Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 11 of 198
Found at i:3747071 original size:43 final size:41
Alignment explanation
Indices: 3746966--3747071 Score: 142
Period size: 43 Copynumber: 2.5 Consensus size: 41
3746956 TTTAAGGTAT
3746966 ATTAAAATATAATTAAAATCATTTTGATTATATAATATTTTTA
1 ATTAAAATATAATTAAAATCATTTTGATTATATAATA--TTTA
*
3747009 ATTGAAATATAATTAAAATCATTTTGATTATATAATA-TTA
1 ATTAAAATATAATTAAAATCATTTTGATTATATAATATTTA
*
3747049 ATATAAAACTATACATTTAAATC
1 AT-TAAAA-TATA-ATTAAAATC
3747072 CAAAATATAA
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
40 5 0.09
41 4 0.07
42 4 0.07
43 44 0.77
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (41 bp):
ATTAAAATATAATTAAAATCATTTTGATTATATAATATTTA
Found at i:3750947 original size:16 final size:16
Alignment explanation
Indices: 3750928--3750969 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3750918 TTATTAAATT
*
3750928 ATATATTTTAATTATA
1 ATATATTTTAATAATA
3750944 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
3750959 AT-TATGTTTAA
1 ATATAT-TTTAA
3750970 ATATGATCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:3750954 original size:15 final size:15
Alignment explanation
Indices: 3750919--3750960 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3750909 NNNNNNAATT
*
3750919 TATTAAATTAT-ATA
1 TATTTAATTATAATA
3750933 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
3750947 TATTTAATAATAAT
1 TATTTAATTATAAT
3750961 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:3751153 original size:39 final size:42
Alignment explanation
Indices: 3751099--3751199 Score: 111
Period size: 45 Copynumber: 2.4 Consensus size: 42
3751089 TTCCATTATG
*
3751099 CTATTACACCTCTATTC-T-ATTCAACCAAACACA-AGA-TTA
1 CTATTACGCCTCTATTCATAATTCAACCAAACA-ATAGATTTA
* *
3751138 CTATTACGCCTCTATTCCATTACATTCAACCAAACAATTGATTTG
1 CTATTACGCCTCTATT-CA-TA-ATTCAACCAAACAATAGATTTA
3751183 CTATTACGCCTCTATTC
1 CTATTACGCCTCTATTC
3751200 CATTACACCT
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
39 15 0.29
40 1 0.02
42 1 0.02
43 1 0.02
44 16 0.31
45 18 0.35
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.35
Consensus pattern (42 bp):
CTATTACGCCTCTATTCATAATTCAACCAAACAATAGATTTA
Found at i:3751195 original size:45 final size:44
Alignment explanation
Indices: 3751117--3751206 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 44
3751107 CCTCTATTCT
3751117 ATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTAC
* *
3751161 ATTCAACCAAACA-ATTGATTTGCTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACACA-AGA-TTACTATTACGCCTCTATTCCATTAC
3751206 A
1 A
3751207 CCTCTATTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 15 0.36
45 26 0.62
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (44 bp):
ATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTAC
Found at i:3751210 original size:16 final size:16
Alignment explanation
Indices: 3751185--3751238 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
3751175 TTGATTTGCT
*
3751185 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
3751201 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
3751217 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
3751233 AATACA
1 ATTACA
3751239 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.26, C:0.35, G:0.04, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:3756283 original size:30 final size:29
Alignment explanation
Indices: 3756221--3756306 Score: 117
Period size: 25 Copynumber: 3.0 Consensus size: 29
3756211 CATATTTATG
3756221 GAAAGTCAAAGATATGGGTATC-AA-A-T
1 GAAAGTCAAAGATATGGGTATCAAATATT
3756247 -AAAGTCAAAGATATGGGTATCAAATATT
1 GAAAGTCAAAGATATGGGTATCAAATATT
*
3756275 GAAAAGTCAAAGATATGGGTATCGAGATATT
1 G-AAAGTCAAAGATATGGGTATC-AAATATT
3756306 G
1 G
3756307 GCATAAGAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
25 21 0.40
26 2 0.04
27 1 0.02
28 1 0.02
30 21 0.40
31 7 0.13
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (29 bp):
GAAAGTCAAAGATATGGGTATCAAATATT
Found at i:3760829 original size:30 final size:27
Alignment explanation
Indices: 3760764--3760842 Score: 117
Period size: 25 Copynumber: 2.9 Consensus size: 27
3760754 ATCCATATTT
3760764 ATGGAAAGTCAAAGATATGGGTATCAA
1 ATGGAAAGTCAAAGATATGGGTATCAA
3760791 AT--AAAGTCAAAGATATGGGTATCAAA
1 ATGGAAAGTCAAAGATATGGGTATC-AA
3760817 TATTGGAAAGTCAAAGATATGGGTAT
1 -A-TGGAAAGTCAAAGATATGGGTAT
3760843 TGAGATATTG
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
25 21 0.45
26 2 0.04
27 3 0.06
28 1 0.02
30 20 0.43
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.25
Consensus pattern (27 bp):
ATGGAAAGTCAAAGATATGGGTATCAA
Found at i:3774746 original size:26 final size:26
Alignment explanation
Indices: 3774717--3774770 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
3774707 CATTCTTGTT
3774717 TCATTATGAACAGGGTTTTGTTTTTA
1 TCATTATGAACAGGGTTTTGTTTTTA
3774743 TCATTATGAACAGGGTTTTGTTTTTA
1 TCATTATGAACAGGGTTTTGTTTTTA
3774769 TC
1 TC
3774771 TGTCTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.09, G:0.19, T:0.50
Consensus pattern (26 bp):
TCATTATGAACAGGGTTTTGTTTTTA
Found at i:3783725 original size:9 final size:9
Alignment explanation
Indices: 3783629--3783770 Score: 62
Period size: 9 Copynumber: 16.6 Consensus size: 9
3783619 AATACTTTTA
*
3783629 TTAAATTTT
1 TTAAATATT
3783638 TTAAAT-TT
1 TTAAATATT
*
3783646 TAAAAT-TT
1 TTAAATATT
3783654 TTAAAATACTT
1 TT-AAATA-TT
* *
3783665 TTTAATTTT
1 TTAAATATT
*
3783674 TTTAA-A-T
1 TTAAATATT
3783681 TT-AATATT
1 TTAAATATT
3783689 TTAAAATACTTT
1 TT-AAATA--TT
3783701 TTAAAT-TT
1 TTAAATATT
3783709 TT--A-A-T
1 TTAAATATT
3783714 TTAAATATT
1 TTAAATATT
3783723 TTAAATACTTT
1 TTAAATA--TT
3783734 TTAAAT-TT
1 TTAAATATT
3783742 TT--A-A-T
1 TTAAATATT
3783747 TTAAATATT
1 TTAAATATT
3783756 TTAAATACTT
1 TTAAATA-TT
3783766 TTAAA
1 TTAAA
3783771 AATACTTTTT
Statistics
Matches: 106, Mismatches: 5, Indels: 43
0.69 0.03 0.28
Matches are distributed among these distances:
5 6 0.06
6 4 0.04
7 6 0.06
8 23 0.22
9 33 0.31
10 14 0.13
11 16 0.15
12 4 0.04
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (9 bp):
TTAAATATT
Found at i:3783729 original size:33 final size:34
Alignment explanation
Indices: 3783595--3783767 Score: 210
Period size: 33 Copynumber: 4.9 Consensus size: 34
3783585 TATTTTTTAT
3783595 TTTTTAATTTTAAAATACTTTTAAAATACTTTTATTAAA
1 TTTTTAA-TTT-AAATA-TTTTAAAATACTT-T-TTAAA
*
3783634 TTTTTTAAATTTTAAA-ATTTTTAAAATACTTTTTAATT
1 -TTTTT-AA-TTTAAATA-TTTTAAAATACTTTTTAA-A
3783672 TTTTTAAATTT-AATATTTTAAAATACTTTTTAAA
1 TTTTT-AATTTAAATATTTTAAAATACTTTTTAAA
3783706 TTTTTAATTTAAATATTTT-AAATACTTTTTAAA
1 TTTTTAATTTAAATATTTTAAAATACTTTTTAAA
3783739 TTTTTAATTTAAATATTTT-AAATACTTTT
1 TTTTTAATTTAAATATTTTAAAATACTTTT
3783768 AAAAATACTT
Statistics
Matches: 126, Mismatches: 3, Indels: 15
0.88 0.02 0.10
Matches are distributed among these distances:
33 48 0.38
34 13 0.10
35 20 0.16
36 4 0.03
37 12 0.10
38 1 0.01
39 14 0.11
40 8 0.06
41 6 0.05
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (34 bp):
TTTTTAATTTAAATATTTTAAAATACTTTTTAAA
Found at i:3784337 original size:14 final size:15
Alignment explanation
Indices: 3784312--3784341 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3784302 NNATTTTTTA
3784312 ATTTTAAAATACTTT
1 ATTTTAAAATACTTT
3784327 ATTTT-AAATACTTT
1 ATTTTAAAATACTTT
3784341 A
1 A
3784342 AATACTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTAAAATACTTT
Found at i:3784360 original size:28 final size:28
Alignment explanation
Indices: 3784328--3784423 Score: 95
Period size: 28 Copynumber: 3.2 Consensus size: 28
3784318 AAATACTTTA
*
3784328 TTTTAAATACTTTAAATACTTTATTAAT
1 TTTTAAATATTTTAAATACTTTATTAAT
* *
3784356 TTTTAATTTAAATTTTTAAATACTTTTATT-TT
1 TTTTAA---ATA-TTTTAAATAC-TTTATTAAT
*
3784388 TATTTAAATATTTTAAATACTTTTTTAAT
1 T-TTTAAATATTTTAAATACTTTATTAAT
3784417 TTTTAAA
1 TTTTAAA
3784424 ATAATTTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
28 17 0.31
29 12 0.22
30 2 0.04
31 2 0.04
32 11 0.20
33 11 0.20
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTTAAATATTTTAAATACTTTATTAAT
Found at i:3784376 original size:32 final size:32
Alignment explanation
Indices: 3784324--3784422 Score: 134
Period size: 29 Copynumber: 3.2 Consensus size: 32
3784314 TTTAAAATAC
* *
3784324 TTTATTTTAAATACTTTAAATACTTTATTAATT
1 TTTAATTTAAATATTTTAAATACTTT-TTAATT
3784357 TTTAATTTAAAT-TTTTAAATAC-TTTT-ATT
1 TTTAATTTAAATATTTTAAATACTTTTTAATT
3784386 TTT-ATTTAAATATTTTAAATACTTTTTTAATT
1 TTTAATTTAAATATTTTAAATAC-TTTTTAATT
3784418 TTTAA
1 TTTAA
3784423 AATAATTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.14
