Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold258
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: 5730937
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 25
Found at i:1577788 original size:20 final size:20
Alignment explanation
Indices: 1577751--1577796 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1577741 AAGAATTGAA
* *
1577751 GAGGGATACAAGATAGGGAT
1 GAGGGATACAAGAGAGGGAG
**
1577771 GAGGGATACTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
1577791 GAGGGA
1 GAGGGA
1577797 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.48, T:0.13
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:1577933 original size:27 final size:27
Alignment explanation
Indices: 1577877--1577942 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
1577867 AGCCTCCATA
*
1577877 TTTGACAAATACAAAGGAAACCATAATT
1 TTTGACAAACACAAA-GAAACCATAATT
1577905 TTTGACAAACACAAA-ATAACCACT-ATT
1 TTTGACAAACACAAAGA-AACCA-TAATT
1577932 TTTGACAAACA
1 TTTGACAAACA
1577943 AATGGGTGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 1 0.03
27 19 0.54
28 15 0.43
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.26
Consensus pattern (27 bp):
TTTGACAAACACAAAGAAACCATAATT
Found at i:1584486 original size:20 final size:20
Alignment explanation
Indices: 1584452--1584497 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1584442 AAGAATTGAA
*
1584452 GAGGGATACAAGAGAGAGAT
1 GAGGGATACAAGAGAGAGAG
** *
1584472 GAGGGATACTTGAGAGGGAG
1 GAGGGATACAAGAGAGAGAG
1584492 GAGGGA
1 GAGGGA
1584498 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.48, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGAGAG
Found at i:1585252 original size:14 final size:14
Alignment explanation
Indices: 1585235--1585279 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
1585225 ACGAATACGA
1585235 TATATTAAATATAT
1 TATATTAAATATAT
*
1585249 TATATT-AAT-CA-
1 TATATTAAATATAT
1585260 TAT-TTAAATATAT
1 TATATTAAATATAT
1585273 TATATTA
1 TATATTA
1585280 TATTTGTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
10 2 0.08
11 6 0.24
12 2 0.08
13 6 0.24
14 9 0.36
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
TATATTAAATATAT
Found at i:1585304 original size:21 final size:22
Alignment explanation
Indices: 1585271--1585312 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1585261 ATTTAAATAT
1585271 ATTATATTATATTTGTTAATTA
1 ATTATATTATATTTGTTAATTA
*
1585293 ATTATA-TATATTTTTTAATT
1 ATTATATTATATTTGTTAATT
1585313 TTTTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
ATTATATTATATTTGTTAATTA
Found at i:1588145 original size:2 final size:2
Alignment explanation
Indices: 1588132--1588165 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1588122 TTTTGCACTG
*
1588132 AT AT AT AC 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
1588166 CAAAACAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1588631 original size:17 final size:17
Alignment explanation
Indices: 1588611--1588713 Score: 75
Period size: 17 Copynumber: 6.5 Consensus size: 17
1588601 ATAAATTTGA
1588611 TAAATATATTATAATAT
1 TAAATATATTATAATAT
*
1588628 TAAA-AT-TTATAAAAT
1 TAAATATATTATAATAT
*
1588643 ATAAAT-TATTAAAATAT
1 -TAAATATATTATAATAT
1588660 T-AA-AT-TT-T-ATA-
1 TAAATATATTATAATAT
1588671 TAAAT-TATTATAAT-T
1 TAAATATATTATAATAT
1588686 TAAATATGATTATAATAT
1 TAAATAT-ATTATAATAT
*
1588704 AAAAATATAT
1 -TAAATATAT
1588714 AAATTATCAA
Statistics
Matches: 67, Mismatches: 5, Indels: 27
0.68 0.05 0.27
Matches are distributed among these distances:
11 1 0.01
12 6 0.09
13 2 0.03
14 3 0.04
15 18 0.27
16 9 0.13
17 19 0.28
18 3 0.04
19 6 0.09
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (17 bp):
TAAATATATTATAATAT
Found at i:1588634 original size:27 final size:23
Alignment explanation
Indices: 1588593--1588657 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 23
1588583 ATATAATAAA
1588593 AAATATATATAAATTTGATAAATATATT
1 AAATAT-TA-AAATTT-ATAAA-ATA-T
1588621 ATAATATTAAAATTTATAAAATAT
1 A-AATATTAAAATTTATAAAATAT
1588645 AAATTATTAAAAT
1 AAA-TATTAAAAT
1588658 ATTAAATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
23 2 0.06
24 11 0.31
25 3 0.09
26 5 0.14
27 6 0.17
28 3 0.09
29 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
AAATATTAAAATTTATAAAATAT
Found at i:1588637 original size:15 final size:16
Alignment explanation
Indices: 1588611--1588719 Score: 74
Period size: 15 Copynumber: 7.1 Consensus size: 16
1588601 ATAAATTTGA
1588611 TAAATATATTATAATAT
1 TAAA-ATATTATAATAT
*
1588628 TAAAAT-TTATAAAAT
1 TAAAATATTATAATAT
* *
1588643 ATAAATTATTAAAATAT
1 -TAAAATATTATAATAT
1588660 T-AAAT-TT-T-ATA-
1 TAAAATATTATAATAT
*
1588671 TAAATTATTATAAT-T
1 TAAAATATTATAATAT
1588686 TAAATATGATTATAATAT
1 TAAA-AT-ATTATAATAT
*
1588704 AAAAATA-TATAA-AT
1 TAAAATATTATAATAT
1588718 TA
1 TA
1588720 TCAATTTTAT
Statistics
Matches: 72, Mismatches: 10, Indels: 23
0.69 0.10 0.22
Matches are distributed among these distances:
11 1 0.01
12 6 0.08
13 2 0.03
14 6 0.08
15 22 0.31
16 10 0.14
17 21 0.29
18 4 0.06
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (16 bp):
TAAAATATTATAATAT
Found at i:1588659 original size:32 final size:34
Alignment explanation
Indices: 1588592--1588675 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 34
1588582 TATATAATAA
* *
1588592 AAAATATATATAAATTTGATAAATATATTATAATATT
1 AAAATTTATATAAA--T-ATAAATATATTAAAATATT
1588629 AAAATTTATA-AAATATAAAT-TATTAAAATATT
1 AAAATTTATATAAATATAAATATATTAAAATATT
*
1588661 AAATTTTATATAAAT
1 AAAATTTATATAAAT
1588676 TATTATAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
32 20 0.47
33 10 0.23
34 1 0.02
36 3 0.07
37 9 0.21
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (34 bp):
AAAATTTATATAAATATAAATATATTAAAATATT
Found at i:1588699 original size:27 final size:27
Alignment explanation
Indices: 1588641--1588717 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
1588631 AATTTATAAA
* *
1588641 ATATAAATTATTAAAATATTAAATTTT
1 ATATAAATTATTAAAATATTAAATATG
*
1588668 ATATAAATTATTATAAT-TTAAATATG
1 ATATAAATTATTAAAATATTAAATATG
*
1588694 AT-TATAA-TATAAAAATATATAAAT
1 ATATA-AATTATTAAAATAT-TAAAT
1588718 TATCAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
25 9 0.21
26 12 0.29
27 21 0.50
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (27 bp):
ATATAAATTATTAAAATATTAAATATG
Found at i:1592520 original size:3 final size:3
Alignment explanation
Indices: 1592514--1592546 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1592504 CATAGATATG
1592514 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1592547 AAAAAAGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1593989 original size:3 final size:3
Alignment explanation
Indices: 1593976--1594006 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1593966 GACATATAGA
*
1593976 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1594007 TATTTTTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:1598619 original size:2 final size:2
Alignment explanation
Indices: 1598612--1598648 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1598602 GTCGAAAAGC
1598612 AT 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 AT A
1598649 ATCTGTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1599042 original size:47 final size:48
Alignment explanation
Indices: 1598978--1599079 Score: 138
Period size: 47 Copynumber: 2.2 Consensus size: 48
1598968 AATTAAATAT
