATATAATT
**
1538716 TAAAAAATAATTAA
1 TAAAATTTAATTAA
1538730 AATATAATAT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
52 9 0.15
53 7 0.12
54 22 0.37
55 21 0.36
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (54 bp):
TAAAATTTAATTAATAAAATTATTAAAAAATATTAAATAAATAAAAATATAATT
Found at i:1538711 original size:11 final size:11
Alignment explanation
Indices: 1538679--1538738 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
1538669 AATTATATAA
1538679 AATATAAAATA-
1 AATA-AAAATAT
* *
1538690 AATTAAGATAT
1 AATAAAAATAT
1538701 AATAAAAATAT
1 AATAAAAATAT
1538712 AATTTAAAAA-AT
1 AA--TAAAAATAT
*
1538724 AATTAAAATAT
1 AATAAAAATAT
1538735 AATA
1 AATA
1538739 TGACACAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 10 0.26
11 19 0.49
12 4 0.10
13 6 0.15
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
AATAAAAATAT
Found at i:1538718 original size:23 final size:23
Alignment explanation
Indices: 1538662--1538737 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 23
1538652 ATTTAAATTT
* *
1538662 AAAATTTAATTATATAAAAT-AT-
1 AAAATATAATT-TAAAAAATAATA
* *
1538684 AAAATA-AA-TTAAGATATAATA
1 AAAATATAATTTAAAAAATAATA
*
1538705 AAAATATAATTTAAAAAATAATT
1 AAAATATAATTTAAAAAATAATA
1538728 AAAATATAAT
1 AAAATATAAT
1538738 ATGACACAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
19 5 0.12
20 3 0.07
21 8 0.19
22 7 0.16
23 20 0.47
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (23 bp):
AAAATATAATTTAAAAAATAATA
Found at i:1539462 original size:29 final size:30
Alignment explanation
Indices: 1539406--1539465 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
1539396 ATTGAGATAT
* *
1539406 AATACAAACACAACATATATATATATATAA
1 AATACAAACACAACATAAAAATATATATAA
1539436 AATA-AAACACAACATGAAAAATA-ATATAA
1 AATACAAACACAACAT-AAAAATATATATAA
1539465 A
1 A
1539466 CACTTAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.65, C:0.12, G:0.02, T:0.22
Consensus pattern (30 bp):
AATACAAACACAACATAAAAATATATATAA
Found at i:1539732 original size:19 final size:18
Alignment explanation
Indices: 1539693--1539778 Score: 88
Period size: 18 Copynumber: 4.8 Consensus size: 18
1539683 TGAAACTTTT
* * *
1539693 TAATATAATAAGATTATA
1 TAATATAAAAATATAATA
1539711 TAATATAAAAATTATAATA
1 TAATATAAAAA-TATAATA
*
1539730 TAATAT-AAAATATGATA
1 TAATATAAAAATATAATA
1539747 TAATATGAAAAA-ATAATA
1 TAATAT-AAAAATATAATA
*
1539765 TAA-ATATAAATATA
1 TAATATAAAAATATA
1539779 CAAATTTATT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
16 4 0.07
17 17 0.29
18 22 0.38
19 15 0.26
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
TAATATAAAAATATAATA
Found at i:1539747 original size:12 final size:12
Alignment explanation
Indices: 1539708--1539783 Score: 50
Period size: 12 Copynumber: 6.2 Consensus size: 12
1539698 TAATAAGATT
1539708 ATATAATATAAAA
1 ATATAATAT-AAA
1539721 ATTATAATAT--A
1 A-TATAATATAAA
* **
1539732 ATATAAAATATG
1 ATATAATATAAA
1539744 ATATAATATGAAA
1 ATATAATAT-AAA
*
1539757 AAATAATAT-AA
1 ATATAATATAAA
1539768 ATATAAATATACAA
1 ATAT-AATATA-AA
1539782 AT
1 AT
1539784 TTATTAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
10 7 0.14
11 7 0.14
12 13 0.27
13 10 0.20
14 12 0.24
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:1540170 original size:25 final size:27
Alignment explanation
Indices: 1540131--1540181 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
1540121 TCGTATATTT
*
1540131 ATATAATATTATAATTATATTTTAAAA
1 ATATAATATTATAATTAAATTTTAAAA
1540158 ATAT-ATATT-TAATTAAATTTTAAA
1 ATATAATATTATAATTAAATTTTAAA
1540182 CAGCGGAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.61
26 5 0.22
27 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATATAATATTATAATTAAATTTTAAAA
Found at i:1540511 original size:17 final size:17
Alignment explanation
Indices: 1540473--1540511 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1540463 TATATACATG
1540473 TTAATTTATTATATTTA
1 TTAATTTATTATATTTA
*
1540490 ATAATTTATTAT-TATTA
1 TTAATTTATTATAT-TTA
1540507 TTAAT
1 TTAAT
1540512 ATATAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTAATTTATTATATTTA
Found at i:1540527 original size:19 final size:18
Alignment explanation
Indices: 1540503--1540559 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
1540493 ATTTATTATT
1540503 ATTATTAATATATAAAATA
1 ATTATTAA-ATATAAAATA
*
1540522 ATTATTTAAATATAATATA
1 ATTA-TTAAATATAAAATA
* *
1540541 TTTAATAAATATAAAATA
1 ATTATTAAATATAAAATA
1540559 A
1 A
1540560 CATAAAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 12 0.38
19 16 0.50
20 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTATTAAATATAAAATA
Found at i:1540558 original size:11 final size:12
Alignment explanation
Indices: 1540508--1540559 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
1540498 TTATTATTAT
1540508 TAATATATAAAA
1 TAATATATAAAA
*
1540520 TAATTATTTAAATA
1 TAA-TATATAAA-A
**
1540534 TAATATATTTAA
1 TAATATATAAAA
1540546 TAA-ATATAAAA
1 TAATATATAAAA
1540557 TAA
1 TAA
1540560 CATAAAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
11 9 0.28
12 7 0.22
13 12 0.38
14 4 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TAATATATAAAA
Found at i:1540748 original size:23 final size:24
Alignment explanation
Indices: 1540712--1540757 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
1540702 TAACATAAAA
*
1540712 TATTTAATATATTTATCATATTTT
1 TATTTAATAAATTTATCATATTTT
1540736 TATTTAA-AAATTTATCATATTT
1 TATTTAATAAATTTATCATATTT
1540758 AATAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTTAATAAATTTATCATATTTT
Found at i:1540818 original size:2 final size:2
Alignment explanation
Indices: 1540813--1540870 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
1540803 TAAATATGAC
*
1540813 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1540855 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1540871 TACACACACA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1551541 original size:14 final size:13
Alignment explanation
Indices: 1551506--1551532 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1551496 CGTGGATGCT
1551506 ACAATAGCAGTAG
1 ACAATAGCAGTAG
1551519 ACAATAGCAGTAG
1 ACAATAGCAGTAG
1551532 A
1 A
1551533 TTGATAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.22, T:0.15
Consensus pattern (13 bp):
ACAATAGCAGTAG
Found at i:1553641 original size:15 final size:15
Alignment explanation
Indices: 1553623--1553791 Score: 76
Period size: 15 Copynumber: 11.5 Consensus size: 15
1553613 AATTAAAATT
1553623 ATTTAAATTTAATAA
1 ATTTAAATTTAATAA
*
1553638 ATTT-AA-TTATTAA
1 ATTTAAATTTAATAA
*
1553651 ATTT-AATTTATTTAA
1 ATTTAAATTTA-ATAA
*
1553666 ATGTTAAATTTAATTA
1 AT-TTAAATTTAATAA
*
1553682 TTTTAAA-TT-AT--
1 ATTTAAATTTAATAA
1553693 -TTTAAA-TTAATTAA
1 ATTTAAATTTAA-TAA
1553707 ATTTAATATTTAAATAA
1 ATTTAA-ATTT-AATAA
*
1553724 A-TTAAATTTTAAGT-G
1 ATTTAAA-TTTAA-TAA
* *
1553739 TTTTAAAATTAA-AA
1 ATTTAAATTTAATAA
1553753 TTATTTAAATTTAA-AA
1 --ATTTAAATTTAATAA
* *
1553769 TAATTAAATTTAAAAA
1 -ATTTAAATTTAATAA
1553785 ATTTAAA
1 ATTTAAA
1553792 AAATTTAAAA
Statistics
Matches: 123, Mismatches: 12, Indels: 38