29 16 0.27
30 2 0.03
31 6 0.10
32 15 0.25
33 12 0.20
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTAATTTAAATATTTTAAATACTTTTTAATT
Found at i:3784497 original size:26 final size:26
Alignment explanation
Indices: 3784461--3784511 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
3784451 TGGGCCGGGC
3784461 CGGGCCCGGGCTTATGAATTTTTTCT
1 CGGGCCCGGGCTTATGAATTTTTTCT
3784487 CGGGCCCGGGCTTATGAATTTTTTC
1 CGGGCCCGGGCTTATGAATTTTTTC
3784512 CCAGGCCGGG
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:0.12, C:0.24, G:0.27, T:0.37
Consensus pattern (26 bp):
CGGGCCCGGGCTTATGAATTTTTTCT
Found at i:3784520 original size:25 final size:26
Alignment explanation
Indices: 3784463--3784522 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
3784453 GGCCGGGCCG
* *
3784463 GGCCCGGGCTTATGAATTTTTTCTCG
1 GGCCCGGGCTTATGAATTTTTTCCCA
3784489 GGCCCGGGCTTATGAATTTTTTCCCA
1 GGCCCGGGCTTATGAATTTTTTCCCA
3784515 GG-CCGGGC
1 GGCCCGGGC
3784523 CTGGGCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 6 0.19
26 26 0.81
ACGTcount: A:0.12, C:0.27, G:0.30, T:0.32
Consensus pattern (26 bp):
GGCCCGGGCTTATGAATTTTTTCCCA
Found at i:3787045 original size:25 final size:25
Alignment explanation
Indices: 3787015--3787064 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3787005 TTTTACACTC
3787015 GTGTAAATATTTCCTTCATTATAAA
1 GTGTAAATATTTCCTTCATTATAAA
3787040 GTGTAAATATTTCCTTCATTATAAA
1 GTGTAAATATTTCCTTCATTATAAA
3787065 TTTACATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (25 bp):
GTGTAAATATTTCCTTCATTATAAA
Found at i:3787835 original size:2 final size:2
Alignment explanation
Indices: 3787824--3787865 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3787814 CAGATACATT
3787824 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3787865 T
1 T
3787866 TAAGTACGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3790178 original size:2 final size:2
Alignment explanation
Indices: 3790171--3790206 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3790161 NNNNNNNNNN
3790171 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
3790207 TTTAAGGCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3791785 original size:5 final size:5
Alignment explanation
Indices: 3791775--3791803 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3791765 TTCTTGGAAA
3791775 AAAAC AAAAC AAAAC AAAAC AAAA- AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
3791804 CCGAGCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:3799729 original size:2 final size:2
Alignment explanation
Indices: 3799722--3799761 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
3799712 GGACATAATC
* * *
3799722 AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT GT 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
3799762 TAGTTTGGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3800939 original size:126 final size:126
Alignment explanation
Indices: 3800713--3801011 Score: 481
Period size: 126 Copynumber: 2.4 Consensus size: 126
3800703 TAATTTAACG
* * * **
3800713 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAGAAAATAATTTTGAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCAAGTAGACGTTT
* * *
3800778 CTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGTTTTGTCAGCAGAAGTACTAAAAA
66 CTAAGCAAACAGTGTCAAAAACGCTTTAAGAAGGATGCTTTGTCAGCAGAAGTACTAAAAA
*
3800839 AAGCTTCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCAAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCAAGTAGACGTTT
* *
3800904 CTAAGCAAACAGTGTCAAAAACGCTTTAAGAAGGATGCTTTGTCAGCAGAAGTACTGAAAG
66 CTAAGCAAACAGTGTCAAAAACGCTTTAAGAAGGATGCTTTGTCAGCAGAAGTACTAAAAA
*
3800965 AAGCTCCCACATGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAAA
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCT-AAAAAAA
3801012 CTCCTACGTG
Statistics
Matches: 159, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
126 152 0.96
127 7 0.04
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.25
Consensus pattern (126 bp):
AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCAAGTAGACGTTT
CTAAGCAAACAGTGTCAAAAACGCTTTAAGAAGGATGCTTTGTCAGCAGAAGTACTAAAAA
Found at i:3804653 original size:18 final size:18
Alignment explanation
Indices: 3804626--3804663 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3804616 GAAAAAAGAA
* *
3804626 ACATATAAGGGTTAGGAT
1 ACATAAAAGGGCTAGGAT
3804644 ACATAAAAGGGCTAGGAT
1 ACATAAAAGGGCTAGGAT
3804662 AC
1 AC
3804664 GCACCTGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (18 bp):
ACATAAAAGGGCTAGGAT
Found at i:3806329 original size:18 final size:18
Alignment explanation
Indices: 3806269--3806331 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 18
3806259 AACAAATAAT
3806269 AAATT-AATAATTATTT-A
1 AAATTAAATAA-TATTTAA
* **
3806286 AAATTACATAA-ATAAAA
1 AAATTAAATAATATTTAA
3806303 AAATCTTAAATAATATTTAA
1 AAA--TTAAATAATATTTAA
3806323 AAATTAAAT
1 AAATTAAAT
3806332 TTAACACTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
16 2 0.06
17 9 0.26
18 10 0.29
19 7 0.20
20 7 0.20
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTAAATAATATTTAA
Found at i:3806514 original size:11 final size:11
Alignment explanation
Indices: 3806498--3806539 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
3806488 TTAAATAGGG
3806498 ATTTGAGAGAA
1 ATTTGAGAGAA
3806509 ATTTGAGAGCAA
1 ATTTGAGAG-AA
3806521 A-TTGAGAGGAA
1 ATTTGAGA-GAA
*
3806532 ATTAGAGA
1 ATTTGAGA
3806540 AAGGATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.45, C:0.02, G:0.29, T:0.24
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:3806763 original size:40 final size:39
Alignment explanation
Indices: 3806684--3806764 Score: 90
Period size: 40 Copynumber: 2.1 Consensus size: 39
3806674 CGCTTACGTG
* ** *
3806684 GTAGGGAAACGCGTCCTTGAGGGCGCGCTTTGTTACCAC
1 GTAGGCAAACGCGTCCTTGAGGAAGCGCTTTCTTACCAC
* * *
3806723 GTAGGCAAAGCGCTTCCTTGAGGAAGCGTTTTCTTGCCAC
1 GTAGGCAAA-CGCGTCCTTGAGGAAGCGCTTTCTTACCAC
3806763 GT
1 GT
3806765 CCCCTGACAT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
39 8 0.24
40 26 0.76
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.26
Consensus pattern (39 bp):
GTAGGCAAACGCGTCCTTGAGGAAGCGCTTTCTTACCAC
Found at i:3812705 original size:5 final size:5
Alignment explanation
Indices: 3812688--3812723 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
3812678 TTTACTATAT
* *
3812688 CGACC CGAAC CGATC CGACC CGACC CGACC CGACC C
1 CGACC CGACC CGACC CGACC CGACC CGACC CGACC C
3812724 CTGACCCAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.22, C:0.56, G:0.19, T:0.03
Consensus pattern (5 bp):
CGACC
Found at i:3813205 original size:24 final size:22
Alignment explanation
Indices: 3813178--3813222 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3813168 TACTCTCATT
3813178 ATTATTGTTATTATTTTATTTTTC
1 ATTATTGTTA-T-TTTTATTTTTC
*
3813202 ATTATTTTTATTTTTATTTTT
1 ATTATTGTTATTTTTATTTTT
3813223 AACATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 1 0.05
24 9 0.45
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (22 bp):
ATTATTGTTATTTTTATTTTTC
Found at i:3813207 original size:15 final size:16
Alignment explanation
Indices: 3813187--3813216 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3813177 TATTATTGTT
3813187 ATTA-TTTTATTTTTC
1 ATTATTTTTATTTTTC
3813202 ATTATTTTTATTTTT
1 ATTATTTTTATTTTT
3813217 ATTTTTAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTATTTTTATTTTTC
Found at i:3813214 original size:21 final size:20
Alignment explanation
Indices: 3813188--3813244 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
3813178 ATTATTGTTA
3813188 TTATTTTATTTTTCATTATTT
1 TTATTTTATTTTT-ATTATTT
**
3813209 TTATTTTTATTTTTAACATTT
1 TTA-TTTTATTTTTATTATTT
*
3813230 TTATATTATTATTTA
1 TTATTTTATT-TTTA
3813245 ATTAGTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 6 0.19
21 15 0.48
22 10 0.32
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATTTTATTTTTATTATTT
Found at i:3814785 original size:41 final size:41
Alignment explanation
Indices: 3814728--3814887 Score: 266
Period size: 41 Copynumber: 3.9 Consensus size: 41
3814718 TGAGTTTTTG
3814728 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
3814769 GGGCCTTTAGCAGCGTTTTTGAAAAAGCGTCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * *
3814810 TGGCCTTTAGCGGCGTTTTTGAAAAAGCGCAGCTAATGCTT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
*
3814851 GGGCCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAAT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
3814888 AATAATAAAA
Statistics