* * *
1598978 TTAAA-TTTAAATATCACTTTTTAAAAAAAT-AACATAAATTAATTAAA
1 TTAAATTTTAAATATCACTTCTT-AAAAAATCAACATAAACTAATCAAA
1599025 TTAAATTTTAAAT-TCACTTCTTAAAAAATCAACATAAACTAATCAAA
1 TTAAATTTTAAATATCACTTCTTAAAAAATCAACATAAACTAATCAAA
*
1599072 TCAAATTT
1 TTAAATTT
1599080 CGAATTTACC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
46 7 0.14
47 35 0.71
48 7 0.14
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (48 bp):
TTAAATTTTAAATATCACTTCTTAAAAAATCAACATAAACTAATCAAA
Found at i:1599564 original size:22 final size:21
Alignment explanation
Indices: 1599528--1599568 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1599518 TAATAATACC
1599528 ATTAAATATTAATATTTTTGT
1 ATTAAATATTAATATTTTTGT
*
1599549 ATTAATATATTTATATTTTT
1 ATTAA-ATATTAATATTTTT
1599569 TAAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTAAATATTAATATTTTTGT
Found at i:1599741 original size:12 final size:12
Alignment explanation
Indices: 1599726--1599761 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1599716 ATTATCATCA
*
1599726 ATATATATATAT
1 ATATGTATATAT
*
1599738 ATATGTATATGT
1 ATATGTATATAT
1599750 ATATGTATATAT
1 ATATGTATATAT
1599762 TCATGAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:1600405 original size:79 final size:83
Alignment explanation
Indices: 1600300--1600453 Score: 226
Period size: 79 Copynumber: 1.9 Consensus size: 83
1600290 AAAAAAAAAA
* *
1600300 TTATAAACAGCAAAATGTTTATAAAATAAATTTTTCCAAAT-AAAGA-A-TCTC-TTGAAACTTT
1 TTATAAACAGCAAAATGTTTATAAAATAAATTTTACCAAATAAAAGACATTCTCTTTGAAACTAT
1600361 ACATAATATAAACATTAT
66 ACATAATATAAACATTAT
* * * *
1600379 TTATATACATCAAAATGTTTATAAAATGAATTTTACCAAGTAAAAGACATTCTCTTTGAAACTAT
1 TTATAAACAGCAAAATGTTTATAAAATAAATTTTACCAAATAAAAGACATTCTCTTTGAAACTAT
1600444 ACATAATATA
66 ACATAATATA
1600454 TATATAAGTA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
79 36 0.55
80 5 0.08
81 1 0.02
82 4 0.06
83 19 0.29
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.36
Consensus pattern (83 bp):
TTATAAACAGCAAAATGTTTATAAAATAAATTTTACCAAATAAAAGACATTCTCTTTGAAACTAT
ACATAATATAAACATTAT
Found at i:1610588 original size:21 final size:23
Alignment explanation
Indices: 1610558--1610601 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
1610548 GAGAGATTTT
1610558 TTAAAAATAATTAT-T-AATATA
1 TTAAAAATAATTATATAAATATA
*
1610579 TTAAATATAATTATATAAATATA
1 TTAAAAATAATTATATAAATATA
1610602 ATATTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 1 0.05
23 6 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAAAAATAATTATATAAATATA
Found at i:1610597 original size:14 final size:14
Alignment explanation
Indices: 1610575--1610709 Score: 54
Period size: 15 Copynumber: 9.6 Consensus size: 14
1610565 TAATTATTAA
1610575 TATATTAAATATAAT
1 TATA-TAAATATAAT
1610590 TATATAAATATAA-
1 TATATAAATATAAT
1610603 TAT-T-AATA-AA-
1 TATATAAATATAAT
*
1610613 -ATAAAAATA-AAT
1 TATATAAATATAAT
** *
1610625 TA-ATATTTTAAAAT
1 TATATA-AATATAAT
1610639 TATAT-AATATAAAT
1 TATATAAATAT-AAT
*
1610653 TATTAATATAATAAAATT
1 TA-T-ATA-AATATAA-T
*
1610671 TATATAAATATATAA
1 TATATAAATATA-AT
*
1610686 TATTTTAAATATAAT
1 TA-TATAAATATAAT
1610701 TATAATAAA
1 TAT-ATAAA
1610710 ATACATAAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 32
0.67 0.10 0.24
Matches are distributed among these distances:
9 2 0.02
10 2 0.02
11 10 0.11
12 3 0.03
13 8 0.09
14 20 0.22
15 21 0.23
16 15 0.16
17 3 0.03
18 7 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TATATAAATATAAT
Found at i:1610659 original size:13 final size:14
Alignment explanation
Indices: 1610635--1610663 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1610625 TAATATTTTA
1610635 AAATTATATAATAT
1 AAATTATATAATAT
1610649 AAATTAT-TAATAT
1 AAATTATATAATAT
1610662 AA
1 AA
1610664 TAAAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATTATATAATAT
Found at i:1610680 original size:20 final size:20
Alignment explanation
Indices: 1610640--1610711 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 20
1610630 TTTTAAAATT
1610640 ATATAATATAAA-TTAT-T-A
1 ATATAATA-AAATTTATATAA
1610658 ATATAATAAAATTTATATAA
1 ATATAATAAAATTTATATAA
*
1610678 ATAT-ATAATATTTTAAATATAA
1 ATATAATAA-AATTT--ATATAA
*
1610700 TTATAATAAAAT
1 ATATAATAAAAT
1610712 ACATAAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
17 3 0.07
18 12 0.27
19 5 0.11
20 9 0.20
22 11 0.25
23 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATAATAAAATTTATATAA
Found at i:1610685 original size:22 final size:23
Alignment explanation
Indices: 1610658--1610711 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 23
1610648 TAAATTATTA
*
1610658 ATATAATAAAATTTATATA-AAT
1 ATATAATAAAATTTAAATATAAT
*
1610680 ATATAAT--ATTTTAAATATAAT
1 ATATAATAAAATTTAAATATAAT
1610701 -TATAATAAAAT
1 ATATAATAAAAT
1610712 ACATAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 14 0.54
21 3 0.12
22 9 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATAATAAAATTTAAATATAAT
Found at i:1610694 original size:27 final size:30
Alignment explanation
Indices: 1610564--1610694 Score: 72
Period size: 27 Copynumber: 4.7 Consensus size: 30
1610554 TTTTTTAAAA
* *
1610564 ATAATTATTAATATATT-AAA-TATAATTAT
1 ATAATTATTAATATTTTAAAATTAT-ATAAT
* * *
1610593 ATAAATA-TAATATTAATAAAA-TA-AAAAT
1 ATAATTATTAATATT-TTAAAATTATATAAT
1610621 A-AATTA--A-TATTTTAAAATTATATAAT
1 ATAATTATTAATATTTTAAAATTATATAAT
**
1610647 ATAAATTATTAATATAATAAAATT-TAT-AT
1 AT-AATTATTAATATTTTAAAATTATATAAT
1610676 A-AA-TATATAATATTTTAAA
1 ATAATTAT-TAATATTTTAAA
1610695 TATAATTATA
Statistics
Matches: 80, Mismatches: 12, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
24 5 0.06
25 6 0.08
26 9 0.11
27 16 0.20
28 15 0.19
29 10 0.12
30 9 0.11
31 10 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
ATAATTATTAATATTTTAAAATTATATAAT
Found at i:1610721 original size:55 final size:54
Alignment explanation
Indices: 1610563--1610728 Score: 150
Period size: 55 Copynumber: 3.0 Consensus size: 54
1610553 ATTTTTTAAA
* *
1610563 AATAATTAT-TAATATATTAAATATAATTAT-ATAAATATAATATTAATAAAA--T
1 AATAAATATATAATATTTTAAATATAATTATAATAAA-ATAATA-TAATAAAATTT
* *
1610615 AA-AAATAAATTAATATTTTAAA-ATTA-TATAATATAAATTATTAATATAATAAAATTT
1 AATAAATATA-TAATATTTTAAATATAATTAT-A-ATAAA--A-TAATATAATAAAATTT
1610672 ATATAAATATATAATATTTTAAATATAATTATAATAAAATACATA-AATAAAATTT
1 A-ATAAATATATAATATTTTAAATATAATTATAATAAAATA-ATATAATAAAATTT
1610727 AA
1 AA
1610729 AACTTACATA
Statistics
Matches: 94, Mismatches: 6, Indels: 26
0.75 0.05 0.21
Matches are distributed among these distances:
51 7 0.07
52 5 0.05
53 11 0.12
54 6 0.06
55 23 0.24
56 9 0.10
57 2 0.02
58 18 0.19
59 10 0.11
60 3 0.03
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (54 bp):
AATAAATATATAATATTTTAAATATAATTATAATAAAATAATATAATAAAATTT
Found at i:1611193 original size:28 final size:28
Alignment explanation
Indices: 1611136--1611242 Score: 92
Period size: 28 Copynumber: 3.8 Consensus size: 28
1611126 ATACATATAC
* *
1611136 ATGTAAATATAATTTTATATATATTT-AT
1 ATGTAAATATAAATTTA-AAATATTTAAT
*
1611164 ATGTAAATATAAATTTAAAATTTTTAAT
1 ATGTAAATATAAATTTAAAATATTTAAT
* * * *
1611192 ATTTAATATAAAAATTTTAAATATTAAAT
1 ATGTAA-ATATAAATTTAAAATATTTAAT
** *
1611221 AAATAGATA-AAATTTAAAATAT
1 ATGTAAATATAAATTTAAAATAT
1611243 AATAAATTAT
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
27 18 0.28
28 26 0.40
29 21 0.32
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (28 bp):