0.71 0.07 0.22
Matches are distributed among these distances:
10 8 0.07
11 1 0.01
12 1 0.01
13 14 0.11
14 7 0.06
15 45 0.37
16 33 0.27
17 12 0.10
18 2 0.02
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
ATTTAAATTTAATAA
Found at i:1553653 original size:13 final size:13
Alignment explanation
Indices: 1553635--1553683 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
1553625 TTAAATTTAA
1553635 TAAATTTAATTAT
1 TAAATTTAATTAT
1553648 TAAATTTAA-T-T
1 TAAATTTAATTAT
* *
1553659 T--ATTTAAATGT
1 TAAATTTAATTAT
1553670 TAAATTTAATTAT
1 TAAATTTAATTAT
1553683 T
1 T
1553684 TTAAATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
9 6 0.20
10 1 0.03
11 4 0.13
12 1 0.03
13 18 0.60
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATTTAATTAT
Found at i:1553653 original size:22 final size:23
Alignment explanation
Indices: 1553619--1553721 Score: 99
Period size: 22 Copynumber: 4.5 Consensus size: 23
1553609 TTCGAATTAA
1553619 AATTATTTAAATTTAATAAATTT
1 AATTATTTAAATTTAATAAATTT
**
1553642 AATTA-TTAAATTTAATTTATTT
1 AATTATTTAAATTTAATAAATTT
* *
1553664 AA--ATGTTAAATTTAATTATTTT
1 AATTAT-TTAAATTTAATAAATTT
1553686 AAATTATTTTAAA-TTAATTAAATTT
1 -AATTA-TTTAAATTTAA-TAAATTT
1553711 AA-TATTTAAAT
1 AATTATTTAAAT
1553722 AAATTAAATT
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
20 1 0.02
22 38 0.58
23 9 0.14
24 6 0.09
25 11 0.17
26 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (23 bp):
AATTATTTAAATTTAATAAATTT
Found at i:1553674 original size:7 final size:6
Alignment explanation
Indices: 1553623--1553732 Score: 50
Period size: 6 Copynumber: 19.7 Consensus size: 6
1553613 AATTAAAATT
*
1553623 ATTTAA ATTT-A A--TAA ATTTAA TTATTAA ATTT-A ATTT-- ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA ATTTAA
*
1553666 ATGTTAA ATTTAA TTATTTTAA A-TT-A TTTTAA A-TT-A A-TTAA ATTTAA
1 AT-TTAA ATTTAA --A-TTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
1553713 TATTTAA A--TAA A-TTAA ATTT
1 -ATTTAA ATTTAA ATTTAA ATTT
1553733 TAAGTGTTTT
Statistics
Matches: 83, Mismatches: 4, Indels: 34
0.69 0.03 0.28
Matches are distributed among these distances:
3 1 0.01
4 15 0.18
5 19 0.23
6 24 0.29
7 18 0.22
8 1 0.01
9 5 0.06
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:1553712 original size:10 final size:10
Alignment explanation
Indices: 1553613--1553713 Score: 52
Period size: 10 Copynumber: 10.3 Consensus size: 10
1553603 CAATAATTCG
*
1553613 AATTAAAATT
1 AATTAAATTT
*
1553623 ATTTAAATTT
1 AATTAAATTT
1553633 AA-TAAATTT
1 AATTAAATTT
*
1553642 AATT--ATTA
1 AATTAAATTT
*
1553650 AATTTAATTT
1 AATTAAATTT
*
1553660 ATTTAAATGTT
1 AATTAAAT-TT
*
1553671 AAATTTAA-TT
1 -AATTAAATTT
*
1553681 ATTTTAAA-TT
1 A-ATTAAATTT
*
1553691 ATTTTAAA-TT
1 A-ATTAAATTT
1553701 AATTAAATTT
1 AATTAAATTT
1553711 AAT
1 AAT
1553714 ATTTAAATAA
Statistics
Matches: 72, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
8 7 0.10
9 15 0.21
10 43 0.60
11 2 0.03
12 5 0.07
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (10 bp):
AATTAAATTT
Found at i:1553729 original size:41 final size:41
Alignment explanation
Indices: 1553625--1553731 Score: 101
Period size: 41 Copynumber: 2.5 Consensus size: 41
1553615 TTAAAATTAT
* * *
1553625 TTAAATTT-AATAAATTTAATTATTAAATTTAATTTATTTAAATG
1 TTAAATTTAAATAAA-TTAA--ATT-ATTTTAAATTAATTAAATG
* **
1553669 TTAAATTTAATTATTTTAAATTATTTTAAATTAATTAAAT-
1 TTAAATTTAAATAAATTAAATTATTTTAAATTAATTAAATG
1553709 TTAATATTTAAATAAATTAAATT
1 TTAA-ATTTAAATAAATTAAATT
1553732 TTAAGTGTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
40 4 0.08
41 30 0.58
42 3 0.06
44 12 0.23
45 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (41 bp):
TTAAATTTAAATAAATTAAATTATTTTAAATTAATTAAATG
Found at i:1553801 original size:16 final size:16
Alignment explanation
Indices: 1553706--1553810 Score: 83
Period size: 16 Copynumber: 6.6 Consensus size: 16
1553696 AAATTAATTA
1553706 AATTTAATATTT-AAAT
1 AATTTAA-ATTTAAAAT
* * *
1553722 AAATTAAATTTTAAGT
1 AATTTAAATTTAAAAT
** *
1553738 GTTTTAAAATTAAAAT
1 AATTTAAATTTAAAAT
*
1553754 TATTTAAATTTAAAAT
1 AATTTAAATTTAAAAT
1553770 AA-TTAAATTTAAAA-
1 AATTTAAATTTAAAAT
1553784 AATTTAAAAAATTTAAAAT
1 AATTT---AAATTTAAAAT
1553803 AA-TTAAAT
1 AATTTAAAT
1553811 CTAGATTGAT
Statistics
Matches: 71, Mismatches: 12, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
14 2 0.03
15 22 0.31
16 33 0.46
18 12 0.17
19 2 0.03
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:1553810 original size:15 final size:15
Alignment explanation
Indices: 1553741--1553810 Score: 70
Period size: 15 Copynumber: 4.4 Consensus size: 15
1553731 TTTAAGTGTT
* *
1553741 TTAAAATTAAAATTAT
1 TTAAATTTAAAA-TAA
1553757 TTAAATTTAAAATAA
1 TTAAATTTAAAATAA
1553772 TTAAATTTAAAA-AA
1 TTAAATTTAAAATAA
1553786 TTTAAAAAATTTAAAATAA
1 -TT---AAATTTAAAATAA
1553805 TTAAAT
1 TTAAAT
1553811 CTAGATTGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
14 2 0.04
15 20 0.43
16 11 0.23
18 12 0.26
19 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAATTTAAAATAA
Found at i:1555767 original size:22 final size:21
Alignment explanation
Indices: 1555732--1555772 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1555722 GAGAATTGAT
1555732 TTAAATTTGATTTTAGATTTTA
1 TTAAATTTGATTTT-GATTTTA
1555754 TTAAATTT-AGTTTTGATTT
1 TTAAATTTGA-TTTTGATTT
1555773 GGATATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (21 bp):
TTAAATTTGATTTTGATTTTA
Found at i:1556492 original size:25 final size:23
Alignment explanation
Indices: 1556442--1556488 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
1556432 TAGGGTTTAT
*
1556442 TTAATATGATGTCATAAATTAAA
1 TTAATATGATATCATAAATTAAA
1556465 TTAA-ATGATATCAATATAATTAAA
1 TTAATATGATATC-ATA-AATTAAA
1556489 ATTATCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 7 0.33
24 7 0.33
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.38
Consensus pattern (23 bp):
TTAATATGATATCATAAATTAAA
Found at i:1557335 original size:2 final size:2
Alignment explanation
Indices: 1557328--1557388 Score: 65
Period size: 2 Copynumber: 32.0 Consensus size: 2
1557318 ATAATAACTG
* * *
1557328 AT AT AT AT AT TT AT AT AT AT CT AT -T AT -T AT -T AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1557367 AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
1557389 TGTAAGGTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
1 3 0.06
2 45 0.94
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (2 bp):
AT
Found at i:1557678 original size:19 final size:19
Alignment explanation
Indices: 1557651--1557693 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1557641 TTTAAGTTTG
*
1557651 ATTTAATTTTATATTTTAA
1 ATTTAATTTAATATTTTAA
* *
1557670 ATTTTATTTAATTTTTTAA
1 ATTTAATTTAATATTTTAA
1557689 ATTTA
1 ATTTA
1557694 TAAATAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTAATTTAATATTTTAA
Found at i:1558321 original size:21 final size:20
Alignment explanation
Indices: 1558292--1558342 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
1558282 AAATTATTAT
* **
1558292 TTAATAATAAAATTATTTTTA
1 TTAAAAATAAAA-TATTAATA