Matches: 109, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 109 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:3814961 original size:2 final size:2
Alignment explanation
Indices: 3814954--3814978 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3814944 ATGTTTCAAT
3814954 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
3814979 TATTTTATAA
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:3816300 original size:49 final size:49
Alignment explanation
Indices: 3816241--3816359 Score: 220
Period size: 49 Copynumber: 2.4 Consensus size: 49
3816231 GATTATCTAT
*
3816241 ATTTAGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
*
3816290 ATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTATA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
3816339 ATTTTGTATGAATATTGTAAT
1 ATTTTGTATGAATATTGTAAT
3816360 GTCGGGATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 67 1.00
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.53
Consensus pattern (49 bp):
ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
Found at i:3816302 original size:27 final size:25
Alignment explanation
Indices: 3816240--3816359 Score: 144
Period size: 27 Copynumber: 4.9 Consensus size: 25
3816230 AGATTATCTA
*
3816240 TATTTAGTATGAATATTGT-A-ATT
1 TATTTTGTATGAATATTGTAATATT
3816263 T-TTTTGTATGAATATTGTAATATT
1 TATTTTGTATGAATATTGTAATATT
*
3816287 ATAATTTTGTATGAATATTG-CA-ATT
1 -T-ATTTTGTATGAATATTGTAATATT
3816312 T-TTTTGTATGAATATTGTAATATT
1 TATTTTGTATGAATATTGTAATATT
3816336 ATAATTTTGTATGAATATTGTAAT
1 -T-ATTTTGTATGAATATTGTAAT
3816360 GTCGGGATAT
Statistics
Matches: 84, Mismatches: 3, Indels: 16
0.82 0.03 0.16
Matches are distributed among these distances:
22 32 0.38
23 3 0.04
24 7 0.08
25 5 0.06
26 1 0.01
27 36 0.43
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.53
Consensus pattern (25 bp):
TATTTTGTATGAATATTGTAATATT
Found at i:3816571 original size:27 final size:27
Alignment explanation
Indices: 3816540--3816606 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
3816530 TAACATAAAT
*
3816540 TTCATTGGCGCCTCTCTATAAGGCACC
1 TTCATTGGCGCCTCTCTATAAGACACC
*
3816567 TTCATTGGCGCCTCTCTATGAGACACC
1 TTCATTGGCGCCTCTCTATAAGACACC
3816594 TTCATTGGCGCCT
1 TTCATTGGCGCCT
3816607 ACCTGATAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.16, C:0.33, G:0.19, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATAAGACACC
Found at i:3817012 original size:44 final size:42
Alignment explanation
Indices: 3816962--3817126 Score: 195
Period size: 44 Copynumber: 3.8 Consensus size: 42
3816952 AGGTTATATT
* * * *
3816962 TTTAGCGGCGTTTTTGTGAGAAGTGCCGCTAAAGCTTCATGATC
1 TTTAGCGGCGTTTTTG-GAAAAGCGCCGCTAAAG-GTCATGGTC
*
3817006 TTTAGCGGCGTTTTCTGAAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTT-TGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
3817049 TATAGCGGCGTTTTTGGGAAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTTT-GG-AAAAGCGCCGCTAAAGGTCATGGTC
* *
3817093 TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAG
1 TTTAGCGGCGTTT-TTGGAAAAGCGCCGCTAAAG
3817127 TTAGCGACGC
Statistics
Matches: 106, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
42 1 0.01
43 36 0.34
44 66 0.62
45 3 0.03
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:3817116 original size:87 final size:87
Alignment explanation
Indices: 3816964--3817126 Score: 213
Period size: 87 Copynumber: 1.9 Consensus size: 87
3816954 GTTATATTTT
* * * * *
3816964 TAGCGGCGTTTTTGTGAGAAGTGCCGCTAAAGCTTCATGATCTTTAGCGGCGTTTTCTGAAAAAG
1 TAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGCGTCATGATCTTTAGCGGCGTTTTCGGAAAAAG
3817029 CGCCGCTAAAGGTCATGGTCTA
66 CGCCGCTAAAGGTCATGGTCTA
* * **
3817051 TAGCGGCGTTTTTGGGAAAAAGCGCCGCTAAAG-GTCTTGGTCTTTAGCGGCGTTTGT-GGGTAA
1 TAGCGGCGTTTTTGGG-AAAAGCGCCGCTAAAGCGTCATGATCTTTAGCGGCGTTT-TCGGAAAA
3817114 AGCGCCGCTAAAG
64 AGCGCCGCTAAAG
3817127 TTAGCGACGC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 50 0.77
88 15 0.23
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (87 bp):
TAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGCGTCATGATCTTTAGCGGCGTTTTCGGAAAAAG
CGCCGCTAAAGGTCATGGTCTA
Found at i:3818744 original size:9 final size:10
Alignment explanation
Indices: 3818721--3818745 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3818711 TAAACAATGG
3818721 AAAAACATAT
1 AAAAACATAT
3818731 AAAAACATAT
1 AAAAACATAT
3818741 AAAAA
1 AAAAA
3818746 AATTTAAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAACATAT
Found at i:3819955 original size:23 final size:23
Alignment explanation
Indices: 3819923--3819967 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3819913 CCGATTTGCT
*
3819923 CCCTCCGTTTCTTTTCTTTTCTG
1 CCCTCCGTTTATTTTCTTTTCTG
*
3819946 CCCTCTGTTTATTTTCTTTTCT
1 CCCTCCGTTTATTTTCTTTTCT
3819968 TTTCTGTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.02, C:0.31, G:0.07, T:0.60
Consensus pattern (23 bp):
CCCTCCGTTTATTTTCTTTTCTG
Found at i:3819982 original size:61 final size:62
Alignment explanation
Indices: 3819909--3820038 Score: 208
Period size: 66 Copynumber: 2.0 Consensus size: 62
3819899 CCTTCTAGCC
3819909 TCTGCCGATTTGCTCCCTCCG-TTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTT
1 TCTGCCGATTTGCTCCCTCCGTTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTT
*
3819970 TCTGTCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTT
1 TCTGCCGATTTGCTCCCTCCG----TTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTT
3820035 T
62 T
3820036 TCT
1 TCT
3820039 TTTCTTTTCT
Statistics
Matches: 63, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
61 20 0.32
66 43 0.68
ACGTcount: A:0.03, C:0.28, G:0.09, T:0.59
Consensus pattern (62 bp):
TCTGCCGATTTGCTCCCTCCGTTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTT
Found at i:3819988 original size:38 final size:38
Alignment explanation
Indices: 3819946--3820096 Score: 180
Period size: 38 Copynumber: 4.0 Consensus size: 38
3819936 TTCTTTTCTG
* *
3819946 CCCTCTGTTTATTTTCTTTTCTTTTCTGTCGATTTGCT
1 CCCTCTGTTTCTTTTCTTTTCTTTTCTGCCGATTTGCT
* * * *
3819984 CCCTCCGTTTCTTTTCTTTTCTTTTCTGCC-CTCTGTTT
1 CCCTCTGTTTCTTTTCTTTTCTTTTCTGCCGATTTG-CT
***
3820022 ATTTTCT-TTTCTTTTCTTTTCTTTTCTGCCGATTTGCT
1 -CCCTCTGTTTCTTTTCTTTTCTTTTCTGCCGATTTGCT
*
3820060 CCCTTTGTTTCTTTTCTTTTCTTTTCTGCCGATTTGC
1 CCCTCTGTTTCTTTTCTTTTCTTTTCTGCCGATTTGC
3820097 CAGTTTCTGC
Statistics
Matches: 92, Mismatches: 17, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
37 5 0.05
38 82 0.89
39 5 0.05
ACGTcount: A:0.03, C:0.26, G:0.09, T:0.61
Consensus pattern (38 bp):
CCCTCTGTTTCTTTTCTTTTCTTTTCTGCCGATTTGCT
Found at i:3820001 original size:5 final size:5
Alignment explanation
Indices: 3819991--3820048 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
3819981 GCTCCCTCCG
** *
3819991 TTTCT TTTCT TTTCT TTTCT GCCCTCT GTTTAT TTTCT TTTCT TTTCT
1 TTTCT TTTCT TTTCT TTTCT --TTTCT -TTTCT TTTCT TTTCT TTTCT
3820039 TTTCT TTTCT
1 TTTCT TTTCT
3820049 GCCGATTTGC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
5 39 0.89
6 2 0.05
7 3 0.07
ACGTcount: A:0.02, C:0.22, G:0.03, T:0.72
Consensus pattern (5 bp):
TTTCT
Found at i:3820015 original size:28 final size:28
Alignment explanation
Indices: 3819984--3820038 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
3819974 TCGATTTGCT
*
3819984 CCCTCCGTTTCTTTTCTTTTCTTTTCTG
1 CCCTCCGTTTATTTTCTTTTCTTTTCTG
*
3820012 CCCTCTGTTTATTTTCTTTTCTTTTCT
1 CCCTCCGTTTATTTTCTTTTCTTTTCT
3820039 TTTCTTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.02, C:0.29, G:0.05, T:0.64
Consensus pattern (28 bp):
CCCTCCGTTTATTTTCTTTTCTTTTCTG
Found at i:3820104 original size:76 final size:76
Alignment explanation
Indices: 3819957--3820104 Score: 208
Period size: 76 Copynumber: 1.9 Consensus size: 76
3819947 CCTCTGTTTA
* * **
3819957 TTTTCTTTTCTTTTCTGTCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTTTTCTGCCCTCTGTTT
1 TTTTCTTTTCTTTTCTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTTTTCTGCCATCTGTCC
*
3820022 ATTTTCTTTTC
66 AGTTTCTTTTC
** *
3820033 TTTTCTTTTCTTTTCTGCCGATTTGCTCCCTTTGTTTCTTTTCTTTTCTTTTCTGCCGATTTG-C
1 TTTTCTTTTCTTTTCTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTTTTCTGCC-ATCTGTC
3820097 CAGTTTCT
65 CAGTTTCT
3820105 GCTGATTTCT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
76 60 0.95
77 3 0.05
ACGTcount: A:0.03, C:0.26, G:0.09, T:0.61
Consensus pattern (76 bp):
TTTTCTTTTCTTTTCTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTTTTCTGCCATCTGTCC
AGTTTCTTTTC
Found at i:3820662 original size:14 final size:14
Alignment explanation
Indices: 3820643--3820669 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3820633 ATTGTTGATA