ATGTAAATATAAATTTAAAATATTTAAT
Found at i:1611206 original size:22 final size:22
Alignment explanation
Indices: 1611167--1611221 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
1611157 TATTTATATG
*
1611167 TAAATA-TAAAT-TTAAAATTT
1 TAAATATTAAATATAAAAATTT
* *
1611187 TTAATATTTAATATAAAAATTT
1 TAAATATTAAATATAAAAATTT
1611209 TAAATATTAAATA
1 TAAATATTAAATA
1611222 AATAGATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 5 0.18
21 4 0.14
22 19 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATATTAAATATAAAAATTT
Found at i:1612101 original size:21 final size:21
Alignment explanation
Indices: 1612077--1612116 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1612067 AATAATGAGA
* *
1612077 TTTAGTTAATTTTAAATTACC
1 TTTAATTAATGTTAAATTACC
*
1612098 TTTAATTACTGTTAAATTA
1 TTTAATTAATGTTAAATTA
1612117 AATTATTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTAATTAATGTTAAATTACC
Found at i:1613799 original size:13 final size:13
Alignment explanation
Indices: 1613783--1613834 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
1613773 CAGTATTTAT
1613783 ATTATATATTAAA
1 ATTATATATTAAA
*
1613796 ATTATATTTTAAAA
1 ATTATATATT-AAA
*
1613810 TATTATATATTTATA
1 -ATTATATA-TTAAA
1613825 ATT-TATATTA
1 ATTATATATTA
1613835 TATAAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 3 0.09
13 13 0.39
14 6 0.18
15 9 0.27
16 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATATATTAAA
Found at i:1613816 original size:15 final size:15
Alignment explanation
Indices: 1613781--1613833 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
1613771 ATCAGTATTT
*
1613781 ATATTATATATT-AA
1 ATATTATATTTTAAA
1613795 A-ATTATATTTTAAA
1 ATATTATATTTTAAA
*
1613809 ATATTATATATTTATA
1 ATATTATAT-TTTAAA
1613825 AT-TTATATT
1 ATATTATATT
1613834 ATATAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 9 0.26
14 5 0.15
15 13 0.38
16 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTATATTTTAAA
Found at i:1613845 original size:23 final size:22
Alignment explanation
Indices: 1613809--1613914 Score: 75
Period size: 20 Copynumber: 5.1 Consensus size: 22
1613799 ATATTTTAAA
*
1613809 ATATTATATAT-TTATA-ATTT
1 ATATTATATATATTTTATATTT
* **
1613829 ATATTATATAAATTTTATCATAA
1 ATATTATATATATTTTAT-ATTT
*
1613852 ATATT-TA-ATATTTTATTTTT
1 ATATTATATATATTTTATATTT
1613872 ATATTATATTATATTTTA-A-TT
1 ATATTATA-TATATTTTATATTT
* *
1613893 AT-TT-TTTATATTTTATAATT
1 ATATTATATATATTTTATATTT
1613913 AT
1 AT
1613915 TTCGTATTTA
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
18 9 0.13
19 2 0.03
20 22 0.32
21 18 0.26
22 2 0.03
23 15 0.22
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATTATATATATTTTATATTT
Found at i:1613854 original size:43 final size:44
Alignment explanation
Indices: 1613807--1613889 Score: 109
Period size: 43 Copynumber: 1.9 Consensus size: 44
1613797 TTATATTTTA
1613807 AAATA-TT-ATATATTTATAATTTATATTATA-TAAATTTTATCAT
1 AAATATTTAATAT-TTTAT-ATTTATATTATATTAAATTTTATCAT
* *
1613850 AAATATTTAATATTTTATTTTTATATTATATTATATTTTA
1 AAATATTTAATATTTTATATTTATATTATATTAAATTTTA
1613890 ATTATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
43 16 0.46
44 15 0.43
45 4 0.11
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (44 bp):
AAATATTTAATATTTTATATTTATATTATATTAAATTTTATCAT
Found at i:1613886 original size:18 final size:19
Alignment explanation
Indices: 1613859--1613907 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
1613849 TAAATATTTA
* *
1613859 ATATTTTATTTTTA-TATT
1 ATATTATATTTTAATTATT
1613877 ATATTATATTTTAATTATT
1 ATATTATATTTTAATTATT
*
1613896 -TTTTATATTTTA
1 ATATTATATTTTA
1613908 TAATTATTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
ATATTATATTTTAATTATT
Found at i:1615518 original size:2 final size:2
Alignment explanation
Indices: 1615511--1615537 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1615501 TTTTCATGGC
1615511 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1615538 TTGCTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1615741 original size:23 final size:23
Alignment explanation
Indices: 1615715--1615761 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1615705 TAGCTACAGA
*
1615715 GCTAAGAGAAGTATTAGTTTTAG
1 GCTAAGAGAAGTACTAGTTTTAG
* *
1615738 GCTAGGAGAAGTACTATTTTTAG
1 GCTAAGAGAAGTACTAGTTTTAG
1615761 G
1 G
1615762 TAATCTTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (23 bp):
GCTAAGAGAAGTACTAGTTTTAG
Found at i:1624897 original size:26 final size:26
Alignment explanation
Indices: 1624868--1624918 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
1624858 AGGCAACTTT
1624868 TCTTCGAAAATGTTTATATTGAAATC
1 TCTTCGAAAATGTTTATATTGAAATC
1624894 TCTTCGAAAATGTTTATATTGAAAT
1 TCTTCGAAAATGTTTATATTGAAAT
1624919 TAAGTGCCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (26 bp):
TCTTCGAAAATGTTTATATTGAAATC
Found at i:1631034 original size:29 final size:28
Alignment explanation
Indices: 1631001--1631077 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 28
1630991 ATAATTTACC
1631001 TAAATATATGATATATAATAAAA-AATATA
1 TAAATATATGATATATAATAAAATAA-A-A
*
1631030 TAAATATATAATATATAATAAAATAAAA
1 TAAATATATGATATATAATAAAATAAAA
1631058 T-AA-ATATGATATAATAATAA
1 TAAATATATGATAT-ATAATAA
1631078 TAATTATGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.18
27 9 0.20
28 2 0.05
29 23 0.52
30 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (28 bp):
TAAATATATGATATATAATAAAATAAAA
Found at i:1631038 original size:24 final size:26
Alignment explanation
Indices: 1631002--1631077 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 26
1630992 TAATTTACCT
*
1631002 AAATATATGATATATAATAA-AAAAT-
1 AAATAAAT-ATATATAATAATAAAATA
*
1631027 ATATAAATATATAATATATAATAAAATA
1 AAATAAATATAT-ATA-ATAATAAAATA
1631055 AAATAAATATGATATAATAATAA
1 AAATAAATAT-ATATAATAATAA
1631078 TAATTATGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
24 4 0.09
25 9 0.21
26 4 0.09
27 12 0.28
28 12 0.28
29 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (26 bp):
AAATAAATATATATAATAATAAAATA
Found at i:1632161 original size:2 final size:2
Alignment explanation
Indices: 1632154--1632178 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1632144 TCACTTCCTC
1632154 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
1632179 AGAACCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1633294 original size:2 final size:2
Alignment explanation
Indices: 1633289--1633315 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1633279 TCTCTCTCTC
1633289 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1633316 TACATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1634341 original size:18 final size:19
Alignment explanation
Indices: 1634307--1634354 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
1634297 AATATATCTC
1634307 AATATATTATAAA-TTAT-T
1 AATATATTA-AAATTTATAT
1634325 AATATATTAAAATTTATAT
1 AATATATTAAAATTTATAT
1634344 AA-ATA-TAAAAT
1 AATATATTAAAAT
1634355 ATTTTAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 9 0.32
18 16 0.57
19 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATATTAAAATTTATAT
Found at i:1637759 original size:2 final size:2
Alignment explanation
Indices: 1637741--1637781 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
1637731 CTAATACTGC
* *
1637741 AT AT A- AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1637782 GTATTCCACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1640591 original size:15 final size:16