1558313 TTAAAAATATAAATATTAATA
1 TTAAAAATA-AAATATTAATA
1558334 -TAAAAATAA
1 TTAAAAATAA
1558343 TTTTTGAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 8 0.31
21 14 0.54
22 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAAAAATAAAATATTAATA
Found at i:1559247 original size:15 final size:14
Alignment explanation
Indices: 1559217--1559258 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1559207 AAAAATTTAT
*
1559217 ATTAAAGTTAATTTA
1 ATTAAA-TTAAATTA
1559232 ATTTAAATTAAATTA
1 A-TTAAATTAAATTA
1559247 ATTAAATTAAAT
1 ATTAAATTAAAT
1559259 AAATAATTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 11 0.44
15 9 0.36
16 5 0.20
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
ATTAAATTAAATTA
Found at i:1559255 original size:5 final size:5
Alignment explanation
Indices: 1559217--1559262 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
1559207 AAAAATTTAT
* *
1559217 ATTAA AGTTAA TTTAA TTTAA ATTAA ATT-A ATTAA ATTAA A-TAA AT
1 ATTAA A-TTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA AT
1559263 AATTCGAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 8 0.22
5 24 0.67
6 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (5 bp):
ATTAA
Found at i:1559573 original size:17 final size:18
Alignment explanation
Indices: 1559541--1559574 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1559531 AAATTTAAAA
1559541 TTTTTGTTTATGCTTATT
1 TTTTTGTTTATGCTTATT
1559559 TTTTTGTTTAT-CTTAT
1 TTTTTGTTTATGCTTAT
1559575 CCAACTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.74
Consensus pattern (18 bp):
TTTTTGTTTATGCTTATT
Found at i:1560745 original size:22 final size:22
Alignment explanation
Indices: 1560720--1560776 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 22
1560710 TTACTATTAA
1560720 TTATATTAATATTTAAAT-ATTT
1 TTATATTAA-ATTTAAATAATTT
1560742 TTATAATTAAATTTAAATAATTT
1 TTAT-ATTAAATTTAAATAATTT
1560765 TTATTATTAAAT
1 TTA-TATTAAAT
1560777 AATAATACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 12 0.38
23 19 0.59
24 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTATATTAAATTTAAATAATTT
Found at i:1563674 original size:16 final size:17
Alignment explanation
Indices: 1563641--1563675 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1563631 ATTCTCTCCG
*
1563641 TCGTCTTTTCCTCTGCA
1 TCGTCTTTTCCACTGCA
1563658 TCGTCTTTT-CACTGCA
1 TCGTCTTTTCCACTGCA
1563674 TC
1 TC
1563676 CCGATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.09, C:0.34, G:0.11, T:0.46
Consensus pattern (17 bp):
TCGTCTTTTCCACTGCA
Found at i:1563819 original size:18 final size:18
Alignment explanation
Indices: 1563798--1563836 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1563788 ATAAATATAT
*
1563798 ATTTTTA-ATTATTTTAAA
1 ATTTTTATA-TATTTAAAA
1563816 ATTTTTATATATTTAAAA
1 ATTTTTATATATTTAAAA
1563834 ATT
1 ATT
1563837 ATATTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTTATATATTTAAAA
Found at i:1565290 original size:78 final size:79
Alignment explanation
Indices: 1565192--1565352 Score: 245
Period size: 78 Copynumber: 2.0 Consensus size: 79
1565182 ACTAAAGAGT
*
1565192 TTTCACTCCATCCAGGAACCTATAATTAACTAGTTTGCTATGTGT-CGC-TCTTTTTGATGTAAC
1 TTTCACTCCATCAAGGAACCTATAATTAACTAGTTTGCTATGT-TCCGCTTCTTTTTGATGTAAC
*
1565255 AATGCTGGATAAACA
65 AATGCTCGATAAACA
* *
1565270 TTTCACTCCATCAAGGAACCTATAATTAACTAGTTTGCTATGTTCCGCTTTTTTTTTTGATGTAG
1 TTTCACTCCATCAAGGAACCTATAATTAACTAGTTTGCTATGTTCCGC--TTCTTTTTGATGTAA
1565335 CAATGCTCGATAAACA
64 CAATGCTCGATAAACA
1565351 TT
1 TT
1565353 CATTTTAAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
77 1 0.01
78 45 0.60
81 29 0.39
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (79 bp):
TTTCACTCCATCAAGGAACCTATAATTAACTAGTTTGCTATGTTCCGCTTCTTTTTGATGTAACA
ATGCTCGATAAACA
Found at i:1569178 original size:11 final size:11
Alignment explanation
Indices: 1569162--1569188 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1569152 GTCTATATTT
1569162 TCACCATTTTA
1 TCACCATTTTA
1569173 TCACCATTTTA
1 TCACCATTTTA
1569184 TCACC
1 TCACC
1569189 TTAATGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.41
Consensus pattern (11 bp):
TCACCATTTTA
Found at i:1570058 original size:31 final size:31
Alignment explanation
Indices: 1570020--1570082 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1570010 GGCAGATACA
1570020 GTTGTATTCTATGTTACTTGGATTCGGTGAT
1 GTTGTATTCTATGTTACTTGGATTCGGTGAT
1570051 GTTGTATTCTATGTTACTTGGATTCGGTGAT
1 GTTGTATTCTATGTTACTTGGATTCGGTGAT
1570082 G
1 G
1570083 ACTGTTAGAT
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:0.16, C:0.10, G:0.27, T:0.48
Consensus pattern (31 bp):
GTTGTATTCTATGTTACTTGGATTCGGTGAT
Found at i:1570343 original size:19 final size:19
Alignment explanation
Indices: 1570319--1570378 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
1570309 TGAATATGAT
1570319 ATGATTATACGGTATAAAC
1 ATGATTATACGGTATAAAC
* * * *
1570338 ATGATT-T--TGAATATGAT
1 ATGATTATACGGTATA-AAC
1570355 ATGATTATACGGTATAAAC
1 ATGATTATACGGTATAAAC
1570374 ATGAT
1 ATGAT
1570379 ACGAAAAAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 2 0.07
19 12 0.41
20 4 0.14
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (19 bp):
ATGATTATACGGTATAAAC
Found at i:1570354 original size:36 final size:36
Alignment explanation
Indices: 1570307--1570378 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
1570297 ACTTGATAAC
1570307 TTTGAATATGATATGATTATACGGTATAAACATGAT
1 TTTGAATATGATATGATTATACGGTATAAACATGAT
1570343 TTTGAATATGATATGATTATACGGTATAAACATGAT
1 TTTGAATATGATATGATTATACGGTATAAACATGAT
1570379 ACGAAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (36 bp):
TTTGAATATGATATGATTATACGGTATAAACATGAT
Found at i:1570685 original size:16 final size:15
Alignment explanation
Indices: 1570670--1570712 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1570660 ATTTTATTAT
1570670 TAAAAAATATTTTTA
1 TAAAAAATATTTTTA
* **
1570685 TAAATAA-ATTTAAA
1 TAAAAAATATTTTTA
1570699 TAAAAAATATTTTT
1 TAAAAAATATTTTT
1570713 TTACTATTCA
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAAAAATATTTTTA
Found at i:1571046 original size:22 final size:23
Alignment explanation
Indices: 1571020--1571082 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 23
1571010 ATTTTTAATA
1571020 ATTTAATTTAATTTAAA-TTATT
1 ATTTAATTTAATTTAAATTTATT
**
1571042 ATTTAA--TAATAAAAATTTTATT
1 ATTTAATTTAATTTAAA-TTTATT
1571064 ATTTATATTTAATTATAAA
1 ATTTA-ATTTAATT-TAAA
1571083 AATAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
20 7 0.23
22 16 0.52
23 1 0.03
25 4 0.13
26 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTTAATTTAATTTAAATTTATT
Found at i:1571500 original size:20 final size:20
Alignment explanation
Indices: 1571445--1571501 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1571435 ATCGACTAAA
*
1571445 TTATTTAATTTAAATCGTTAAT
1 TTATTT-ATTTAAAT-ATTAAT
* *
1571467 TTATTTAATAAAATATTAAT
1 TTATTTATTTAAATATTAAT
*
1571487 TTTTTTATTTAAATA
1 TTATTTATTTAAATA
1571502 AATTATAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 17 0.59
21 6 0.21