3820643 CTGTTGTTTGTTGT
1 CTGTTGTTTGTTGT
3820657 CTGTTGTTTGTTG
1 CTGTTGTTTGTTG
3820670 ATGTGTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.07, G:0.30, T:0.63
Consensus pattern (14 bp):
CTGTTGTTTGTTGT
Found at i:3826358 original size:11 final size:11
Alignment explanation
Indices: 3826344--3826381 Score: 67
Period size: 11 Copynumber: 3.4 Consensus size: 11
3826334 TTTTTTTTAA
3826344 TTTTAAAATAT
1 TTTTAAAATAT
3826355 TTTTAAAATAT
1 TTTTAAAATAT
3826366 TTTTAAAATACT
1 TTTTAAAATA-T
3826378 TTTT
1 TTTT
3826382 TAATTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 21 0.81
12 5 0.19
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:3826397 original size:57 final size:57
Alignment explanation
Indices: 3826224--3826400 Score: 177
Period size: 57 Copynumber: 3.1 Consensus size: 57
3826214 AATATATATA
* **
3826224 TTTTAATTTTAAAATATTTTT-TACTA-TTTTATATTTACTTTTTTAA-TTTTAAATT
1 TTTTAATTTTAAAATATTTTTATAATATTTTTA-AAATACTTTTTTAATTTTTAAATT
* * * * *
3826279 TAAATTAATTTTAAATTTACTTTTACTAA-ATTTTAAAAATA--TTTTTAATTTTTAATTTT
1 T--TTTAATTTTAAA-ATATTTTTA-TAATATTTTTAAAATACTTTTTTAATTTTTAA-ATT
*
3826338 TTTTAATTTTAAAATATTTTTAAAATATTTTTAAAATACTTTTTTAATTTTTAAATT
1 TTTTAATTTTAAAATATTTTTATAATATTTTTAAAATACTTTTTTAATTTTTAAATT
3826395 TTTTAA
1 TTTTAA
3826401 ATAAAAATGG
Statistics
Matches: 97, Mismatches: 14, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
55 3 0.03
56 18 0.19
57 37 0.38
58 26 0.27
59 7 0.07
60 6 0.06
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (57 bp):
TTTTAATTTTAAAATATTTTTATAATATTTTTAAAATACTTTTTTAATTTTTAAATT
Found at i:3828622 original size:16 final size:16
Alignment explanation
Indices: 3828601--3828642 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3828591 TTATTAAATT
*
3828601 ATATATTTTAATTATA
1 ATATATTTTAATAATA
3828617 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
3828632 AT-TATGTTTAA
1 ATATAT-TTTAA
3828643 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:3828627 original size:15 final size:15
Alignment explanation
Indices: 3828592--3828633 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3828582 TTAAGAATTT
*
3828592 TATTAAATTAT-ATA
1 TATTTAATTATAATA
3828606 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
3828620 TATTTAATAATAAT
1 TATTTAATTATAAT
3828634 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:3828870 original size:45 final size:44
Alignment explanation
Indices: 3828787--3828877 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
3828777 ACCTCTATTC
* *
3828787 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACATCTATTCCATTA
*** *
3828831 CATTCAACCAAACAGTTGATTTGCTATTACACATCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACATCTATTCCATTA
3828876 CA
1 CA
3828878 CCTCTATTCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACATCTATTCCATTA
Found at i:3828877 original size:16 final size:16
Alignment explanation
Indices: 3828856--3828909 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
3828846 TTGATTTGCT
*
3828856 ATTACACATCTATTCC
1 ATTACACCTCTATTCC
3828872 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
3828888 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
3828904 AATACA
1 ATTACA
3828910 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.30, C:0.33, G:0.02, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:3843401 original size:28 final size:31
Alignment explanation
Indices: 3843367--3843436 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 31
3843357 AGTCCATTTT
3843367 TTATTTTCTTTATTTAA-T-TTTTTTAAA-A
1 TTATTTTCTTTATTTAATTATTTTTTAAATA
*
3843395 TTATTTT-TCATATTTAATTATTTTTTAAATA
1 TTATTTTCT-TTATTTAATTATTTTTTAAATA
3843426 TATATTTTCTT
1 T-TATTTTCTT
3843437 ATACATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
27 1 0.03
28 14 0.41
29 1 0.03
30 9 0.26
31 2 0.06
32 6 0.18
33 1 0.03
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (31 bp):
TTATTTTCTTTATTTAATTATTTTTTAAATA
Found at i:3843492 original size:17 final size:17
Alignment explanation
Indices: 3843462--3843506 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
3843452 ACATACGCAT
3843462 ATTTTTTTTA-ATGTA-
1 ATTTTTTTTATATGTAG
3843477 ATTATTTTTTATATGTAG
1 ATT-TTTTTTATATGTAG
*
3843495 CTTTTTTTTATA
1 ATTTTTTTTATA
3843507 AACTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 3 0.12
16 7 0.27
17 14 0.54
18 2 0.08
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (17 bp):
ATTTTTTTTATATGTAG
Found at i:3843928 original size:15 final size:15
Alignment explanation
Indices: 3843905--3843939 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3843895 TTTTTATGCC
*
3843905 ATTAATGTATTTATT
1 ATTATTGTATTTATT
3843920 ATTATTGTATTTATT
1 ATTATTGTATTTATT
3843935 ATTAT
1 ATTAT
3843940 AGCATTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (15 bp):
ATTATTGTATTTATT
Found at i:3843946 original size:15 final size:15
Alignment explanation
Indices: 3843913--3843946 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3843903 CCATTAATGT
* *
3843913 ATTTATTATTATTGT
1 ATTTATTATTATAGC
3843928 ATTTATTATTATAGC
1 ATTTATTATTATAGC
3843943 ATTT
1 ATTT
3843947 GTATGTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (15 bp):
ATTTATTATTATAGC
Found at i:3847018 original size:15 final size:14
Alignment explanation
Indices: 3846998--3847028 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
3846988 GTAAAACCAT
3846998 CCTTAAAATCATAAA
1 CCTTAAAATCA-AAA
3847013 CCTTAAAATCAAAA
1 CCTTAAAATCAAAA
3847027 CC
1 CC
3847029 AGCAACTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (14 bp):
CCTTAAAATCAAAA
Found at i:3849114 original size:2 final size:2
Alignment explanation
Indices: 3849109--3849136 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3849099 AAACCTAGAT
3849109 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
3849137 AAGCGTGTTT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3853308 original size:15 final size:17
Alignment explanation
Indices: 3853272--3853306 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3853262 AATATGTTCT
*
3853272 AAATTACATATATATAA
1 AAATAACATATATATAA
3853289 AAATAACATA-ATATAA
1 AAATAACATATATATAA
3853305 AA
1 AA
3853307 TATTGTAAAC
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:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAACATATATATAA
Found at i:3853586 original size:19 final size:19
Alignment explanation
Indices: 3853551--3853589 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3853541 TTTTTAAATG
*
3853551 AATTTAAATTTTGATATAA
1 AATTTAAATTATGATATAA
3853570 AATTTAAAATTAT-ATATAA
1 AATTT-AAATTATGATATAA
3853589 A
1 A
3853590 CTTTGATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
AATTTAAATTATGATATAA
Found at i:3854301 original size:15 final size:15
Alignment explanation
Indices: 3854281--3854311 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3854271 TTAATTTCGA
3854281 TTAATTTGATTAATT
1 TTAATTTGATTAATT
*
3854296 TTAATTTGGTTAATT
1 TTAATTTGATTAATT
3854311 T
1 T
3854312 GGTTAAATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (15 bp):
TTAATTTGATTAATT
Found at i:3854345 original size:2 final size:2
Alignment explanation
Indices: 3854338--3854370 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3854328 CCAATTTGTT
3854338 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3854371 CTTGTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3859030 original size:2 final size:2
Alignment explanation
Indices: 3859025--3859051 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3859015 CAAAACACAC
3859025 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 A
3859052 CTTGGGTATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3862967 original size:51 final size:51
Alignment explanation
Indices: 3862891--3862993 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
3862881 ACGAGAAAAA
*
3862891 AATCGAAACCCAGCACGTTTTCTCGAATTTCCAAACGCAAAACATTTCCTT
1 AATCGAAACCCAACACGTTTTCTCGAATTTCCAAACGCAAAACATTTCCTT
*
3862942 AATCGAAACCCAACACGTTTTCTCGAATTTTCAAACGCAAAACATTTCCTT
1 AATCGAAACCCAACACGTTTTCTCGAATTTCCAAACGCAAAACATTTCCTT
3862993 A
1 A
3862994 CTTCGAAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.35, C:0.28, G:0.09, T:0.28
Consensus pattern (51 bp):
AATCGAAACCCAACACGTTTTCTCGAATTTCCAAACGCAAAACATTTCCTT
Found at i:3862977 original size:27 final size:27
Alignment explanation
Indices: 3862896--3862977 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
3862886 AAAAAAATCG
* *
3862896 AAACCCAGCACGTTTTCTCGAATTTCC
1 AAACCCAACACGTTTTCTCGAATTTTC
* * * * *
3862923 AAACGCAAAACATTTCCT-TAA---TC