Alignment explanation
Indices: 1640571--1640609 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
1640561 AAATTATTTT
1640571 TAAAAAA-TTTAAAAA
1 TAAAAAATTTTAAAAA
1640586 TAAAAAATTTTAAAAA
1 TAAAAAATTTTAAAAA
1640602 TAATAAAA
1 TAA-AAAA
1640610 AAATCTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.32
16 11 0.50
17 4 0.18
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAAAAATTTTAAAAA
Found at i:1640850 original size:2 final size:2
Alignment explanation
Indices: 1640803--1640832 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1640793 ACACACACAC
*
1640803 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1640833 TTTGAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1644272 original size:3 final size:3
Alignment explanation
Indices: 1644259--1644301 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
1644249 CATCATTTAA
1644259 AAT ACAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1644302 GTCCTCGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1644407 original size:52 final size:51
Alignment explanation
Indices: 1644333--1644434 Score: 127
Period size: 52 Copynumber: 2.0 Consensus size: 51
1644323 AGATATTAGT
* *
1644333 AAAAATTATTTAATTTATTTTTTTAAAAAATATATTATTTTTA-TTAAATTAA
1 AAAAATTAATTAATTTATTTTTTTAAAAAATATA--ATTTTAATTTAAATTAA
**
1644385 AAAAATTAATTAATTGTA-TTTTTTATTAAATATAATTTTAATTTAAATTA
1 AAAAATTAATTAATT-TATTTTTTTAAAAAATATAATTTTAATTTAAATTA
1644435 TTAGATAGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
50 6 0.14
51 8 0.18
52 28 0.64
53 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (51 bp):
AAAAATTAATTAATTTATTTTTTTAAAAAATATAATTTTAATTTAAATTAA
Found at i:1645538 original size:2 final size:2
Alignment explanation
Indices: 1645531--1645555 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1645521 TTTTATATTT
1645531 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1645556 GTATTTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1647263 original size:42 final size:42
Alignment explanation
Indices: 1647216--1647304 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
1647206 ATTTTTGGGA
1647216 TATTTTATGTTAACTGGTGACCAGTCCTTTTATGTTTTCATG
1 TATTTTATGTTAACTGGTGACCAGTCCTTTTATGTTTTCATG
*
1647258 TATTTTATGTTACCTGGTGACCAGTCCTTTTATGTTTTCATG
1 TATTTTATGTTAACTGGTGACCAGTCCTTTTATGTTTTCATG
1647300 TATTT
1 TATTT
1647305 GAAGAGCAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.18, C:0.15, G:0.16, T:0.52
Consensus pattern (42 bp):
TATTTTATGTTAACTGGTGACCAGTCCTTTTATGTTTTCATG
Found at i:1647598 original size:20 final size:20
Alignment explanation
Indices: 1647560--1647598 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1647550 ACGAAATTTA
*
1647560 ATGATAAATAAATATTAAAT
1 ATGATAAATAAATAATAAAT
* *
1647580 ATGATTAATAATTAATAAA
1 ATGATAAATAAATAATAAA
1647599 AATATGTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (20 bp):
ATGATAAATAAATAATAAAT
Found at i:1648019 original size:29 final size:23
Alignment explanation
Indices: 1647960--1648019 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 23
1647950 ATTCAAACAT
1647960 AATATAAATATAAAATTTTTTAA
1 AATATAAATATAAAATTTTTTAA
1647983 AAT-TAAATCATAATAATTAATTTTACAA
1 AATATAAAT-ATAA-AATT--TTTT--AA
1648011 AATATAAAT
1 AATATAAAT
1648020 TGAATTAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
22 5 0.17
23 7 0.23
24 4 0.13
26 4 0.13
28 5 0.17
29 5 0.17
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (23 bp):
AATATAAATATAAAATTTTTTAA
Found at i:1648066 original size:24 final size:23
Alignment explanation
Indices: 1648039--1648261 Score: 93
Period size: 23 Copynumber: 9.3 Consensus size: 23
1648029 ATATGATACA
*
1648039 TAAATAATATAAATAAAAAGTAAT
1 TAAA-AATATAAATAAAAAATAAT
1648063 T-AAAATATAACATAAAAAATTAACAT
1 TAAAAATATAA-ATAAAAAA-T-A-AT
*
1648089 GAATATAATATAAATATAAAAAT-AT
1 TAA-A-AATATAAATA-AAAAATAAT
*
1648114 GTAAAAATATACATAAATAAATAAT
1 -TAAAAATATAAATAAA-AAATAAT
** * ** *
1648139 TAATTTATAAAAATTTATAAT-AT
1 TAA-AAATATAAATAAAAAATAAT
**
1648162 TTTAAATAT--ATAAAAAATAA-
1 TAAAAATATAAATAAAAAATAAT
* *
1648182 TATAAATATGATATAAAAAATAAT
1 TAAAAATAT-AAATAAAAAATAAT
*
1648206 T-AAAATATAATATAAAAAAATAAA
1 TAAAAATATAA-AT-AAAAAATAAT
* * *
1648230 T-ATAACATGAATATAAAAATATAT
1 TAAAAATATAAATA-AAAAATA-AT
1648254 TAAAAATA
1 TAAAAATA
1648262 GATAAATATT
Statistics
Matches: 148, Mismatches: 29, Indels: 43
0.67 0.13 0.20
Matches are distributed among these distances:
20 14 0.09
21 1 0.01
22 12 0.08
23 42 0.28
24 40 0.27
25 17 0.11
26 4 0.03
27 1 0.01
28 5 0.03
29 12 0.08
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
TAAAAATATAAATAAAAAATAAT
Found at i:1648183 original size:14 final size:12
Alignment explanation
Indices: 1648165--1648261 Score: 80
Period size: 11 Copynumber: 8.4 Consensus size: 12
1648155 ATAATATTTT
1648165 AAAT-ATATAAA
1 AAATAATATAAA
1648176 AAATAATAT-AA
1 AAATAATATAAA
* *
1648187 ATATGATATAAA
1 AAATAATATAAA
1648199 AAATAAT-TAAA
1 AAATAATATAAA
*
1648210 ATATAATATAAAA
1 AAATAATAT-AAA
*
1648223 AAATAA-ATATA
1 AAATAATATAAA
*
1648234 ACATGAATAT-AA
1 AAAT-AATATAAA
*
1648246 AAAT-ATATTAA
1 AAATAATATAAA
1648257 AAATA
1 AAATA
1648262 GATAAATATT
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
10 4 0.06
11 34 0.50
12 20 0.29
13 10 0.15
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (12 bp):
AAATAATATAAA
Found at i:1648225 original size:48 final size:48
Alignment explanation
Indices: 1648166--1648258 Score: 129
Period size: 48 Copynumber: 1.9 Consensus size: 48
1648156 TAATATTTTA
*
1648166 AATATATAAAAAAT-AATATAAATATG-ATATAAAAA-ATAATTAAAATAT
1 AATATA-AAAAAATAAATAT-AACATGAATATAAAAATAT-ATTAAAATAT
1648214 AATATAAAAAAATAAATATAACATGAATATAAAAATATATTAAAA
1 AATATAAAAAAATAAATATAACATGAATATAAAAATATATTAAAA
1648259 ATAGATAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
47 12 0.29
48 27 0.66
49 2 0.05
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (48 bp):
AATATAAAAAAATAAATATAACATGAATATAAAAATATATTAAAATAT
Found at i:1648258 original size:10 final size:10
Alignment explanation
Indices: 1648102--1648278 Score: 65
Period size: 11 Copynumber: 16.7 Consensus size: 10
1648092 TATAATATAA
1648102 ATATAAAAAT
1 ATATAAAAAT
*
1648112 ATGTAAAAAT
1 ATATAAAAAT
* *
1648122 ATACATAAAT
1 ATATAAAAAT
* *
1648132 AAATAATTAAT
1 ATATAA-AAAT
*
1648143 TTATAAAAAT
1 ATATAAAAAT
* *
1648153 TTAT-AATAT
1 ATATAAAAAT
* *
1648162 -TTTAAATAT
1 ATATAAAAAT
1648171 ATA-AAAAAT
1 ATATAAAAAT
*
1648180 AATATAAATAT
1 -ATATAAAAAT
1648191 GATATAAAAA-
1 -ATATAAAAAT
1648201 ATAATTAAAATAT
1 AT-A-TAAAA-AT
1648214 AATATAAAAAAAT
1 -ATAT--AAAAAT
* *
1648227 AAATATAACAT
1 ATATA-AAAAT
1648238 GAATATAAAAAT
1 --ATATAAAAAT
1648250 ATATTAAAAAT
1 ATA-TAAAAAT
* *
1648261 AGATAAATATT
1 ATATAAA-AAT
1648272 ATATAAA
1 ATATAAA
1648279 TTTATAATAT
Statistics
Matches: 125, Mismatches: 25, Indels: 33
0.68 0.14 0.18
Matches are distributed among these distances:
8 2 0.02
9 16 0.13
10 39 0.31
11 46 0.37
12 9 0.07
13 7 0.06
14 6 0.05
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:1657399 original size:20 final size:20
Alignment explanation
Indices: 1657362--1657400 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1657352 AACTCTTATT
* *
1657362 TTAAATAAGTCTATTTTTTC
1 TTAAATAAATCTAATTTTTC
*
1657382 TTAAATAAATTTAATTTTT
1 TTAAATAAATCTAATTTTT