22 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTATTTATTTAAATATTAAT
Found at i:1571864 original size:21 final size:20
Alignment explanation
Indices: 1571835--1571914 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 20
1571825 AGCGATAAGT
1571835 TTAAAATTTAAATTTTAATA
1 TTAAAATTTAAATTTTAATA
1571855 TTATAAATTT---TTTTAATAA
1 TTA-AAATTTAAATTTTAAT-A
*
1571874 TTAAAATTTAATTTTTAATTA
1 TTAAAATTTAAATTTTAA-TA
* *
1571895 TTAAAATTAAAAATTTAATA
1 TTAAAATTTAAATTTTAATA
1571915 CTATATTCAC
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
18 13 0.25
19 4 0.08
20 5 0.10
21 28 0.55
22 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAAAATTTAAATTTTAATA
Found at i:1577785 original size:11 final size:11
Alignment explanation
Indices: 1577769--1577814 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
1577759 ATACAAGATG
1577769 TAATATAATTA
1 TAATATAATTA
**
1577780 TAATATAAAAA
1 TAATATAATTA
1577791 TAAT-TAATATA
1 TAATATAAT-TA
1577802 TAATATAATTA
1 TAATATAATTA
1577813 TA
1 TA
1577815 TAAATATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 3 0.10
11 22 0.76
12 4 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TAATATAATTA
Found at i:1577800 original size:15 final size:15
Alignment explanation
Indices: 1577780--1577818 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1577770 AATATAATTA
1577780 TAATATAAAAATAAT
1 TAATATAAAAATAAT
*
1577795 TAATATATAATATAAT
1 TAATATA-AAAATAAT
1577811 T-ATATAAA
1 TAATATAAA
1577819 TATATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 2 0.09
15 12 0.55
16 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATATAAAAATAAT
Found at i:1577835 original size:33 final size:33
Alignment explanation
Indices: 1577792--1577872 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
1577782 ATATAAAAAT
* * *
1577792 AATTAATATATAATATAATTATATAAATATATTAA
1 AATTTATATAAAATA-AATTAT-TAAATAAATTAA
**
1577827 AATTTATATAAAATAAATTATTTTATAAATTAA
1 AATTTATATAAAATAAATTATTAAATAAATTAA
1577860 AATTTATA-AAAAT
1 AATTTATATAAAAT
1577873 TTAATTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
32 5 0.12
33 17 0.41
34 6 0.15
35 13 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
AATTTATATAAAATAAATTATTAAATAAATTAA
Found at i:1577872 original size:43 final size:44
Alignment explanation
Indices: 1577816--1577916 Score: 100
Period size: 43 Copynumber: 2.3 Consensus size: 44
1577806 ATAATTATAT
* * *
1577816 AAATATATTAAAATTT-ATATAAAATAAATTATT-TT-ATAAATTA
1 AAATTTATAAAAATTTAATAT-AAATAAA-AATTATTAATAAATTA
* *
1577859 AAATTTATAAAAATTTAATTTAAATAAAAATTATTAATATATTA
1 AAATTTATAAAAATTTAATATAAATAAAAATTATTAATAAATTA
*
1577903 AAATCTCATAAAAA
1 AAAT-TTATAAAAA
1577917 GTAAAAAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
42 3 0.06
43 23 0.48
44 14 0.29
45 8 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (44 bp):
AAATTTATAAAAATTTAATATAAATAAAAATTATTAATAAATTA
Found at i:1578095 original size:5 final size:5
Alignment explanation
Indices: 1578085--1578114 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
1578075 AACAATTGAT
1578085 TTTTA TTTTA TTTTA TTTTA TTTTAA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTT-A TTTT
1578115 TCCAAACAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:1578278 original size:19 final size:18
Alignment explanation
Indices: 1578246--1578291 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 18
1578236 TTTATAAATA
1578246 TAAATATAATT-AAATTAT
1 TAAATATAATTAAAATT-T
1578264 TAAATATATATTAAAATTT
1 TAAATATA-ATTAAAATTT
1578283 TAAATATAA
1 TAAATATAA
1578292 AAATAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.35
19 12 0.46
20 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAATATAATTAAAATTT
Found at i:1578336 original size:24 final size:24
Alignment explanation
Indices: 1578299--1578386 Score: 65
Period size: 28 Copynumber: 3.5 Consensus size: 24
1578289 TAAAAATAAA
*
1578299 AAATAAAAAATTTATTATTTTATTT
1 AAAT-AAAATTTTATTATTTTATTT
1578324 AAATAAAATTTTACTTATTTATTATATT
1 AAATAAAATTTTA-TTA-TT-TTAT-TT
* *
1578352 AAA-ATAAATTTTA-AATATT-TTT
1 AAATA-AAATTTTATTATTTTATTT
*
1578374 AAATAAATTTTTA
1 AAATAAAATTTTA
1578387 AATAAATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
22 12 0.23
23 2 0.04
24 10 0.19
25 8 0.15
26 3 0.06
27 5 0.09
28 13 0.25
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATAAAATTTTATTATTTTATTT
Found at i:1578370 original size:28 final size:29
Alignment explanation
Indices: 1578313--1578371 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
1578303 AAAAAATTTA
* * **
1578313 TTATTTTATTTAAATAAAATTTTACTTAT
1 TTATTATATTAAAATAAAATTTTAAATAT
1578342 TTATTATATTAAAAT-AAATTTTAAATAT
1 TTATTATATTAAAATAAAATTTTAAATAT
1578370 TT
1 TT
1578372 TTAAATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (29 bp):
TTATTATATTAAAATAAAATTTTAAATAT
Found at i:1578383 original size:12 final size:12
Alignment explanation
Indices: 1578353--1578394 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
1578343 TATTATATTA
1578353 AAATAAA-TTTT
1 AAATAAATTTTT
1578364 AAAT--ATTTTT
1 AAATAAATTTTT
1578374 AAATAAATTTTT
1 AAATAAATTTTT
1578386 AAATAAATT
1 AAATAAATT
1578395 AATATTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 1 0.04
10 8 0.29
11 4 0.14
12 15 0.54
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAAATTTTT
Found at i:1578396 original size:21 final size:21
Alignment explanation
Indices: 1578353--1578396 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1578343 TATTATATTA
**
1578353 AAATAAATTTTAAATATTTTT
1 AAATAAATTTTAAATATAATT
1578374 AAATAAATTTTTAAATA-AATT
1 AAATAAA-TTTTAAATATAATT
1578395 AA
1 AA
1578397 TATTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATAAATTTTAAATATAATT
Found at i:1578477 original size:22 final size:22
Alignment explanation
Indices: 1578452--1578493 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1578442 AAAATGAAGA
*
1578452 AAAAAAGTGATGTACTTTAACT
1 AAAAAAGTGAAGTACTTTAACT
*
1578474 AAAAAAGTTAAGTACTTTAA
1 AAAAAAGTGAAGTACTTTAA
1578494 ACACTCTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (22 bp):
AAAAAAGTGAAGTACTTTAACT
Found at i:1578820 original size:21 final size:19
Alignment explanation
Indices: 1578763--1578821 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 19
1578753 AAATTCAATA
1578763 TAAA-CAAATTAAATTTA-T
1 TAAATCAAA-TAAATTTATT
*
1578781 TAAATCAAATAAA-TAATT
1 TAAATCAAATAAATTTATT
*
1578799 TAATTCATAAATAAATTTATT
1 TAAATC--AAATAAATTTATT
1578820 TA
1 TA
1578822 CTAAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 2 0.06
18 14 0.42
19 4 0.12
20 7 0.21
21 6 0.18
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATCAAATAAATTTATT
Found at i:1579005 original size:2 final size:2
Alignment explanation
Indices: 1578994--1579034 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1578984 ATACCTACAA
1578994 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1579035 TTTGTGGCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1579292 original size:10 final size:11
Alignment explanation
Indices: 1579277--1579324 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