1 AAACCCAACACGTTTTCTCGAATTTTC
3862946 GAAACCCAACACGTTTTCTCGAATTTTC
1 -AAACCCAACACGTTTTCTCGAATTTTC
3862974 AAAC
1 AAAC
3862978 GCAAAACATT
Statistics
Matches: 38, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
23 1 0.03
24 14 0.37
25 2 0.05
26 2 0.05
27 17 0.45
28 2 0.05
ACGTcount: A:0.34, C:0.29, G:0.09, T:0.28
Consensus pattern (27 bp):
AAACCCAACACGTTTTCTCGAATTTTC
Found at i:3863841 original size:12 final size:11
Alignment explanation
Indices: 3863824--3863859 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
3863814 AACAAATCCT
3863824 CTCTCATATTTC
1 CTCTCA-ATTTC
*
3863836 CTCTCAATTTT
1 CTCTCAATTTC
3863847 CTCTCAATTTC
1 CTCTCAATTTC
3863858 CT
1 CT
3863860 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:3863870 original size:22 final size:23
Alignment explanation
Indices: 3863823--3863870 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
3863813 AAACAAATCC
**
3863823 TCTCTCATATTTCCTCTCAATTT
1 TCTCTCATATTTCCTCTCAAAAT
3863846 TCTCTCA-ATTTCCT-TCCAAAAT
1 TCTCTCATATTTCCTCT-CAAAAT
3863868 TCT
1 TCT
3863871 TATAAATCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 1 0.05
22 14 0.64
23 7 0.32
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.48
Consensus pattern (23 bp):
TCTCTCATATTTCCTCTCAAAAT
Found at i:3863904 original size:51 final size:51
Alignment explanation
Indices: 3863839--3863962 Score: 178
Period size: 51 Copynumber: 2.4 Consensus size: 51
3863829 ATATTTCCTC
* * * *
3863839 TCAATTTTCTCTCAATTTCCTTCCAAAATTCT-TATAAATCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCCAAAAATCTCT-CAAACCCATATTTAATT
*
3863890 TCAATTTCCTCTCAATTTCATTCCAAAAATCTCTCAAACCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCCAAAAATCTCTCAAACCCATATTTAATT
*
3863941 TCAATTTGCTCTCAATTTCCTT
1 TCAATTTCCTCTCAATTTCCTT
3863963 TTTTAAAATA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 64 0.98
52 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.01, T:0.44
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCCAAAAATCTCTCAAACCCATATTTAATT
Found at i:3864893 original size:22 final size:23
Alignment explanation
Indices: 3864865--3864917 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
3864855 TATAAATAAG
3864865 TATATATTAAAAAA-ATAATG-TA
1 TATATATTAAAAAATAT-ATGCTA
*
3864887 TATATATTATAAAATATATGCCTA
1 TATATATTAAAAAATATATG-CTA
3864911 TATATAT
1 TATATAT
3864918 GAATAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 16 0.59
23 2 0.07
24 9 0.33
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (23 bp):
TATATATTAAAAAATATATGCTA
Found at i:3864971 original size:6 final size:6
Alignment explanation
Indices: 3864957--3865007 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
3864947 TAAATAAGTA
* * *
3864957 AATAAT AATATT AATATT AATGATGT AATA-T AATAGT AATAAT AATATT
1 AATATT AATATT AATATT AAT-AT-T AATATT AATATT AATATT AATATT
3865006 AA
1 AA
3865008 AATAATTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
5 5 0.13
6 27 0.69
7 3 0.08
8 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (6 bp):
AATATT
Found at i:3866290 original size:2 final size:2
Alignment explanation
Indices: 3866283--3866311 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3866273 TCTAAATTGA
3866283 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
3866312 CTACTTTTAC
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:3867067 original size:40 final size:40
Alignment explanation
Indices: 3867012--3867272 Score: 461
Period size: 40 Copynumber: 6.5 Consensus size: 40
3867002 AGGCTTGTGC
*
3867012 CTAGCAGGCTTAATGCCGGTCAAATATTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
*
3867052 CTAGCAGGCTTAATGCCGGTGAAATATTCAGATTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
3867092 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
3867132 CTAGCAGGCTTAATGCCGGTGAAATATTCAGA-TCATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACT-ATACGT
3867172 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
*
3867212 CCAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
* *
3867252 CTAGCAGGCTTCATGTCGGTG
1 CTAGCAGGCTTAATGCCGGTG
3867273 TACGGAATCA
Statistics
Matches: 212, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
39 1 0.00
40 210 0.99
41 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (40 bp):
CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
Found at i:3869332 original size:2 final size:2
Alignment explanation
Indices: 3869325--3869372 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
3869315 CATCCGCATG
3869325 AT AT 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 AT AT
3869367 AT AT AT
1 AT AT AT
3869373 GTATGTATGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3870416 original size:19 final size:20
Alignment explanation
Indices: 3870379--3870418 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3870369 TGGACGACGA
3870379 CGGTGGCAGAGAGTAGGTGG
1 CGGTGGCAGAGAGTAGGTGG
*
3870399 CGGTGGCAG-GAGTTGGTGG
1 CGGTGGCAGAGAGTAGGTGG
3870418 C
1 C
3870419 TGCTAAAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.15, C:0.12, G:0.55, T:0.17
Consensus pattern (20 bp):
CGGTGGCAGAGAGTAGGTGG
Found at i:3870797 original size:10 final size:10
Alignment explanation
Indices: 3870784--3870808 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3870774 TTAAAAATAT
3870784 AAATTCATAA
1 AAATTCATAA
3870794 AAATTCATAA
1 AAATTCATAA
3870804 AAATT
1 AAATT
3870809 AAAAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATTCATAA
Found at i:3870811 original size:25 final size:24
Alignment explanation
Indices: 3870763--3870822 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
3870753 ATTGAATTAT
*
3870763 TTCAAAAAATTTTAAAAATATAAA
1 TTCAAAAAATTATAAAAATATAAA
*
3870787 TTCATAAAAATTCATAAAAATTAAAAA
1 TTCA-AAAAATT-ATAAAAA-TATAAA
*
3870814 TTAAAAAAA
1 TTCAAAAAA
3870823 ACATAATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 4 0.13
25 7 0.23
26 11 0.37
27 8 0.27
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (24 bp):
TTCAAAAAATTATAAAAATATAAA
Found at i:3872689 original size:40 final size:39
Alignment explanation
Indices: 3872598--3872693 Score: 124
Period size: 39 Copynumber: 2.4 Consensus size: 39
3872588 ACCAGAATGG
** *
3872598 CACCCAGTGTCTCATCGGATAATTCGAAGCAATAGTTGA
1 CACCCAGTGTCTCATCGGATAAGCCGAAGAAATAGTTGA
3872637 CACCCAGTGTCTCATCGGCA-AAGCCGAAGAAATA-TAGTGA
1 CACCCAGTGTCTCATCGG-ATAAGCCGAAGAAATAGT--TGA
3872677 CACCCAGTGTCTCATCG
1 CACCCAGTGTCTCATCG
3872694 ACTCGAGGTC
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
38 1 0.02
39 29 0.57
40 21 0.41
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (39 bp):
CACCCAGTGTCTCATCGGATAAGCCGAAGAAATAGTTGA
Found at i:3873946 original size:8 final size:8
Alignment explanation
Indices: 3873933--3874068 Score: 130
Period size: 8 Copynumber: 16.2 Consensus size: 8
3873923 TGTTTTATAT
3873933 ATATAATA
1 ATATAATA
3873941 ATATAATA
1 ATATAATA
*
3873949 TTATAATA
1 ATATAATA
3873957 ATATAATTAA
1 ATATAA-T-A
3873967 TATTATAATA
1 -A-TATAATA
3873977 ATATAATTA
1 ATATAA-TA
3873986 ATATAATA
1 ATATAATA
*
3873994 TTATAATA
1 ATATAATA
*
3874002 TTATAATTA
1 ATATAA-TA
**
3874011 ATATTGTA
1 ATATAATA
*
3874019 ATATTATA
1 ATATAATA
*
3874027 ATATTATA
1 ATATAATA
3874035 AT-TAATA
1 ATATAATA
*
3874042 TTATAATA
1 ATATAATA
3874050 ATATAATTA
1 ATATAA-TA
3874059 ATATAATA
1 ATATAATA
3874067 AT
1 AT
3874069 TATTTATTAA
Statistics
Matches: 110, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
7 5 0.05
8 73 0.66
9 23 0.21
10 2 0.02
11 2 0.02
12 5 0.05
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.46
Consensus pattern (8 bp):
ATATAATA
Found at i:3873960 original size:28 final size:28
Alignment explanation
Indices: 3873929--3874068 Score: 157
Period size: 28 Copynumber: 5.1 Consensus size: 28
3873919 CTTTTGTTTT
*
3873929 ATATATATAATAATATAATATTATAATA
1 ATATATATAATATTATAATATTATAATA
*
3873957 ATATA-ATTAATATTATAATAATATAAT-
1 ATATATA-TAATATTATAATATTATAATA
3873984 -TA-ATATAATATTATAATATTATAATTA
1 ATATATATAATATTATAATATTATAA-TA
*
3874011 ATAT-TGTAATATTATAATATTATAATTA
1 ATATATATAATATTATAATATTATAA-TA
* *
3874039 ATAT-TATAATAATATAATTAATATAATA
1 ATATATATAATATTATAA-TATTATAATA
3874067 AT
1 AT
3874069 TATTTATTAA
Statistics
Matches: 98, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
25 19 0.19
26 4 0.04
27 1 0.01
28 67 0.68
29 7 0.07
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
ATATATATAATATTATAATATTATAATA
Found at i:3873967 original size:20 final size:20
Alignment explanation
Indices: 3873938--3874068 Score: 154
Period size: 20 Copynumber: 6.8 Consensus size: 20