1657401 TATTCAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (20 bp):
TTAAATAAATCTAATTTTTC
Found at i:1659311 original size:21 final size:20
Alignment explanation
Indices: 1659285--1659331 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1659275 TTTTAGCCTG
*
1659285 AAAAAAAATGAAATCAAAGA
1 AAAAAAAATGAAAACAAAGA
*
1659305 AAAAAAAATGAAAAGAAAGA
1 AAAAAAAATGAAAACAAAGA
*
1659325 TAAAAAA
1 AAAAAAA
1659332 TTTATATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.79, C:0.02, G:0.11, T:0.09
Consensus pattern (20 bp):
AAAAAAAATGAAAACAAAGA
Found at i:1660198 original size:20 final size:19
Alignment explanation
Indices: 1660162--1660200 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1660152 TAAAATAATT
**
1660162 TTTTAAAATTTTAATTTTA
1 TTTTAAAATAATAATTTTA
1660181 TTTTAAAATAATATATTTTA
1 TTTTAAAATAATA-ATTTTA
1660201 AAAAATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAAAATAATAATTTTA
Found at i:1660860 original size:76 final size:76
Alignment explanation
Indices: 1660719--1660860 Score: 212
Period size: 76 Copynumber: 1.9 Consensus size: 76
1660709 CAAAAAAAAT
* * * * **
1660719 AATAAAGGAGTTAATGATCATAATATTGAAATAATATATATTTTAATGTTAATTTGTACTGTAGG
1 AATAAAAGAGTTAATGAGCATAATATTAAAATAATATATATTTTAATATTAATTTGTACCATAGG
1660784 TCAAGAAACGC
66 TCAAGAAACGC
**
1660795 AATAAAAGAGTTAATGAGCATAATATTAAAATAATATATATTTTAATATTTCTTTGTACCATAGG
1 AATAAAAGAGTTAATGAGCATAATATTAAAATAATATATATTTTAATATTAATTTGTACCATAGG
1660860 T
66 T
1660861 TGATTTAGTA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 58 1.00
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.37
Consensus pattern (76 bp):
AATAAAAGAGTTAATGAGCATAATATTAAAATAATATATATTTTAATATTAATTTGTACCATAGG
TCAAGAAACGC
Found at i:1661556 original size:5 final size:5
Alignment explanation
Indices: 1661546--1661570 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1661536 TAATAAATTA
1661546 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
1661571 AATAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:1661791 original size:27 final size:27
Alignment explanation
Indices: 1661761--1661812 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1661751 AAAATGATTA
1661761 TTAAGA-TATTTAATATATAATAAAAAT
1 TTAAGATTATTTAATAT-TAATAAAAAT
* *
1661788 TTAAGATTATTTGATATTTATAAAA
1 TTAAGATTATTTAATATTAATAAAA
1661813 TTAATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (27 bp):
TTAAGATTATTTAATATTAATAAAAAT
Found at i:1662259 original size:21 final size:21
Alignment explanation
Indices: 1662235--1662282 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1662225 ATATTATAAA
1662235 ATATAT-AATA-AAAATTACAT
1 ATATATAAATATAAAATTA-AT
1662255 GATATATAAATATAAAATTAAT
1 -ATATATAAATATAAAATTAAT
1662277 ATATAT
1 ATATAT
1662283 TATATAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.48
22 6 0.24
23 7 0.28
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
ATATATAAATATAAAATTAAT
Found at i:1672653 original size:15 final size:16
Alignment explanation
Indices: 1672633--1672663 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1672623 ATTGGCTCAC
1672633 GGCGCA-GACAATTAT
1 GGCGCAGGACAATTAT
1672648 GGCGCAGGACAATTAT
1 GGCGCAGGACAATTAT
1672664 AGTACCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.19
Consensus pattern (16 bp):
GGCGCAGGACAATTAT
Found at i:1682372 original size:23 final size:26
Alignment explanation
Indices: 1682333--1682384 Score: 74
Period size: 23 Copynumber: 2.1 Consensus size: 26
1682323 ACCCATAATA
1682333 AATTTAATAATTTTAAATAAAATT-T
1 AATTTAATAATTTTAAATAAAATTAT
*
1682358 AATTT-AT-ATTTTAAATATAATTAT
1 AATTTAATAATTTTAAATAAAATTAT
1682382 AAT
1 AAT
1682385 AAATAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 14 0.56
24 6 0.24
25 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
AATTTAATAATTTTAAATAAAATTAT
Found at i:1683459 original size:11 final size:11
Alignment explanation
Indices: 1683443--1683478 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1683433 AACTCTCCCG
1683443 TTTATTTTCTT
1 TTTATTTTCTT
1683454 TTTATTTTCTT
1 TTTATTTTCTT
* *
1683465 ATTATTTTATT
1 TTTATTTTCTT
1683476 TTT
1 TTT
1683479 CGGTGCCCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTATTTTCTT
Found at i:1683719 original size:18 final size:17
Alignment explanation
Indices: 1683685--1683717 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1683675 TATATTAAAT
*
1683685 TTTTTAATTATATTTTA
1 TTTTTAAATATATTTTA
1683702 TTTTTAAATATATTTT
1 TTTTTAAATATATTTT
1683718 TAAAATATGT
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTAAATATATTTTA
Found at i:1684844 original size:18 final size:18
Alignment explanation
Indices: 1684800--1684845 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1684790 AGAGATGATC
*
1684800 AAATATCTTATTTTATAA
1 AAATATTTTATTTTATAA
* *
1684818 AAATTTTTTATTTTTTAA
1 AAATATTTTATTTTATAA
*
1684836 ATATATTTTA
1 AAATATTTTA
1684846 AATATACGAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
AAATATTTTATTTTATAA
Found at i:1685174 original size:34 final size:36
Alignment explanation
Indices: 1685108--1685190 Score: 104
Period size: 35 Copynumber: 2.4 Consensus size: 36
1685098 TAGACTTAAG
* *
1685108 TAAAAA-ATTTATAATTTAATTAAATTTAAATAATA
1 TAAAAATATTTAAAATTTAATTAAATATAAATAATA
1685143 -AAAAATATTTAAAATTTAATTATAA-AT-AATAATA
1 TAAAAATATTTAAAATTTAATTA-AATATAAATAATA
1685177 TAAAAAT-TTTAAAA
1 TAAAAATATTTAAAA
1685191 AAATTTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
34 19 0.44
35 22 0.51
36 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (36 bp):
TAAAAATATTTAAAATTTAATTAAATATAAATAATA
Found at i:1685180 original size:25 final size:25
Alignment explanation
Indices: 1685129--1685181 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1685119 TAATTTAATT
*
1685129 AAATTTAAATAATAAAAAATATTTA
1 AAATTTAAATAATAAAAAATATATA
* *
1685154 AAATTT-AATTATAAATAATAATATA
1 AAATTTAAATAATAAAAAAT-ATATA
1685179 AAA
1 AAA
1685182 ATTTTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
AAATTTAAATAATAAAAAATATATA
Found at i:1686663 original size:19 final size:19
Alignment explanation
Indices: 1686626--1686660 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1686616 TATAAATATT
1686626 TATATCTTTTTAATTTTTA
1 TATATCTTTTTAATTTTTA
1686645 TATAT-TTTTT-ATTTTT
1 TATATCTTTTTAATTTTT
1686661 TTAAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (19 bp):
TATATCTTTTTAATTTTTA
Found at i:1691672 original size:20 final size:20
Alignment explanation
Indices: 1691647--1691692 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1691637 TGATATCATA
*
1691647 AATTAATTAAA-TATTAATTT
1 AATTAATAAAATTATT-ATTT
1691667 AATTAATAAAATTATTATTT
1 AATTAATAAAATTATTATTT
*
1691687 GATTAA
1 AATTAA
1691693 AATATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AATTAATAAAATTATTATTT
Found at i:1695688 original size:31 final size:31
Alignment explanation
Indices: 1695650--1695711 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1695640 TTTTAAGAGG
1695650 TTCTTTTATTGATTATCGTTGTTTGGAATAT
1 TTCTTTTATTGATTATCGTTGTTTGGAATAT
*
1695681 TTCTTTTATTGATTATCTTTGTTTGGAATAT
1 TTCTTTTATTGATTATCGTTGTTTGGAATAT
1695712 ATGTTTGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.19, C:0.06, G:0.15, T:0.60
Consensus pattern (31 bp):
TTCTTTTATTGATTATCGTTGTTTGGAATAT
Found at i:1698654 original size:2 final size:2
Alignment explanation