1579267 AAAATCTAAT
1579277 TTTAAAAT-AA
1 TTTAAAATAAA
1579287 TTTAAAAATAAA
1 TTT-AAAATAAA
1579299 TTT-AAATAAA
1 TTTAAAATAAA
*
1579309 TTTAAGATAAA
1 TTTAAAATAAA
1579320 TTTAA
1 TTTAA
1579325 TATTATTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
10 13 0.38
11 16 0.47
12 5 0.15
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TTTAAAATAAA
Found at i:1579307 original size:21 final size:21
Alignment explanation
Indices: 1579281--1579338 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
1579271 TCTAATTTTA
1579281 AAATAATTTAAAAATAAATTT
1 AAATAATTTAAAAATAAATTT
*
1579302 AAATAAATTT-AAGATAAATTT
1 AAAT-AATTTAAAAATAAATTT
*
1579323 AATATTATTATAAAAA
1 AA-ATAATT-TAAAAA
1579339 AATAAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 19 0.63
22 8 0.27
23 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AAATAATTTAAAAATAAATTT
Found at i:1579565 original size:2 final size:2
Alignment explanation
Indices: 1579560--1579589 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1579550 ATCCCCCCCC
1579560 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
1579590 ATATGCAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1588516 original size:38 final size:39
Alignment explanation
Indices: 1588437--1588522 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
1588427 TAGATTAAGT
* *
1588437 AAAA-TTCCCACACATAATGCTGTAGGATTCGCCCATAA
1 AAAATTTCCCACACATAATGCCGTAGGAGTCGCCCATAA
1588475 AAAATTTCCCACACATAATGCCGTAGGAGTCGCCCATAA
1 AAAATTTCCCACACATAATGCCGTAGGAGTCGCCCATAA
1588514 AAAATTTCC
1 AAAATTTCC
1588523 TTTTAATTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 4 0.09
39 41 0.91
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (39 bp):
AAAATTTCCCACACATAATGCCGTAGGAGTCGCCCATAA
Found at i:1589635 original size:15 final size:17
Alignment explanation
Indices: 1589614--1589646 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1589604 CATTATTTAT
*
1589614 TTTTTTATT-TAAAATA
1 TTTTTAATTATAAAATA
1589630 TTTTTAATTATAAAATA
1 TTTTTAATTATAAAATA
1589647 ATGAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTTAATTATAAAATA
Found at i:1589706 original size:26 final size:26
Alignment explanation
Indices: 1589668--1589719 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1589658 ATTAATCTTA
1589668 AAATTATATTTAA-TTACTATTAAATT
1 AAATTATATTTAAGTTA-TATTAAATT
*
1589694 AAATTAT-TATTAAGTTATATTTAATT
1 AAATTATAT-TTAAGTTATATTAAATT
1589720 CAAGTACATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 1 0.04
26 19 0.83
27 3 0.13
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
AAATTATATTTAAGTTATATTAAATT
Found at i:1590311 original size:18 final size:17
Alignment explanation
Indices: 1590288--1590331 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1590278 TTGACAGTAA
1590288 TTAAAAATAATTTTATAG
1 TTAAAAATAATTTTA-AG
*
1590306 TTAAAAAT-GTTTTAAG
1 TTAAAAATAATTTTAAG
*
1590322 TAAAAAATAA
1 TTAAAAATAA
1590332 AAAAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 9 0.41
17 5 0.23
18 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (17 bp):
TTAAAAATAATTTTAAG
Found at i:1592319 original size:23 final size:23
Alignment explanation
Indices: 1592269--1592326 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
1592259 ATTTAAAAAA
1592269 ATAAAT-ATTATTTTTAATTATAT
1 ATAAATAATT-TTTTTAATTATAT
*
1592292 TTAAATAATTTTTTT-ATTATTAT
1 ATAAATAATTTTTTTAATTA-TAT
1592315 ATAAAATAATTT
1 AT-AAATAATTT
1592327 AAATTGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 4 0.13
23 14 0.47
24 12 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATAAATAATTTTTTTAATTATAT
Found at i:1594274 original size:207 final size:207
Alignment explanation
Indices: 1593919--1594340 Score: 790
Period size: 207 Copynumber: 2.0 Consensus size: 207
1593909 GACTTCAGTT
* *
1593919 GAACATTTAGAGATGGAACATTCAACTGGCTTTTCAGAAAATGGGTCAGATGGAGTACAGGTTAT
1 GAACATTTAGAGACGGAACATTCAACTGGCTTTCCAGAAAATGGGTCAGATGGAGTACAGGTTAT
1593984 GGAGGAAGCTATTGGCAACATCGCAGTCACTGAATCTGCAGTCAAAGGAAGAAAAAGAAAGAAAA
66 GGAGGAAGCTATTGGCAACATCGCAGTCACTGAATCTGCAGTCAAAGGAAGAAAAAGAAAGAAAA
*
1594049 GAAAGGAAGGAAAGAAGTTGGAGTCATCGGAAAAGTATCCAGACCAAAAGGATGTTGAGATAGGA
131 GAAAGAAAGGAAAGAAGTTGGAGTCATCGGAAAAGTATCCAGACCAAAAGGATGTTGAGATAGGA
1594114 ACCAAGACAGAA
196 ACCAAGACAGAA
1594126 GAACATTTAGAGACGGAACATTCAACTGGCTTTCCAGAAAATGGGTCAGATGGAGTACAGGTTAT
1 GAACATTTAGAGACGGAACATTCAACTGGCTTTCCAGAAAATGGGTCAGATGGAGTACAGGTTAT
*
1594191 GGAGGAAGCTATTGGCAACATCGCAGTCACTGAATCTGCAGTCGAAGGAAGAAAAAGAAAGAAAA
66 GGAGGAAGCTATTGGCAACATCGCAGTCACTGAATCTGCAGTCAAAGGAAGAAAAAGAAAGAAAA
*
1594256 GAAAGAAAGGAAAGAAGTTGGAGTCATCGGACAAGTATCCAGACCAAAAGGATGTTGAGATAGGA
131 GAAAGAAAGGAAAGAAGTTGGAGTCATCGGAAAAGTATCCAGACCAAAAGGATGTTGAGATAGGA
*
1594321 ACCAAGAGAGAA
196 ACCAAGACAGAA
1594333 GAACATTT
1 GAACATTT
1594341 GCCTTCTCTC
Statistics
Matches: 209, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
207 209 1.00
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.18
Consensus pattern (207 bp):
GAACATTTAGAGACGGAACATTCAACTGGCTTTCCAGAAAATGGGTCAGATGGAGTACAGGTTAT
GGAGGAAGCTATTGGCAACATCGCAGTCACTGAATCTGCAGTCAAAGGAAGAAAAAGAAAGAAAA
GAAAGAAAGGAAAGAAGTTGGAGTCATCGGAAAAGTATCCAGACCAAAAGGATGTTGAGATAGGA
ACCAAGACAGAA
Found at i:1597302 original size:2 final size:2
Alignment explanation
Indices: 1597297--1597330 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1597287 GGGGGAGGGG
1597297 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1597331 AGCGCAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1599978 original size:2 final size:2
Alignment explanation
Indices: 1599971--1600008 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1599961 CATAATCATA
1599971 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1600009 GATGCCAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1600213 original size:14 final size:15
Alignment explanation
Indices: 1600196--1600235 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
1600186 TTTCACCCTT
1600196 TTTTTTTCTTTTT-C
1 TTTTTTTCTTTTTAC
*
1600210 TTTTTTTTTTTTTAC
1 TTTTTTTCTTTTTAC
*
1600225 TTTTTTACTTT
1 TTTTTTTCTTT
1600236 GATTTATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTTCTTTTTAC
Found at i:1600215 original size:15 final size:15
Alignment explanation
Indices: 1600193--1600230 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1600183 TCTTTTCACC
*
1600193 CTTTTTTTTTCTTTTT
1 CTTTTTTTTT-TTTTA
1600209 CTTTTTTTTTTTTTA
1 CTTTTTTTTTTTTTA
1600224 CTTTTTT
1 CTTTTTT
1600231 ACTTTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.87
Consensus pattern (15 bp):
CTTTTTTTTTTTTTA
Found at i:1600474 original size:2 final size:2
Alignment explanation
Indices: 1600462--1600493 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1600452 TCCGCATGAC
*
1600462 AT AT AT GT 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
1600494 GAAAAGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1601329 original size:2 final size:2
Alignment explanation
Indices: 1601322--1601361 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1601312 TTCAGCATGT