3873928 TATATATATA
3873938 ATAATATAATATTATAATAAT
1 ATAAT-TAATATTATAATAAT
3873959 ATAATTAATATTATAATAAT
1 ATAATTAATATTATAATAAT
3873979 ATAATT-A-A-TATAAT-AT
1 ATAATTAATATTATAATAAT
3873995 -T-A-TAATATTATAATTAAT
1 ATAATTAATATTATAA-TAAT
*
3874013 AT--TGTAATATTATAATATT
1 ATAAT-TAATATTATAATAAT
3874032 ATAATTAATATTATAATAAT
1 ATAATTAATATTATAATAAT
*
3874052 ATAATTAATATAATAAT
1 ATAATTAATATTATAAT
3874069 TATTTATTAA
Statistics
Matches: 97, Mismatches: 3, Indels: 21
0.80 0.02 0.17
Matches are distributed among these distances:
13 1 0.01
14 2 0.02
15 2 0.02
16 7 0.07
17 7 0.07
18 3 0.03
19 7 0.07
20 62 0.64
21 6 0.06
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (20 bp):
ATAATTAATATTATAATAAT
Found at i:3874094 original size:73 final size:71
Alignment explanation
Indices: 3873932--3874095 Score: 224
Period size: 73 Copynumber: 2.3 Consensus size: 71
3873922 TTGTTTTATA
3873932 TATATAAT-AATATAATATTATAATAATATAATTAATATTATAATAATATAATTAATATAATATT
1 TATA-AATAAATATAATATTATAATAATATAATTAATATTATAATAATATAATTAATATAATATT
3873996 ATAATAT
65 ATAATAT
* * *
3874003 TATAATTAATATTGTAATATTATAATATTATAATTAATATTATAATAATATAATTAATATAATAA
1 TATAAATAA-A-TATAATATTATAATAATATAATTAATATTATAATAATATAATTAATATAAT-A
*
3874068 TTAT-TTAT
63 TTATAATAT
3874076 TAAGTAAATAAATATAATAT
1 T-A-TAAATAAATATAATAT
3874096 ATATTAACTA
Statistics
Matches: 81, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
70 2 0.02
71 5 0.06
72 1 0.01
73 60 0.74
74 7 0.09
75 6 0.07
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (71 bp):
TATAAATAAATATAATATTATAATAATATAATTAATATTATAATAATATAATTAATATAATATTA
TAATAT
Found at i:3874317 original size:13 final size:13
Alignment explanation
Indices: 3874299--3874325 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3874289 ACAACTAACT
3874299 TCATAAATATTTA
1 TCATAAATATTTA
3874312 TCATAAATATTTA
1 TCATAAATATTTA
3874325 T
1 T
3874326 GAGTCCAATT
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:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
TCATAAATATTTA
Found at i:3878350 original size:14 final size:15
Alignment explanation
Indices: 3878328--3878404 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
3878318 CAATCAAACA
3878328 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
3878342 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
3878357 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
3878377 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
3878391 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
3878405 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:3878369 original size:20 final size:20
Alignment explanation
Indices: 3878344--3878383 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3878334 AATATTTTCC
*
3878344 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
3878364 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
3878384 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:3878389 original size:34 final size:35
Alignment explanation
Indices: 3878332--3878398 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3878322 CAAACACCAG
*
3878332 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
3878367 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
3878399 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:3881304 original size:20 final size:20
Alignment explanation
Indices: 3881275--3881313 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3881265 AATATTTTCT
*
3881275 GTAAATCATTTTACAGAAAA
1 GTAAAACATTTTACAGAAAA
*
3881295 GTAAAACATTTTCCAGAAA
1 GTAAAACATTTTACAGAAA
3881314 TCATTTTACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (20 bp):
GTAAAACATTTTACAGAAAA
Found at i:3881672 original size:89 final size:88
Alignment explanation
Indices: 3881444--3881672 Score: 280
Period size: 89 Copynumber: 2.6 Consensus size: 88
3881434 GGTTTAAGCT
* * * * *
3881444 TCAAAAAGCCCTCAAATTTAAAAAAAAAAAAACAATTAAGTTCTTGCTTTTTTTTTTACTCATTT
1 TCAAAAAGCCCTCAAACTT-AAAAAAAAAAAGCAATTAAGCTCTTGCTTTTTTTTGTACTCAATT
3881509 GGGTACTTAAACTTTCAAAATGCA
65 GGGTACTTAAACTTTCAAAATGCA
* * *** * * *
3881533 TTAAGAATGCCCTCAAACCTT-TTCAGAAAAAGTAATTAAGCTCTTACTTTTTTTTGTACTCAAT
1 TCAA-AAAGCCCTCAAA-CTTAAAAAAAAAAAGCAATTAAGCTCTTGCTTTTTTTTGTACTCAAT
*
3881597 TGGGTACTTGAACTTTCAAAATGCA
64 TGGGTACTTAAACTTTCAAAATGCA
*
3881622 TCAAAAAGACCCTCAAACTTAAAAAAAAAAAGCAATTAAGCTCATGCTTTT
1 TCAAAAAG-CCCTCAAACTTAAAAAAAAAAAGCAATTAAGCTCTTGCTTTT
3881673 ATTAAAAATT
Statistics
Matches: 113, Mismatches: 23, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
88 6 0.05
89 94 0.83
90 11 0.10
91 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (88 bp):
TCAAAAAGCCCTCAAACTTAAAAAAAAAAAGCAATTAAGCTCTTGCTTTTTTTTGTACTCAATTG
GGTACTTAAACTTTCAAAATGCA
Found at i:3881781 original size:18 final size:18
Alignment explanation
Indices: 3881752--3881799 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
3881742 TAAAAAATTC
3881752 AAATATTAAAAATTAG-AAA
1 AAATA-TAAAAA-TAGTAAA
3881771 AAATATAAAAATAGTAAA
1 AAATATAAAAATAGTAAA
*
3881789 AAATGTAAAAA
1 AAATATAAAAA
3881800 AATGTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 3 0.11
18 19 0.70
19 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (18 bp):
AAATATAAAAATAGTAAA
Found at i:3881809 original size:27 final size:25
Alignment explanation
Indices: 3881743--3881809 Score: 64
Period size: 28 Copynumber: 2.5 Consensus size: 25
3881733 AATTTTAATT
* *
3881743 AAAAAATTCAAATATTAAAAATTAG
1 AAAAAATTAAAATATAAAAAATTAG
3881768 AAAAAATATAAAAATAGTAAAAAATGTA-
1 AAAAAAT-T-AAAATA-TAAAAAAT-TAG
3881796 AAAAAATGTAAAAT
1 AAAAAAT-TAAAAT
3881810 TTTATAAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 7 0.20
26 1 0.03
27 10 0.29
28 15 0.43
29 2 0.06
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.24
Consensus pattern (25 bp):
AAAAAATTAAAATATAAAAAATTAG
Found at i:3882098 original size:30 final size:28
Alignment explanation
Indices: 3882008--3882101 Score: 82
Period size: 30 Copynumber: 3.2 Consensus size: 28
3881998 GTCGTTAATT
3882008 TTTTTTATGATTTTTA-TAAAATTTTATAA
1 TTTTTTAT-ATTTTTATTAAAA-TTTATAA
* * * * *
3882037 TTTGTTACGATTTTTATAAAAAAATTCTAA
1 TTTTTTA-TATTTTTAT-TAAAATTTATAA
3882067 TTTTTCTATATTTTTATTAAAATTTAATAA
1 TTTTT-TATATTTTTATTAAAATTT-ATAA
3882097 TTTTT
1 TTTTT
3882102 ATAAAATTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
29 19 0.38
30 25 0.50
31 6 0.12
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (28 bp):
TTTTTTATATTTTTATTAAAATTTATAA
Found at i:3882100 original size:29 final size:28
Alignment explanation
Indices: 3882009--3882104 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 28
3881999 TCGTTAATTT
*
3882009 TTTTTATGATTTTTA-TAAAATTTTATAA
1 TTTTTAT-ATTTTTATTAAAATTTAATAA
* *
3882037 TTTGTTACGATTTTTATAAAAAAATTCTAAT--
1 TTT-TTA-TATTTTTAT--TAAAATT-TAATAA
3882068 TTTTCTATATTTTTATTAAAATTTAATAA
1 TTTT-TATATTTTTATTAAAATTTAATAA
3882097 TTTTTATA
1 TTTTTATA
3882105 AAATTTATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 18
0.70 0.06 0.23
Matches are distributed among these distances:
27 4 0.07
28 13 0.24
29 14 0.26
30 9 0.17
31 5 0.09
32 6 0.11
33 3 0.06
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.57
Consensus pattern (28 bp):
TTTTTATATTTTTATTAAAATTTAATAA
Found at i:3882121 original size:18 final size:19
Alignment explanation
Indices: 3882076--3882124 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
3882066 ATTTTTCTAT
3882076 ATTTTTATTAAAATTTAATA
1 ATTTTTA-TAAAATTTAATA
*
3882096 ATTTTTATAAAATTTATTA
1 ATTTTTATAAAATTTAATA
3882115 A-TTTTATAAA
1 ATTTTTATAAA
3882125 TTATTTTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 9 0.32
19 12 0.43
20 7 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTTATAAAATTTAATA
Found at i:3882312 original size:86 final size:85
Alignment explanation
Indices: 3882160--3882319 Score: 230
Period size: 86 Copynumber: 1.9 Consensus size: 85
3882150 AGGGGTTTAA
* *
3882160 TTGCTTTTTTGAAAAAATTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAG
1 TTGCTTTTTTGAAAAAATTTGAGAGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAG
*
3882225 TGAACAAAATATAGGCTCAG
66 TGAAAAAAATATAGGCTCAG
* * * * * *
3882245 TTGCTTTGTTTGAAGAAGTTTGAGAGCCTTTTTGATGGATTTTGAAAGTTTAAGTGCTCAATTGA
1 TTGCTTT-TTTGAAAAAATTTGAGAGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGA
3882310 GTGAAAAAAA
65 GTGAAAAAAA
3882320 AAAAGAAGGG
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 7 0.11
86 58 0.89
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (85 bp):
TTGCTTTTTTGAAAAAATTTGAGAGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAG
TGAAAAAAATATAGGCTCAG