Indices: 1698647--1698687 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1698637 CTTTCTGTGG
1698647 AT AT AT 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 AT AT AT A
1698688 AAATAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1702264 original size:2 final size:2
Alignment explanation
Indices: 1702257--1702286 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1702247 CCTCAAACTC
1702257 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
1702287 CCATCAATTT
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:1708125 original size:2 final size:2
Alignment explanation
Indices: 1708118--1708142 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1708108 TAAGATATTC
1708118 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 A
1708143 ATTATTACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1710500 original size:2 final size:2
Alignment explanation
Indices: 1710493--1710522 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1710483 TTTAGTTTGC
1710493 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
1710523 GTATGATTAT
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:1714249 original size:2 final size:2
Alignment explanation
Indices: 1714242--1714270 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1714232 AAAGGGTAAA
1714242 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
1714271 GTTTTAAATC
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:1715846 original size:14 final size:14
Alignment explanation
Indices: 1715814--1715862 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
1715804 GAGAAGAAAT
*
1715814 AAATATATATACTGAA
1 AAATATATATAAT--A
1715830 AAATATATATAATA
1 AAATATATATAATA
*
1715844 AAATTTATATAATA
1 AAATATATATAATA
1715858 TAAAT
1 -AAAT
1715863 TATTTATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 14 0.47
15 4 0.13
16 12 0.40
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (14 bp):
AAATATATATAATA
Found at i:1715853 original size:18 final size:18
Alignment explanation
Indices: 1715836--1715934 Score: 68
Period size: 18 Copynumber: 5.7 Consensus size: 18
1715826 TGAAAAATAT
1715836 ATATAATAAAATTTATATA
1 ATATAATAAAATTTATA-A
**
1715855 ATATAA-ATTATTTAT--
1 ATATAATAAAATTTATAA
1715870 ATAT--TAAAATTTA-AA
1 ATATAATAAAATTTATAA
* *
1715885 AAATAAATAATATTT-TAA
1 ATAT-AATAAAATTTATAA
*
1715903 ATATAATAAAAATATATAA
1 ATATAAT-AAAATTTATAA
1715922 ATATAATATAAAT
1 ATATAATA-AAAT
1715935 AGGTAATTGA
Statistics
Matches: 61, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
14 6 0.10
15 7 0.11
17 3 0.05
18 25 0.41
19 20 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATAATAAAATTTATAA
Found at i:1715881 original size:14 final size:14
Alignment explanation
Indices: 1715829--1715882 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1715819 TATATACTGA
* *
1715829 AAAATATATATAAT
1 AAAATTTATATATT
1715843 AAAATTTATATAATAT
1 AAAATTTATAT-AT-T
1715859 AAATTATTTATATATT
1 AAA--ATTTATATATT
1715875 AAAATTTA
1 AAAATTTA
1715883 AAAAATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 15 0.44
15 1 0.03
16 8 0.24
17 2 0.06
18 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATTTATATATT
Found at i:1715899 original size:32 final size:32
Alignment explanation
Indices: 1715835--1715927 Score: 84
Period size: 32 Copynumber: 2.8 Consensus size: 32
1715825 CTGAAAAATA
*
1715835 TATATAATAAAATTTATATAATATAAATTATT
1 TATATAATAAAATTTATATAAAATAAATTATT
*
1715867 TATATATTAAAATTTA-A-AAAATAAATAATATTT
1 TATATAATAAAATTTATATAAAATAAAT--TA-TT
*
1715900 TAAATATAATAAAA-ATATATAAATATAA
1 T--ATATAATAAAATTTATATAAA-ATAA
1715928 TATAAATAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
30 8 0.16
31 1 0.02
32 17 0.35
33 3 0.06
34 2 0.04
35 11 0.22
36 3 0.06
37 4 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
TATATAATAAAATTTATATAAAATAAATTATT
Found at i:1715941 original size:13 final size:11
Alignment explanation
Indices: 1715900--1715935 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1715890 AATAATATTT
1715900 TAAATATAATA
1 TAAATATAATA
1715911 -AAA-AT-ATA
1 TAAATATAATA
1715919 TAAATATAATA
1 TAAATATAATA
1715930 TAAATA
1 TAAATA
1715936 GGTAATTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 3 0.14
9 5 0.23
10 5 0.23
11 9 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATATAATA
Found at i:1717516 original size:20 final size:19
Alignment explanation
Indices: 1717462--1717522 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
1717452 ATTTTAGATT
*
1717462 TAATTAATATTTAATAATCAA
1 TAATTAATATTTAAAAAT--A
1717483 TAATTAA-A-TTAAAAATA
1 TAATTAATATTTAAAAATA
1717500 TAATTATATATTTAAAAATA
1 TAATTA-ATATTTAAAAATA
1717520 TAA
1 TAA
1717523 AATATTAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
17 7 0.19
18 1 0.03
19 8 0.22
20 13 0.36
21 7 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATTAATATTTAAAAATA
Found at i:1717898 original size:17 final size:18
Alignment explanation
Indices: 1717859--1717907 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
1717849 GTTATATATT
*
1717859 TTTTTTAATTTAATTAAA
1 TTTTTTAAATTAATTAAA
* *
1717877 -ATTTTAAATTAATTTAA
1 TTTTTTAAATTAATTAAA
1717894 TTTTTTAAATTAAT
1 TTTTTTAAATTAAT
1717908 ATGATATTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTTAAATTAATTAAA
Found at i:1718170 original size:22 final size:23
Alignment explanation
Indices: 1718147--1718213 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
1718137 TAACATAAAT
1718147 AATTTTAATAAATATGAAATATAA
1 AATTTTAATAAATATGAAATAT-A
*
1718171 AATTTTAATTAA-AT-AAATATA
1 AATTTTAATAAATATGAAATATA
*
1718192 AATTATATAACAAATATGAAAT
1 AATT-T-TAATAAATATGAAAT
1718214 GAGTGCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
21 5 0.14
22 7 0.19
23 7 0.19
24 13 0.36
25 4 0.11
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.37
Consensus pattern (23 bp):
AATTTTAATAAATATGAAATATA
Found at i:1718973 original size:3 final size:3
Alignment explanation
Indices: 1718965--1718998 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1718955 GGCGCTCCCT
1718965 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1718999 CCCGCGGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1730221 original size:22 final size:23
Alignment explanation
Indices: 1730191--1730234 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1730181 TTAATATATT
* *
1730191 ATTTTTTAAA-TTTAATAAAATA
1 ATTTATTAAATTTTAAAAAAATA
1730213 ATTTATTAAATTTTAAAAAAAT
1 ATTTATTAAATTTTAAAAAAAT
1730235 TAAAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTATTAAATTTTAAAAAAATA
Found at i:1730957 original size:2 final size:2
Alignment explanation
Indices: 1730950--1730976 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1730940 ATTTATGTAT
1730950 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1730977 GAAAATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1733869 original size:3 final size:3
Alignment explanation
Indices: 1733861--1733893 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1733851 TCTTTTTTCT
1733861 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1733894 CTACTACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1734548 original size:4 final size:4
Alignment explanation
Indices: 1734539--1734563 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1734529 CTTAATTTAT
1734539 TCTA TCTA TCTA TCTA TCTA TCTA T
1 TCTA TCTA TCTA TCTA TCTA TCTA T