1601322 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
1601362 AAGCTTTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1601650 original size:2 final size:2
Alignment explanation
Indices: 1601643--1601672 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1601633 CACTTCAATC
1601643 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
1601673 TTCAAATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1601796 original size:2 final size:2
Alignment explanation
Indices: 1601789--1601816 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1601779 TGTGAGCAAT
1601789 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
1601817 CATTGATATC
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:1603054 original size:2 final size:2
Alignment explanation
Indices: 1603047--1603080 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1603037 TATGAAATTA
1603047 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1603081 GATTTAGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1603189 original size:2 final size:2
Alignment explanation
Indices: 1603182--1603207 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1603172 GTCTTGATTT
1603182 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
1603208 AAAAGTTAAA
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):
TA
Found at i:1605754 original size:4 final size:4
Alignment explanation
Indices: 1605745--1605777 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
1605735 AGGTTAACTT
*
1605745 CATA CATA CATA CATA CATA CATA CATA TATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA C
1605778 TAGGGACCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:1607721 original size:2 final size:2
Alignment explanation
Indices: 1607714--1607751 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1607704 AGTTTCTTGA
* *
1607714 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1607752 TTAATGGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1607990 original size:24 final size:22
Alignment explanation
Indices: 1607941--1607992 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
1607931 AAAAGATTTG
* * *
1607941 TAATTTGAATTAATTTAATTAT
1 TAATTTAAATTAATTTAAATAA
1607963 TAATTTAAATTACTATTTAAATAA
1 TAATTTAAATTA--ATTTAAATAA
1607987 TAATTT
1 TAATTT
1607993 TTTTAAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.44
24 14 0.56
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TAATTTAAATTAATTTAAATAA
Found at i:1609508 original size:2 final size:2
Alignment explanation
Indices: 1609501--1609530 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1609491 AAGTGTTATG
1609501 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
1609531 CATACATGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1611177 original size:31 final size:31
Alignment explanation
Indices: 1611142--1611201 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
1611132 TTAAATTTTG
1611142 ATATAAAAATATAATTT-TA-AAAATATATAAA
1 ATAT-AAAATAT-ATTTATATAAAATATATAAA
*
1611173 ATATAAAATATATTTATATCAAATATATA
1 ATATAAAATATATTTATATAAAATATATA
1611202 TTCATACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 4 0.15
30 9 0.35
31 13 0.50
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
ATATAAAATATATTTATATAAAATATATAAA
Found at i:1611920 original size:17 final size:17
Alignment explanation
Indices: 1611898--1611930 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1611888 TGCATATATA
*
1611898 TATATATATATTAAATC
1 TATATATAAATTAAATC
1611915 TATATATAAATTAAAT
1 TATATATAAATTAAAT
1611931 TATTTTCTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TATATATAAATTAAATC
Found at i:1612909 original size:26 final size:26
Alignment explanation
Indices: 1612856--1612909 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
1612846 GTTTAAAATA
* *
1612856 TTTACAATTTATTTTATATTAATATT
1 TTTACAATTTATTTAAAATTAATATT
*
1612882 TTTATAATTTAATTTAAAATTAAT-TT
1 TTTACAATTT-ATTTAAAATTAATATT
1612908 TT
1 TT
1612910 ATTAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTACAATTTATTTAAAATTAATATT
Found at i:1614489 original size:17 final size:18
Alignment explanation
Indices: 1614448--1614491 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
1614438 CTAATAAAAT
1614448 ATATATTATATAAATGTAC
1 ATATA-TATATAAATGTAC
* *
1614467 AAATATATCTAAAT-TAC
1 ATATATATATAAATGTAC
1614484 ATATATAT
1 ATATATAT
1614492 GTGTATGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 10 0.45
18 8 0.36
19 4 0.18
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (18 bp):
ATATATATATAAATGTAC
Found at i:1619964 original size:20 final size:21
Alignment explanation
Indices: 1619926--1619965 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1619916 TATTAAAAAA
1619926 TATTTTTTAATTAATAATTAT
1 TATTTTTTAATTAATAATTAT
1619947 TATTTTTATAA-TAA-AATTA
1 TATTTTT-TAATTAATAATTA
1619966 AATAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 10 0.56
22 3 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTTTAATTAATAATTAT
Found at i:1619983 original size:35 final size:34
Alignment explanation
Indices: 1619944--1620009 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
1619934 AATTAATAAT
**
1619944 TATTATTTTTATAATAAAATTAAATAAAATTTTTA
1 TATTATTTAAATAAT-AAATTAAATAAAATTTTTA
* *
1619979 TATTATTTAAATAATAATTTAAATTAAATTT
1 TATTATTTAAATAATAAATTAAATAAAATTT
1620010 AAATTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 14 0.52
35 13 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
TATTATTTAAATAATAAATTAAATAAAATTTTTA
Found at i:1620005 original size:17 final size:17
Alignment explanation
Indices: 1619985--1620022 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1619975 TTTATATTAT
1619985 TTAAATA-ATAATTTAAA
1 TTAAATATA-AATTTAAA
*
1620002 TTAAATTTAAATTTAAA
1 TTAAATATAAATTTAAA
1620019 TTAA
1 TTAA
1620023 CTTATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAAATATAAATTTAAA
Found at i:1620536 original size:12 final size:12
Alignment explanation
Indices: 1620519--1620545 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1620509 TTGAAGGGCC
1620519 TTTTTTTTTTTG
1 TTTTTTTTTTTG
1620531 TTTTTTTTTTTG
1 TTTTTTTTTTTG
1620543 TTT
1 TTT
1620546 CTTCTAATCG
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:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:1628292 original size:21 final size:21
Alignment explanation
Indices: 1628227--1628294 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
1628217 ATATAAATAA
1628227 AATTATATTTATATAATAATTT
1 AATTATA-TTATATAATAATTT
** * *
1628249 AAAAATAATATAATATATCATTT
1 AATTATATTAT-ATA-ATAATTT
1628272 ATATTATATTATATAAT-ATTT
1 A-ATTATATTATATAATAATTT
1628293 AA
1 AA
1628295 GATATAATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
20 1 0.03
21 8 0.22
22 10 0.28
23 10 0.28
24 7 0.19
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTATATTATATAATAATTT
Found at i:1628338 original size:19 final size:19
Alignment explanation
Indices: 1628208--1628343 Score: 57
Period size: 21 Copynumber: 6.8 Consensus size: 19