1734564 TATTATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TCTA
Found at i:1735197 original size:21 final size:21
Alignment explanation
Indices: 1735173--1735245 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
1735163 TTTAATATAA
1735173 ATATAAAATATATTAAAAATT
1 ATATAAAATATATTAAAAATT
* *
1735194 ATATAATATA-ATT-ATAA-T
1 ATATAAAATATATTAAAAATT
* *
1735212 ATATAAAA-ATATATAAATATA
1 ATATAAAATATAT-TAAAAATT
1735233 ATATAAATATATA
1 ATATAAA-ATATA
1735246 AATTATTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
17 1 0.03
18 10 0.25
19 4 0.10
20 5 0.12
21 16 0.40
22 1 0.03
23 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATAAAATATATTAAAAATT
Found at i:1735238 original size:11 final size:11
Alignment explanation
Indices: 1735153--1735243 Score: 64
Period size: 11 Copynumber: 8.3 Consensus size: 11
1735143 AATTAAAAAA
*
1735153 ATAATATTAAT
1 ATAATATAAAT
*
1735164 TTAATATAAAT
1 ATAATATAAAT
* *
1735175 ATAAAATATAT
1 ATAATATAAAT
1735186 -TAA-A-AATTAT
1 ATAATATAA--AT
*
1735196 ATAATATAATT
1 ATAATATAAAT
1735207 ATAATATATAA-
1 ATAATATA-AAT
*
1735218 AAATATATAAAT
1 ATA-ATATAAAT
1735230 ATAATATAAAT
1 ATAATATAAAT
1735241 ATA
1 ATA
1735244 TAAATTATTA
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
8 1 0.02
9 1 0.02
10 5 0.08
11 44 0.71
12 9 0.15
13 2 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1735246 original size:29 final size:29
Alignment explanation
Indices: 1735165--1735247 Score: 107
Period size: 29 Copynumber: 2.8 Consensus size: 29
1735155 AATATTAATT
1735165 TAATATAAATATAAAATATATTAAAAATTATA
1 TAATAT-AATAT-AAATATA-TAAAAATTATA
1735197 TAATATAAT-TATAATATATAAAAA-TATA
1 TAATATAATATA-AATATATAAAAATTATA
1735225 TAAATATAATATAAATATATAAA
1 T-AATATAATATAAATATATAAA
1735248 TTATTAAAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
28 5 0.10
29 25 0.52
30 9 0.19
31 3 0.06
32 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
TAATATAATATAAATATATAAAAATTATA
Found at i:1737457 original size:2 final size:2
Alignment explanation
Indices: 1737450--1737485 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1737440 CCTAAAAACT
*
1737450 GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1737486 AATAGTATAT
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:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1740234 original size:2 final size:2
Alignment explanation
Indices: 1740229--1740261 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1740219 GAACCTTAAT
1740229 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1740262 TTTGTAGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1744889 original size:28 final size:27
Alignment explanation
Indices: 1744858--1744915 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
1744848 ATTTAAAATA
1744858 TAATAAAAATTTTAAAA-ATTATTTAATT
1 TAATAAAAATTTTAAAATA-T-TTTAATT
** *
1744886 TAATTTATATTTTAAAATATTTTAATT
1 TAATAAAAATTTTAAAATATTTTAATT
1744913 TAA
1 TAA
1744916 ACACCATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 10 0.38
28 15 0.58
29 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TAATAAAAATTTTAAAATATTTTAATT
Found at i:1750840 original size:155 final size:151
Alignment explanation
Indices: 1750559--1750843 Score: 365
Period size: 155 Copynumber: 1.9 Consensus size: 151
1750549 TCGGTCCTAA
* * ** **
1750559 ATTTATTTTTCTATTTGATTAATTTTTTAGGAAATTTTAATTTTTTTATTTGTTATAAAATGGGA
1 ATTTATTTTCCCATTTGATTAACCTTTTAGGAAATTTTAATTTTTTTATTTGTTATAAAATGAAA
* * * * *
1750624 AAATTTTAAGGTTAAAGTGGAACTCAAGTGTAATGATAAGCTCTTGATCTTGGACCCCATGTTTG
66 AAAATTTAAGGTTAAAGTGGAACTCAAGTGCAATGACAAGCTCTTGATCTTGAACCACATGTTTG
1750689 GGTTGTGGCCAATAGACCCAC
131 GGTTGTGGCCAATAGACCCAC
1750710 ATTTATTTTCCCATTTGATTAACCTTTTAGGAAATTTTAATTTATTCTTTTATTTGTTATAAAAT
1 ATTTATTTTCCCATTTGATTAACCTTTTAGGAAATTTTAA--T-TT-TTTTATTTGTTATAAAAT
* ** * * *
1750775 GAAAAAAAATTTAAGGTTGAAG-GGGGCTTAAGTGCAGTGACAATCTCTTGATCTTGAACCACAT
62 G-AAAAAAATTTAAGGTTAAAGTGGAACTCAAGTGCAATGACAAGCTCTTGATCTTGAACCACAT
1750839 GTTTG
126 GTTTG
1750844 CGGCCAATGG
Statistics
Matches: 112, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
151 36 0.32
153 1 0.01
154 2 0.02
155 57 0.51
156 16 0.14
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (151 bp):
ATTTATTTTCCCATTTGATTAACCTTTTAGGAAATTTTAATTTTTTTATTTGTTATAAAATGAAA
AAAATTTAAGGTTAAAGTGGAACTCAAGTGCAATGACAAGCTCTTGATCTTGAACCACATGTTTG
GGTTGTGGCCAATAGACCCAC
Found at i:1751075 original size:15 final size:17
Alignment explanation
Indices: 1751055--1751108 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
1751045 AGATTTATAA
1751055 AATAAAATTATT-A-TT
1 AATAAAATTATTAATTT
*
1751070 AATAAAATTTTTAATTT
1 AATAAAATTATTAATTT
* * *
1751087 AATAAAAATAATAATTA
1 AATAAAATTATTAATTT
1751104 AATAA
1 AATAA
1751109 TTTTTAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 11 0.34
16 1 0.03
17 20 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAAAATTATTAATTT
Found at i:1751090 original size:17 final size:15
Alignment explanation
Indices: 1751055--1751093 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1751045 AGATTTATAA
1751055 AATAAAATTATTATT
1 AATAAAATTATTATT
*
1751070 AATAAAATTTTTAATTT
1 AATAAAATTATT-A-TT
1751087 AATAAAA
1 AATAAAA
1751094 ATAATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.52
16 1 0.05
17 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATAAAATTATTATT
Found at i:1751091 original size:32 final size:30
Alignment explanation
Indices: 1751055--1751121 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 30
1751045 AGATTTATAA
* *
1751055 AATAAAATTATTATTAATAAAATTTTTAATTT
1 AATAAAATAATAATTAA-AAAATTTTTAA-TT
*
1751087 AATAAAAATAATAATTAAATAATTTTTAATT
1 AAT-AAAATAATAATTAAAAAATTTTTAATT
1751118 AATA
1 AATA
1751122 TTTAAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 1 0.03
31 5 0.16
32 13 0.42
33 12 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
AATAAAATAATAATTAAAAAATTTTTAATT
Found at i:1754117 original size:7 final size:7
Alignment explanation
Indices: 1754100--1754132 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
1754090 CGTGCATACC
1754100 TGCCA-T
1 TGCCATT
1754106 TGCCATT
1 TGCCATT
1754113 TGCCATT
1 TGCCATT
1754120 TGCCATT
1 TGCCATT
1754127 TGCCAT
1 TGCCAT
1754133 CCCTCCACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.15, C:0.30, G:0.15, T:0.39
Consensus pattern (7 bp):
TGCCATT
Found at i:1758493 original size:18 final size:18
Alignment explanation
Indices: 1758472--1758507 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1758462 AGTTGCAAGT
1758472 TGAAACAGAATTGCAGAA
1 TGAAACAGAATTGCAGAA
* *
1758490 TGAAATATAATTGCAGAA
1 TGAAACAGAATTGCAGAA
1758508 ACCATTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.22
Consensus pattern (18 bp):
TGAAACAGAATTGCAGAA
Found at i:1760126 original size:2 final size:2
Alignment explanation
Indices: 1760119--1760143 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1760109 ATGATTTTTA
1760119 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 A
1760144 ATGTTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1762037 original size:16 final size:16
Alignment explanation
Indices: 1761955--1762081 Score: 80
Period size: 16 Copynumber: 7.9 Consensus size: 16
1761945 TAATTGTTCG
1761955 AATCATTTCAAATTCA
1 AATCATTTCAAATTCA
* * *
1761971 AATTATTT-GAACTCA
1 AATCATTTCAAATTCA
* *
1761986 AATTATTTTAAATT-A
1 AATCATTTCAAATTCA
* *
1762001 AACTTATTTCAAGA-TCG