1628198 TAATTATATA
*
1628208 TTATATATAATATAAATAAAA
1 TTATAT-TAATATAAAT-AAT
*
1628229 TTATATTTATAT-AATAAT
1 TTATATTAATATAAATAAT
* *
1628247 TTAAAAATAATATAATATATCAT
1 TT-ATATTAATATAA-ATA--AT
1628270 TTATATTATATTATATAAT-AT
1 TTATATTA-A-TATA-AATAAT
* * *
1628291 TTA-A--GATATAATTATTT
1 TTATATTAATATAAATA-AT
1628308 TTATATAATAATATAAATAAT
1 TTATAT--TAATATAAATAAT
*
1628329 TTATATTAATTTAAA
1 TTATATTAATATAAA
1628344 ATCGATTTAA
Statistics
Matches: 86, Mismatches: 14, Indels: 32
0.65 0.11 0.24
Matches are distributed among these distances:
15 2 0.02
16 4 0.05
17 5 0.06
18 5 0.06
19 18 0.21
20 7 0.08
21 21 0.24
22 12 0.14
23 5 0.06
24 6 0.07
25 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (19 bp):
TTATATTAATATAAATAAT
Found at i:1628622 original size:31 final size:32
Alignment explanation
Indices: 1628555--1628632 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 32
1628545 AAATAATTAA
*
1628555 AATAAAATATAAATATCTTAAAATCTTGTAAT
1 AATAAAATATAAATATCTTAAAATCTTATAAT
* * * *
1628587 -ATAAATTATTAATGTCTTAAAAT-TTATATT
1 AATAAAATATAAATATCTTAAAATCTTATAAT
*
1628617 AATAAAATTTAAATAT
1 AATAAAATATAAATAT
1628633 AATTATAAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
30 5 0.14
31 31 0.86
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (32 bp):
AATAAAATATAAATATCTTAAAATCTTATAAT
Found at i:1628909 original size:22 final size:22
Alignment explanation
Indices: 1628884--1628925 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1628874 TTGAATTTAT
*
1628884 ATTTTTATTAATATTT-TTTAAA
1 ATTTTTAATAAT-TTTATTTAAA
1628906 ATTTTTAATAATTTTATTTA
1 ATTTTTAATAATTTTATTTA
1628926 TCAAGTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTTTTAATAATTTTATTTAAA
Found at i:1629445 original size:20 final size:22
Alignment explanation
Indices: 1629392--1629456 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
1629382 TTAATGTAAC
*
1629392 AATTTTTTAATTAATAAAATTA
1 AATTTTTTAAATAATAAAATTA
***
1629414 AATTTAAAAAATAA-AAAA-TA
1 AATTTTTTAAATAATAAAATTA
* *
1629434 AATTTTTTAAATATTAATATTA
1 AATTTTTTAAATAATAAAATTA
1629456 A
1 A
1629457 TGATATCATA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
20 12 0.38
21 7 0.22
22 13 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTTTTTAAATAATAAAATTA
Found at i:1632689 original size:16 final size:17
Alignment explanation
Indices: 1632611--1632692 Score: 64
Period size: 16 Copynumber: 4.8 Consensus size: 17
1632601 GTTAATATAG
1632611 ATATATAAATATTTTAAAAT
1 ATATATAAATA---TAAAAT
* *
1632631 TTATAT-AATATAAATT
1 ATATATAAATATAAAAT
*
1632647 AT-TAT-CATATTAAAAT
1 ATATATAAATA-TAAAAT
*
1632663 TTATATAAATATAAAAT
1 ATATATAAATATAAAAT
1632680 ATAT-TAAATATAA
1 ATATATAAATATAA
1632693 TTATGTTATA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
15 6 0.12
16 21 0.41
17 12 0.24
18 3 0.06
19 4 0.08
20 5 0.10
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATATAAATATAAAAT
Found at i:1632979 original size:15 final size:16
Alignment explanation
Indices: 1632948--1632981 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1632938 AAATTGATTG
1632948 AAAATTTAAATAAAAT
1 AAAATTTAAATAAAAT
*
1632964 AAAATTTTAA-AAAAT
1 AAAATTTAAATAAAAT
1632979 AAA
1 AAA
1632982 GAACATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTTAAATAAAAT
Found at i:1638980 original size:263 final size:263
Alignment explanation
Indices: 1638511--1639027 Score: 750
Period size: 263 Copynumber: 2.0 Consensus size: 263
1638501 ACTCATACTC
* * * *
1638511 ATGTGTGCGTATTGGACATAAATATATGTACAATATGATTATATTTAATTATTTTAAGTTTTTTT
1 ATGTGTGCGTATTAGACATAAATATATGTACAACACGAATATATTTAATTATTTTAAGTTTTTTT
* *
1638576 CATATATTTAGAAAGTTATAGAAAGATCATATCTTTATATTCATATCCAGATATATATAAGATAT
66 CATATATTTAAAAAGTTATAGAAAGATCATATCTTTATATTCATATCCAAATATATATAAGATAT
* *
1638641 GAGTATCGAACATTGTTATCTATCTTTTGCTGCAATTTTCGTTGACATAAGTACGAAGATAAAAT
131 GAGTATCGAACATTGTTATCTATCTTTTGCTACAATTTTCGTTGACATAAGTACAAAGATAAAAT
* * *
1638706 TTTTTAAATATATAAAAACTTTCAAAAAAATATTAAATATATTCATGTCGAATGTATATATTAGA
196 CTTTCAAATATATAAAAACTTTCAAAAAAATATTAAATATATTCATGTCAAATGTATATATTAGA
1638771 CTT
261 CTT
* *
1638774 ATGTGTGCGTATTAGACATGAATATATGTACAACACGAATATATTTAATTTTTTTAAAGTTTTTT
1 ATGTGTGCGTATTAGACATAAATATATGTACAACACGAATATATTTAATTATTTT-AAGTTTTTT
* *
1638839 T-ATATATTTAAAAAGTCT-TAGAATGATCATTTCTTTATATTCATATCCAAATATATATAAGAT
65 TCATATATTTAAAAAGT-TATAGAAAGATCATATCTTTATATTCATATCCAAATATATATAAGAT
* * ** * *
1638902 ATGAGTATCGAACATTGTTATTTATCTTTTGTTACTTTTTTCGTTGACATAAGTATAAATATAAA
129 ATGAGTATCGAACATTGTTATCTATCTTTTGCTACAATTTTCGTTGACATAAGTACAAAGATAAA
*** *** *
1638967 ATCTTTCAAATATATAAATTTTTTTTTAAAAATATTAAATATATTGATGTCAAATGTATAT
194 ATCTTTCAAATATATAAAAACTTTCAAAAAAATATTAAATATATTCATGTCAAATGTATAT
1639028 CTATATTTAT
Statistics
Matches: 224, Mismatches: 28, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
263 213 0.95
264 11 0.05
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.43
Consensus pattern (263 bp):
ATGTGTGCGTATTAGACATAAATATATGTACAACACGAATATATTTAATTATTTTAAGTTTTTTT
CATATATTTAAAAAGTTATAGAAAGATCATATCTTTATATTCATATCCAAATATATATAAGATAT
GAGTATCGAACATTGTTATCTATCTTTTGCTACAATTTTCGTTGACATAAGTACAAAGATAAAAT
CTTTCAAATATATAAAAACTTTCAAAAAAATATTAAATATATTCATGTCAAATGTATATATTAGA
CTT
Found at i:1640220 original size:17 final size:17
Alignment explanation
Indices: 1640200--1640249 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
1640190 ACATATCATA
*
1640200 TTTATATTATTTTTTAT
1 TTTATATTATATTTTAT
*
1640217 TTTATATTATATTATAT
1 TTTATATTATATTTTAT
1640234 TTTATATTATATTTTA
1 TTTATATTATATTTTA
1640250 ACTATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATATTATATTTTAT
Found at i:1640221 original size:12 final size:12
Alignment explanation
Indices: 1640200--1640249 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
1640190 ACATATCATA
1640200 TTTATATTAT-T
1 TTTATATTATAT
*
1640211 TTT-TATTTTAT
1 TTTATATTATAT
*
1640222 ATTATATTATAT
1 TTTATATTATAT
1640234 TTTATATTATAT
1 TTTATATTATAT
1640246 TTTA
1 TTTA
1640250 ACTATTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 5 0.15
11 6 0.18
12 22 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:1640293 original size:2 final size:2
Alignment explanation
Indices: 1640286--1640314 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1640276 TAAAATTATC
1640286 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
1640315 AAGTTTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1643855 original size:15 final size:15
Alignment explanation
Indices: 1643837--1643891 Score: 83
Period size: 15 Copynumber: 3.7 Consensus size: 15
1643827 GGAGGTGGCA
1643837 GCTATGGTGGTGGTG
1 GCTATGGTGGTGGTG
*
1643852 GCTATGGCGGTGGTG
1 GCTATGGTGGTGGTG
* *
1643867 GCTATGGTGGCGGCG
1 GCTATGGTGGTGGTG
1643882 GCTATGGTGG
1 GCTATGGTGG
1643892 CAGCAGCGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.07, C:0.13, G:0.53, T:0.27
Consensus pattern (15 bp):
GCTATGGTGGTGGTG
Found at i:1643902 original size:18 final size:15
Alignment explanation
Indices: 1643837--1643909 Score: 74
Period size: 15 Copynumber: 4.7 Consensus size: 15