1 AA-TCATTTCAA-ATTCA
* *
1762018 AATCATTTCGAATTTA
1 AATCATTTCAAATTCA
*
1762034 AATCAATTCAAATTCA
1 AATCATTTCAAATTCA
* * *
1762050 AATCATTTTAGATTTA
1 AATCATTTCAAATTCA
*
1762066 AATTATTTTCAAATTC
1 AATCA-TTTCAAATTC
1762082 GAATTAATCA
Statistics
Matches: 83, Mismatches: 22, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
15 17 0.20
16 56 0.67
17 10 0.12
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.43
Consensus pattern (16 bp):
AATCATTTCAAATTCA
Found at i:1762051 original size:64 final size:63
Alignment explanation
Indices: 1761952--1762073 Score: 147
Period size: 64 Copynumber: 1.9 Consensus size: 63
1761942 AGTTAATTGT
* ** *
1761952 TCGAATCATTTCAAATTCAAATTATTTGAACTCAAATTATTTTA-AATTAAACTTATTTCAAGA
1 TCGAATCATTTCAAATTCAAATAATTCAAACTCAAATCATTTTAGAATTAAA-TTATTTCAAGA
* * * *
1762015 TCGAATCATTTCGAATTTAAATCAATTCAAATTCAAATCATTTTAGATTTAAATTATTT
1 TCGAATCATTTCAAATTCAAAT-AATTCAAACTCAAATCATTTTAGAATTAAATTATTT
1762074 TCAAATTCGA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
63 20 0.41
64 23 0.47
65 6 0.12
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (63 bp):
TCGAATCATTTCAAATTCAAATAATTCAAACTCAAATCATTTTAGAATTAAATTATTTCAAGA
Found at i:1762671 original size:6 final size:6
Alignment explanation
Indices: 1762660--1762684 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1762650 GATGATAACT
1762660 TTAGAA TTAGAA TTAGAA TTAGAA T
1 TTAGAA TTAGAA TTAGAA TTAGAA T
1762685 ATGATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (6 bp):
TTAGAA
Found at i:1762869 original size:2 final size:2
Alignment explanation
Indices: 1762864--1762888 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1762854 ACACACACAC
1762864 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 A
1762889 CACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1765951 original size:22 final size:22
Alignment explanation
Indices: 1765926--1765971 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1765916 ATAGAACATA
1765926 TAGAATTAGAAAGCTTCAGCTC
1 TAGAATTAGAAAGCTTCAGCTC
1765948 TAGAATTAGAAAGCTTCAGCTC
1 TAGAATTAGAAAGCTTCAGCTC
1765970 TA
1 TA
1765972 ATCACTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (22 bp):
TAGAATTAGAAAGCTTCAGCTC
Found at i:1783013 original size:30 final size:30
Alignment explanation
Indices: 1782977--1783033 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
1782967 GCCCACGTTA
1782977 GTTGAAAGGACAGACTTTCTATCAACTTTT
1 GTTGAAAGGACAGACTTTCTATCAACTTTT
*
1783007 GTTGAAAGGATAGACTTTCTATCAACT
1 GTTGAAAGGACAGACTTTCTATCAACT
1783034 CTACGATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (30 bp):
GTTGAAAGGACAGACTTTCTATCAACTTTT
Found at i:1788454 original size:21 final size:21
Alignment explanation
Indices: 1788430--1788474 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1788420 AATTTTATTA
*
1788430 ATAAAATAAATAA-AATAATAC
1 ATAAAATAAA-AATAATAAAAC
1788451 ATAAAATAAAAATAATAAAAC
1 ATAAAATAAAAATAATAAAAC
1788472 ATA
1 ATA
1788475 TACCATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (21 bp):
ATAAAATAAAAATAATAAAAC
Found at i:1788477 original size:27 final size:28
Alignment explanation
Indices: 1788432--1788485 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
1788422 TTTTATTAAT
*
1788432 AAAATAAATAAAATAATA-CATAAAATA
1 AAAATAAATAAAACAATACCATAAAATA
1788459 AAAAT-AATAAAACATATACCATAAAAT
1 AAAATAAATAAAACA-ATACCATAAAAT
1788486 TCTAATACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 8 0.33
27 8 0.33
28 8 0.33
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (28 bp):
AAAATAAATAAAACAATACCATAAAATA
Found at i:1793336 original size:16 final size:16
Alignment explanation
Indices: 1793312--1793342 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1793302 TTATATTAAT
1793312 TTAAGAATTTTAAATA
1 TTAAGAATTTTAAATA
*
1793328 TTAATAATTTTAAAT
1 TTAAGAATTTTAAAT
1793343 CATCAAAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TTAAGAATTTTAAATA
Found at i:1795633 original size:26 final size:26
Alignment explanation
Indices: 1795597--1795646 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1795587 AACGTACAAA
* *
1795597 ATTTTAATTTATATTTTATAAATAGT
1 ATTTAAATTTATATATTATAAATAGT
*
1795623 ATTTAAATTTATATATTATTAATA
1 ATTTAAATTTATATATTATAAATA
1795647 AATCAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
ATTTAAATTTATATATTATAAATAGT
Found at i:1796378 original size:5 final size:5
Alignment explanation
Indices: 1796368--1796392 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1796358 ACAGGAAAAA
1796368 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
1796393 TATTTTCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:1797045 original size:25 final size:25
Alignment explanation
Indices: 1797017--1797064 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1797007 TTTTTATTAA
* *
1797017 TTAAATTATAATAATTTAAATCAAG
1 TTAAATTAAAAAAATTTAAATCAAG
*
1797042 TTAAATTAAAAAAATTTGAATCA
1 TTAAATTAAAAAAATTTAAATCA
1797065 TTAAATATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (25 bp):
TTAAATTAAAAAAATTTAAATCAAG
Found at i:1798354 original size:16 final size:16
Alignment explanation
Indices: 1798335--1798382 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1798325 TTTTTGTAAA
1798335 AAAAAATTTTAAAAAT
1 AAAAAATTTTAAAAAT
** *
1798351 AAAAAAAATTACAAAT
1 AAAAAATTTTAAAAAT
*
1798367 ATTAAAATTTTAAAAA
1 A-AAAAATTTTAAAAA
1798383 AATAATTAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAAATTTTAAAAAT
Found at i:1799748 original size:29 final size:29
Alignment explanation
Indices: 1799692--1799748 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1799682 AATTCATACT
* *
1799692 ATACCATTGAATCACACAACTATAGATCC
1 ATACCATCGAATCACACAACAATAGATCC
* *
1799721 ATACCATCGAATCAGACAACAATTGATC
1 ATACCATCGAATCACACAACAATAGATC
1799749 AATAAAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.42, C:0.26, G:0.09, T:0.23
Consensus pattern (29 bp):
ATACCATCGAATCACACAACAATAGATCC
Found at i:1799911 original size:3 final size:3
Alignment explanation
Indices: 1799903--1799935 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1799893 TGTGCTTAAC
1799903 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1799936 CCGTGTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1800520 original size:22 final size:22
Alignment explanation
Indices: 1800492--1800541 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
1800482 TCATTTCATC
1800492 ACCATTGTTTTCAATATCACTT
1 ACCATTGTTTTCAATATCACTT
1800514 ACCATTGTTTTCAATATCACTT
1 ACCATTGTTTTCAATATCACTT
*
1800536 TCCATT
1 ACCATT
1800542 CTAATAGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.26, C:0.24, G:0.04, T:0.46
Consensus pattern (22 bp):
ACCATTGTTTTCAATATCACTT
Found at i:1803177 original size:20 final size:21
Alignment explanation
Indices: 1803152--1803190 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1803142 TTAAATAATT
1803152 AAATAATATTATTT-TATTAA
1 AAATAATATTATTTATATTAA
1803172 AAATAATATTATTTATATT
1 AAATAATATTATTTATATT
1803191 TATTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATAATATTATTTATATTAA
Found at i:1804215 original size:2 final size:2
Alignment explanation
Indices: 1804208--1804237 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1804198 TGTGTAACAA
1804208 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
1804238 TGTAATAAAA
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
Done.