1643827 GGAGGTGGCA
* *
1643837 GCTATGGTGGTGGTG
1 GCTATGGTGGCGGCG
* * *
1643852 GCTATGGCGGTGGTG
1 GCTATGGTGGCGGCG
1643867 GCTATGGTGGCGGCG
1 GCTATGGTGGCGGCG
1643882 GCTATGGTGGCAGCAGCG
1 GCTATGGTGGC-G--GCG
1643900 GCTATGGTGG
1 GCTATGGTGG
1643910 TGGTAATTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
15 37 0.73
16 1 0.02
18 13 0.25
ACGTcount: A:0.10, C:0.15, G:0.51, T:0.25
Consensus pattern (15 bp):
GCTATGGTGGCGGCG
Found at i:1653603 original size:31 final size:29
Alignment explanation
Indices: 1653521--1653614 Score: 72
Period size: 29 Copynumber: 3.2 Consensus size: 29
1653511 TAATGATAAT
1653521 TTTTTTAAT-TTTATAAGTAATATT-AAAAA
1 TTTTTTAATATTTATAA-T-ATATTAAAAAA
* * *
1653550 TTTTAT-ATATTT-T-ATTTTTTAAAATTAA
1 TTTTTTAATATTTATAATATATTAAAA--AA
1653578 TTTTTTAATATTTATAATATATTAAAAAGA
1 TTTTTTAATATTTATAATATATTAAAAA-A
*
1653608 ATTTTTA
1 TTTTTTA
1653615 TTTTATTAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
25 3 0.06
26 4 0.08
27 1 0.02
28 10 0.20
29 15 0.30
30 8 0.16
31 9 0.18
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (29 bp):
TTTTTTAATATTTATAATATATTAAAAAA
Found at i:1654036 original size:38 final size:37
Alignment explanation
Indices: 1653985--1654059 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 37
1653975 CCTGAGGTCC
1653985 CAAAATTCTGCTAATAAATATTTATTTTTTTTAATGAA
1 CAAAATTCTGCTAATAAATATTTA-TTTTTTTAATGAA
1654023 CAAAATTCTGCTAATAAATATTTATTTTTTTAATGAA
1 CAAAATTCTGCTAATAAATATTTATTTTTTTAATGAA
1654060 AAAGGGGTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 13 0.35
38 24 0.65
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (37 bp):
CAAAATTCTGCTAATAAATATTTATTTTTTTAATGAA
Found at i:1654393 original size:33 final size:33
Alignment explanation
Indices: 1654355--1654418 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1654345 TATGAGTGAC
*
1654355 ATAAATATACTAAT-TTTTAAAAATTTATATACT
1 ATAAAT-TACTAATATATTAAAAATTTATATACT
* *
1654388 ATAAATTATTAATATATTAAAATTTTATATA
1 ATAAATTACTAATATATTAAAAATTTATATA
1654419 AATAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 6 0.22
33 21 0.78
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (33 bp):
ATAAATTACTAATATATTAAAAATTTATATACT
Found at i:1655066 original size:12 final size:12
Alignment explanation
Indices: 1655041--1655078 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1655031 AAATACGATA
1655041 AAAAAATAAT-T
1 AAAAAATAATAT
*
1655052 AAAATATAATAT
1 AAAAAATAATAT
*
1655064 AAAAAATAACAT
1 AAAAAATAATAT
1655076 AAA
1 AAA
1655079 TATTTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAAATAATAT
Found at i:1659756 original size:23 final size:21
Alignment explanation
Indices: 1659712--1659756 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
1659702 ATCCGCGTTC
*
1659712 TAAAATTGTTATTTTTTCTAT
1 TAAAATTGTTATTTTTTATAT
*
1659733 TAAAATATTTTATATTTTTATAT
1 TAAAAT-TGTTAT-TTTTTATAT
1659756 T
1 T
1659757 TTTAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 5 0.25
23 9 0.45
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
TAAAATTGTTATTTTTTATAT
Found at i:1661109 original size:18 final size:18
Alignment explanation
Indices: 1661086--1661121 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1661076 TTAAGCTTAT
1661086 TTTACTTATATACACAGA
1 TTTACTTATATACACAGA
1661104 TTTACTTATATACACAGA
1 TTTACTTATATACACAGA
1661122 CACATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (18 bp):
TTTACTTATATACACAGA
Found at i:1665394 original size:26 final size:26
Alignment explanation
Indices: 1665365--1665414 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1665355 TTGAAATTTA
*
1665365 AAAATAATTTAAATTTAAAATAATAC
1 AAAATAATTTAAATCTAAAATAATAC
* * *
1665391 AAAATGATTTGAATCTGAAATAAT
1 AAAATAATTTAAATCTAAAATAAT
1665415 TCGAATTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (26 bp):
AAAATAATTTAAATCTAAAATAATAC
Found at i:1665450 original size:23 final size:25
Alignment explanation
Indices: 1665403--1665450 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
1665393 AATGATTTGA
*
1665403 ATCTGAAATAATTCGAATTTGAAATG
1 ATCTGAAATAATTC-AATTTAAAATG
1665429 ATCTG-AATAATT-AATTTAAAAT
1 ATCTGAAATAATTCAATTTAAAAT
1665451 AATTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
25 7 0.33
26 5 0.24
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (25 bp):
ATCTGAAATAATTCAATTTAAAATG
Found at i:1665504 original size:19 final size:19
Alignment explanation
Indices: 1665468--1665511 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1665458 ATTTAAATTT
** *
1665468 AAATATTATTTTATTTAAA
1 AAATATTAAATTAATTAAA
1665487 AAATATTAAATTAATTAAA
1 AAATATTAAATTAATTAAA
1665506 ATAATA
1 A-AATA
1665512 CTTATAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATATTAAATTAATTAAA
Found at i:1666395 original size:22 final size:23
Alignment explanation
Indices: 1666316--1666381 Score: 96
Period size: 23 Copynumber: 2.8 Consensus size: 23
1666306 TGAGATTTAT
* *
1666316 TAAATTCAAATTTTACTTAAATAA
1 TAAATTTAAATTTT-TTTAAATAA
*
1666340 TAAATTTAATTTTTTTTAAATAA
1 TAAATTTAAATTTTTTTAAATAA
1666363 TAAATTTAAATTTTTTTAA
1 TAAATTTAAATTTTTTTAA
1666382 TGCTTAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
23 26 0.68
24 12 0.32
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAATTTAAATTTTTTTAAATAA
Found at i:1666900 original size:2 final size:2
Alignment explanation
Indices: 1666895--1666929 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1666885 ACACACACAC
1666895 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
1666930 AACATGCCTA
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:1667654 original size:24 final size:25
Alignment explanation
Indices: 1667609--1667655 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1667599 AATAATTTAA
*
1667609 TTTAATATTATATTATATTTAAAAT
1 TTTAATATTATATTATAATTAAAAT
1667634 TTTAAT-TTAT-TTAATAATTAAA
1 TTTAATATTATATT-ATAATTAAA
1667656 TCCTCGAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 12 0.60
25 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTAATATTATATTATAATTAAAAT
Found at i:1668849 original size:23 final size:23
Alignment explanation
Indices: 1668823--1668871 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1668813 ATTTAATACT
*
1668823 TATAGTAAATCTAATTAACATAA
1 TATAGTAAATCCAATTAACATAA
*
1668846 TATATTAAATCCAATTAACATAA
1 TATAGTAAATCCAATTAACATAA
1668869 TAT
1 TAT
1668872 GTTATTGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (23 bp):
TATAGTAAATCCAATTAACATAA
Found at i:1670012 original size:30 final size:31
Alignment explanation
Indices: 1669952--1670034 Score: 73
Period size: 30 Copynumber: 2.7 Consensus size: 31
1669942 ATTTAATTTT
* * * *
1669952 TTTAAAAATTTACTTAAA-CTTAATTTAAAA
1 TTTAAAATTTTATTTAAATATTAATTAAAAA
1669982 TTTAAAATTTTATTTAAATATTAA-TAAAAA
1 TTTAAAATTTTATTTAAATATTAATTAAAAA
**
1670012 TAAAAATATTTTATATT-AATATT
1 TTTAAA-ATTTTAT-TTAAATATT
1670035 TATATATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
30 25 0.57
31 17 0.39
32 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (31 bp):
TTTAAAATTTTATTTAAATATTAATTAAAAA
Done.