Found at i:3885400 original size:14 final size:14
Alignment explanation
Indices: 3885381--3885409 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3885371 TGTGATTCTC
3885381 AGATTTTTTTTAAA
1 AGATTTTTTTTAAA
3885395 AGATTTTTTTTAAA
1 AGATTTTTTTTAAA
3885409 A
1 A
3885410 TTTGAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
AGATTTTTTTTAAA
Found at i:3892621 original size:12 final size:12
Alignment explanation
Indices: 3892604--3892633 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3892594 AATTGTTTTT
*
3892604 ATTTAATATTAA
1 ATTTAATATAAA
3892616 ATTTAATATAAA
1 ATTTAATATAAA
3892628 ATTTAA
1 ATTTAA
3892634 ATTTATTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTTAATATAAA
Found at i:3893384 original size:19 final size:17
Alignment explanation
Indices: 3893354--3893401 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 17
3893344 ATTTTAGATT
3893354 TTTTTAATTTTTCT-ATA
1 TTTTTAATTTTT-TAATA
3893371 TTCTTTAGATTTTTTAATA
1 TT-TTTA-ATTTTTTAATA
3893390 TTTTTAAATTTT
1 TTTTT-AATTTT
3893402 ATAAATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 2 0.07
18 13 0.48
19 12 0.44
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTTAATTTTTTAATA
Found at i:3893409 original size:27 final size:27
Alignment explanation
Indices: 3893353--3893409 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
3893343 TATTTTAGAT
* *
3893353 TTTTTTAATTTTTCTATATTCTTTAGA
1 TTTTTTAATTTTTCTAAATTCTTTAAA
3893380 TTTTTTAATATTTT-TAAATT-TTATAAA
1 TTTTTTAAT-TTTTCTAAATTCTT-TAAA
3893407 TTT
1 TTT
3893410 AAAAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 2 0.08
27 20 0.77
28 4 0.15
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (27 bp):
TTTTTTAATTTTTCTAAATTCTTTAAA
Found at i:3893439 original size:18 final size:19
Alignment explanation
Indices: 3893416--3893451 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3893406 ATTTAAAAAA
3893416 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
3893434 TATAAATATTTTGAATTT
1 TATAAATATTTGGAATTT
3893452 ATTTTGTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:3895142 original size:29 final size:30
Alignment explanation
Indices: 3895109--3895195 Score: 90
Period size: 29 Copynumber: 2.9 Consensus size: 30
3895099 ATTGGACCTG
3895109 AAATT-TAAAATATAAAAAGTAAAAAAACT
1 AAATTCTAAAATATAAAAAGTAAAAAAACT
* *
3895138 AAATTCCTAAAA-ATAAAAA-TATAAAGACT
1 AAATT-CTAAAATATAAAAAGTAAAAAAACT
* * *
3895167 AAATTCTAAATTTATGAAAAGTAGAAAAA
1 AAATTCTAAA-ATATAAAAAGTAAAAAAA
3895196 TTTATGACAT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
28 5 0.11
29 18 0.38
30 13 0.28
31 11 0.23
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (30 bp):
AAATTCTAAAATATAAAAAGTAAAAAAACT
Found at i:3896932 original size:2 final size:2
Alignment explanation
Indices: 3896925--3896965 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3896915 TCCATGGGGG
*
3896925 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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
3896966 CATGACTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3899343 original size:42 final size:42
Alignment explanation
Indices: 3899284--3899368 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
3899274 ACCCCCCTAG
3899284 ATTCGCCTCTGCTAGTGAAGAACAGCAAATGAAACTAACATA
1 ATTCGCCTCTGCTAGTGAAGAACAGCAAATGAAACTAACATA
3899326 ATTCGCCTCTGCTAGTGAAGAACAGCAAATGAAACTAACATA
1 ATTCGCCTCTGCTAGTGAAGAACAGCAAATGAAACTAACATA
3899368 A
1 A
3899369 AGGCACCTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21
Consensus pattern (42 bp):
ATTCGCCTCTGCTAGTGAAGAACAGCAAATGAAACTAACATA
Found at i:3904216 original size:19 final size:19
Alignment explanation
Indices: 3904176--3904217 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
3904166 TTAAATCATG
* *
3904176 TTATTACCCTTAGTTTATA
1 TTATTACCCTAAGCTTATA
3904195 TTATTAACCCTAAGCTTA-A
1 TTATT-ACCCTAAGCTTATA
3904214 TTAT
1 TTAT
3904218 CAAGCAAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.48
Consensus pattern (19 bp):
TTATTACCCTAAGCTTATA
Found at i:3907147 original size:18 final size:18
Alignment explanation
Indices: 3907126--3907170 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
3907116 TAAATTATAT
3907126 TTGATATGTGAATTAATA
1 TTGATATGTGAATTAATA
3907144 TTGATATGTGAATTAATA
1 TTGATATGTGAATTAATA
3907162 TTGA-ATGTG
1 TTGATATGTG
3907171 GAAGGAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (18 bp):
TTGATATGTGAATTAATA
Found at i:3907302 original size:8 final size:8
Alignment explanation
Indices: 3907289--3907317 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3907279 CACTAGAGAC
3907289 CAGTGTTA
1 CAGTGTTA
3907297 CAGTGTTA
1 CAGTGTTA
3907305 CAGTGTTA
1 CAGTGTTA
3907313 CAGTG
1 CAGTG
3907318 AGTCCCGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:3907456 original size:22 final size:23
Alignment explanation
Indices: 3907404--3907501 Score: 135
Period size: 23 Copynumber: 4.3 Consensus size: 23
3907394 AGTGTTATTG
*
3907404 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGTTACAT
* *
3907427 CTCAGTGGTAGTTTCGGTTACAT
1 ATCAGTGGTAGCTTCGGTTACAT
*
3907450 -TCAGTGGTAACTTCGGTTACAT
1 ATCAGTGGTAGCTTCGGTTACAT
* *
3907472 ATCAGTGGTAGCTTCGGCTATAT
1 ATCAGTGGTAGCTTCGGTTACAT
3907495 ATCAGTG
1 ATCAGTG
3907502 TGACACTTAT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
22 20 0.30
23 46 0.70
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGTTACAT
Found at i:3939579 original size:21 final size:23
Alignment explanation
Indices: 3939523--3939579 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 23
3939513 AAAAAATAAG
*
3939523 ATATATATTTATAGTTTGTTTAA
1 ATATATTTTTATAGTTTGTTTAA
* *
3939546 ATTTATTTGTT-TA-TTGTTTTTAA
1 ATATATTT-TTATAGTT-TGTTTAA
3939569 ATATATTTTTA
1 ATATATTTTTA
3939580 ATTTTTCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
22 4 0.15
23 21 0.78
24 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (23 bp):
ATATATTTTTATAGTTTGTTTAA
Found at i:3939720 original size:30 final size:31
Alignment explanation
Indices: 3939684--3939743 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
3939674 AAGGTGTAAT
*
3939684 TGTATACAT-AAACTCTAATTGTGGTTTAAA
1 TGTATACATGAAACTCTAATTGTGATTTAAA
* * *
3939714 TGTATACTTGAAACTTTAATTTTGATTTAA
1 TGTATACATGAAACTCTAATTGTGATTTAA
3939744 TCATACACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (31 bp):
TGTATACATGAAACTCTAATTGTGATTTAAA
Found at i:3949610 original size:15 final size:17
Alignment explanation
Indices: 3949576--3949612 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
3949566 TCCTTTTCTT
3949576 TTCACAATTATATAACA
1 TTCACAATTATATAACA
*
3949593 TTCACAA-TAT-TCACA
1 TTCACAATTATATAACA
3949608 TTCAC
1 TTCAC
3949613 TTACCATCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 9 0.47
16 3 0.16
17 7 0.37
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (17 bp):
TTCACAATTATATAACA
Found at i:3951867 original size:40 final size:40
Alignment explanation
Indices: 3951812--3951890 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
3951802 CGTTTGGATA
* *
3951812 AAAAAACGCCGCTAAAAATCGAGCATTAGCAGCGCTTTAC
1 AAAAAACACCGCTAAAAATCGAGCATTAGCAGCACTTTAC
* * *
3951852 AAAAAACACCGCTAAAGATCTAGCATTAGCGGCACTTTA
1 AAAAAACACCGCTAAAAATCGAGCATTAGCAGCACTTTA
3951891 AAGCGCCGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (40 bp):
AAAAAACACCGCTAAAAATCGAGCATTAGCAGCACTTTAC
Found at i:3952038 original size:41 final size:41
Alignment explanation
Indices: 3951979--3952367 Score: 544
Period size: 41 Copynumber: 9.5 Consensus size: 41
3951969 TGACCTTTCG
* * * *
3951979 GGGCTTTAACGGCATTTTTGGAGAAGCGCCGCTAATGCTCC
1 GGGCTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCA
* * *
3952020 GGGCTTTAACGGCGTTTTTTGAGAAGCGCCGCTAATGCTCC
1 GGGCTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCA
* * * * *
3952061 GGGCTTGAGTGGCGTTTTTTGAGAAGAGCCGCTAATGCTCC
1 GGGCTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCA
* ** *
3952102 GGGCTTTAGCGGTGTTTTTAGAGAAAAGCCGCTAATGCTCC
1 GGGCTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCA
* *
3952143 GGGCTTTAGCGGTGTTTTTAGAGAAGTGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCA
* *
3952184 GGGCTTTAGCGGTGTTTTTAGAGAAGTGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCA
* *
3952225 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTTA
1 GGGCTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCA
* *
3952266 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCACA
1 GGGCTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCA
* *
3952307 AGGCTTTAGCAGCGTTTTTAGAGAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCA
3952348 GGGCTTTAGCGGCGTTTTTA
1 GGGCTTTAGCGGCGTTTTTA
3952368 AAAAAGCACC
Statistics
Matches: 322, Mismatches: 26, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 322 1.00
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.29
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCA
Found at i:3952807 original size:14 final size:15
Alignment explanation
Indices: 3952779--3952808 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3952769 AAGGTTTATA
3952779 GATTATGGAATTAGG
1 GATTATGGAATTAGG
3952794 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
3952808 G
1 G
3952809 GTTCTAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:3953052 original size:21 final size:21
Alignment explanation
Indices: 3953028--3953073 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3953018 TAAATAAGGT
3953028 TTAGGGGTCAGTAGTTAGGGG
1 TTAGGGGTCAGTAGTTAGGGG
** *
3953049 TTAGGGGTTTGTGGTTAGGGG
1 TTAGGGGTCAGTAGTTAGGGG
3953070 TTAG
1 TTAG
3953074 AGCTTAGAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.02, G:0.48, T:0.35
Consensus pattern (21 bp):
TTAGGGGTCAGTAGTTAGGGG
Found at i:3953080 original size:7 final size:7
Alignment explanation
Indices: 3953070--3953096 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3953060 TGGTTAGGGG
3953070 TTAGAGC
1 TTAGAGC
3953077 TTAGAGC
1 TTAGAGC
3953084 TTAGAGC
1 TTAGAGC
3953091 TTAGAG
1 TTAGAG
3953097 GTTAAGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (7 bp):
TTAGAGC
Found at i:3953080 original size:14 final size:14
Alignment explanation
Indices: 3953063--3953100 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
3953053 GGGTTTGTGG
*
3953063 TTAGGGGTTAGAGC
1 TTAGAGGTTAGAGC
*
3953077 TTAGAGCTTAGAGC
1 TTAGAGGTTAGAGC
3953091 TTAGAGGTTA
1 TTAGAGGTTA
3953101 AGAATTAGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.26, C:0.08, G:0.34, T:0.32
Consensus pattern (14 bp):
TTAGAGGTTAGAGC
Found at i:3955867 original size:27 final size:26
Alignment explanation
Indices: 3955837--3955893 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 26
3955827 AATTTCGAGG
*
3955837 TTTACAATTTTTAATTTTTATTAATT
1 TTTACAATTTTTAATGTTTATTAATT
* *
3955863 ATTTACATTTTTTCATGTTTATTAATT
1 -TTTACAATTTTTAATGTTTATTAATT
3955890 TTTA
1 TTTA
3955894 TTATTATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTACAATTTTTAATGTTTATTAATT
Found at i:3956044 original size:20 final size:19
Alignment explanation
Indices: 3955998--3956047 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
3955988 TAAAAAATAA
3955998 ATTAAAATATAATATTTATC
1 ATTAAAATA-AATATTTATC
* * *
3956018 ATAAAAATAAATATTATTTG
1 ATTAAAATAAATATT-TATC
3956038 ATTAAAATAA
1 ATTAAAATAA
3956048 TTTTTTTGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
ATTAAAATAAATATTTATC
Found at i:3961399 original size:634 final size:634
Alignment explanation
Indices: 3960191--3961451 Score: 2522
Period size: 634 Copynumber: 2.0 Consensus size: 634
3960181 CAAATCCAAA
3960191 GTGGGAACGGTGGGAAAATCATTCCATTACCGAAGACAGAGCAGCAAAAACGAGTCTATTTGTTC
1 GTGGGAACGGTGGGAAAATCATTCCATTACCGAAGACAGAGCAGCAAAAACGAGTCTATTTGTTC
3960256 AAAACTGACTTTTCAACGAGTATGGATGAGAAGGTACAATTTTCGTTTCATTTTTCTTGGATACA
66 AAAACTGACTTTTCAACGAGTATGGATGAGAAGGTACAATTTTCGTTTCATTTTTCTTGGATACA
3960321 ATTAATTTCACCACTTTGCTAAGCTCAAGGTAGACTTTGATTTCGACCAAGTCAAAAAATAAAAC
131 ATTAATTTCACCACTTTGCTAAGCTCAAGGTAGACTTTGATTTCGACCAAGTCAAAAAATAAAAC
3960386 CCGAAAGAAAAGTCCTTGGACTTTATTATCTGTCAACTTCAACCTCCTAAAGGAGGAAACATGGA
196 CCGAAAGAAAAGTCCTTGGACTTTATTATCTGTCAACTTCAACCTCCTAAAGGAGGAAACATGGA
3960451 ATTATCTCATTACAAAATGGTAATACACAATTAGTAGCTCTGGTGATTCCAGAGCACAACCTCCA
261 ATTATCTCATTACAAAATGGTAATACACAATTAGTAGCTCTGGTGATTCCAGAGCACAACCTCCA
3960516 AAATGAGGTTTCAATTTCGGGCATACTTCCTCGATAAGGTTTGAATATTCTGAAAACCATCATCC
326 AAATGAGGTTTCAATTTCGGGCATACTTCCTCGATAAGGTTTGAATATTCTGAAAACCATCATCC
3960581 TATATGTGGTTCAAATAAAATCAAATTATCAATGCTTTCCATATGCAAAGTAGGGGCTGAAGTCC
391 TATATGTGGTTCAAATAAAATCAAATTATCAATGCTTTCCATATGCAAAGTAGGGGCTGAAGTCC
3960646 CATTAGAATCTACCGTATTAAGTATTAACTAGCTCAATGATTCTGAAAAACTGGCCTATAACAGG
456 CATTAGAATCTACCGTATTAAGTATTAACTAGCTCAATGATTCTGAAAAACTGGCCTATAACAGG
3960711 CACGTAGTATTGTATGAACAATGAAACCAAAGGAACTTCAAAAATAGTGAGAACAGTAGAAAAAT
521 CACGTAGTATTGTATGAACAATGAAACCAAAGGAACTTCAAAAATAGTGAGAACAGTAGAAAAAT
3960776 CATTCCATTGCCGCTGATAGTCAGTGTTGGATTTTTTTATTACCGAACG
586 CATTCCATTGCCGCTGATAGTCAGTGTTGGATTTTTTTATTACCGAACG
3960825 GTGGGAACGGTGGGAAAATCATTCCATTACCGAAGACAGAGCAGCAAAAACGAGTCTATTTGTTC
1 GTGGGAACGGTGGGAAAATCATTCCATTACCGAAGACAGAGCAGCAAAAACGAGTCTATTTGTTC
3960890 AAAACTGACTTTTCAACGAGTATGGATGAGAAGGTACAATTTTCGTTTCATTTTTCTTGGATACA
66 AAAACTGACTTTTCAACGAGTATGGATGAGAAGGTACAATTTTCGTTTCATTTTTCTTGGATACA
3960955 ATTAATTTCACCACTTTGCTAAGCTCAAGGTAGACTTTGATTTCGACCAAGTCAAAAAATAAAAC
131 ATTAATTTCACCACTTTGCTAAGCTCAAGGTAGACTTTGATTTCGACCAAGTCAAAAAATAAAAC
3961020 CCGAAAGAAAAGTCCTTGGACTTTATTATCTGTCAACTTCAACCTCCTAAAGGAGGAAACATGGA
196 CCGAAAGAAAAGTCCTTGGACTTTATTATCTGTCAACTTCAACCTCCTAAAGGAGGAAACATGGA
3961085 ATTATCTCATTACAAAATGGTAATACACAATTAGTAGCTCTGGTGATTCCAGAGCACAACCTCCA
261 ATTATCTCATTACAAAATGGTAATACACAATTAGTAGCTCTGGTGATTCCAGAGCACAACCTCCA
3961150 AAATGAGGTTTCAATTTCGGGCATACTTCCTCGATAAGGTTTGAATATTCTGAAAACCATCATCC
326 AAATGAGGTTTCAATTTCGGGCATACTTCCTCGATAAGGTTTGAATATTCTGAAAACCATCATCC
3961215 TATATGTGGTTCAAATAAAATCAAATTATCAATGCTTTCCATATGCAAAGTAGGGGCTGAAGTCC
391 TATATGTGGTTCAAATAAAATCAAATTATCAATGCTTTCCATATGCAAAGTAGGGGCTGAAGTCC
3961280 CATTAGAATCTACCGTATTAAGTATTAACTAGCTCAATGATTCTGAAAAACTGGCCTATAACAGG
456 CATTAGAATCTACCGTATTAAGTATTAACTAGCTCAATGATTCTGAAAAACTGGCCTATAACAGG
3961345 CACGTAGTATTGTATGAACAATGAAACCAAAGGAACTTCAAAAATAGTGAGAACAGTAGAAAAAT
521 CACGTAGTATTGTATGAACAATGAAACCAAAGGAACTTCAAAAATAGTGAGAACAGTAGAAAAAT
3961410 CATTCCATTGCCGCTGATAGTCAGTGTTGGATTTTTTTATTA
586 CATTCCATTGCCGCTGATAGTCAGTGTTGGATTTTTTTATTA
3961452 AAAGTTTAGG
Statistics
Matches: 627, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
634 627 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (634 bp):
GTGGGAACGGTGGGAAAATCATTCCATTACCGAAGACAGAGCAGCAAAAACGAGTCTATTTGTTC
AAAACTGACTTTTCAACGAGTATGGATGAGAAGGTACAATTTTCGTTTCATTTTTCTTGGATACA
ATTAATTTCACCACTTTGCTAAGCTCAAGGTAGACTTTGATTTCGACCAAGTCAAAAAATAAAAC
CCGAAAGAAAAGTCCTTGGACTTTATTATCTGTCAACTTCAACCTCCTAAAGGAGGAAACATGGA
ATTATCTCATTACAAAATGGTAATACACAATTAGTAGCTCTGGTGATTCCAGAGCACAACCTCCA
AAATGAGGTTTCAATTTCGGGCATACTTCCTCGATAAGGTTTGAATATTCTGAAAACCATCATCC
TATATGTGGTTCAAATAAAATCAAATTATCAATGCTTTCCATATGCAAAGTAGGGGCTGAAGTCC
CATTAGAATCTACCGTATTAAGTATTAACTAGCTCAATGATTCTGAAAAACTGGCCTATAACAGG
CACGTAGTATTGTATGAACAATGAAACCAAAGGAACTTCAAAAATAGTGAGAACAGTAGAAAAAT
CATTCCATTGCCGCTGATAGTCAGTGTTGGATTTTTTTATTACCGAACG
Found at i:3961528 original size:11 final size:11
Alignment explanation
Indices: 3961502--3961534 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3961492 GGATTTAATG
3961502 AAAATA-TTTA
1 AAAATATTTTA
3961512 AAAATATTTTA
1 AAAATATTTTA
*
3961523 AGAATATTTTA
1 AAAATATTTTA
3961534 A
1 A
3961535 CATTATAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
AAAATATTTTA
Found at i:3971504 original size:41 final size:40
Alignment explanation
Indices: 3971449--3971741 Score: 338
Period size: 41 Copynumber: 7.2 Consensus size: 40
3971439 CCTTCGGGAT
** * *
3971449 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGGTCAGAGA
1 TTTAGCGGCGTTTTT-GGAAAGCGCCGCTAATACTCAGGGC
3971490 TTTAGCGGCGTTTTTTGGAAAGCGCCGCTAATGA-TCAGGGC
1 TTTAGCGGCG-TTTTTGGAAAGCGCCGCTAAT-ACTCAGGGC
*
3971531 TTTAGCGGCATTTTTGGGAAAGCGCCGCTAATGA-TCAGGGC
1 TTTAGCGGCGTTTTT-GGAAAGCGCCGCTAAT-ACTCAGGGC
* * * *
3971572 TTTAGAGGCGTTTTTGGGAAAGCGACACTAATACTGAGGGC
1 TTTAGCGGCGTTTTT-GGAAAGCGCCGCTAATACTCAGGGC
* * *
3971613 TTTAGCGTCGTTTTTGAAGAAGCGCCGCTAATACTTAGGGC
1 TTTAGCGGCGTTTTTGGA-AAGCGCCGCTAATACTCAGGGC
* *
3971654 TTTAGCGGCATTTTTGAAGAAGCGCCGCTAATACTCAGGGC
1 TTTAGCGGCGTTTTTGGA-AAGCGCCGCTAATACTCAGGGC
* * *
3971695 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATACTTAGTGC
1 TTTAGCGGCGTTTTTGGA-AAGCGCCGCTAATACTCAGGGC
3971736 TTTAGC
1 TTTAGC
3971742 TACTTTTTTG
Statistics
Matches: 226, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
40 8 0.04
41 213 0.94
42 5 0.02
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.29
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTGGAAAGCGCCGCTAATACTCAGGGC
Found at i:3971668 original size:123 final size:123
Alignment explanation
Indices: 3971449--3971767 Score: 389
Period size: 123 Copynumber: 2.6 Consensus size: 123
3971439 CCTTCGGGAT
** * * *
3971449 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGGTCAGAGATTTAGCGGCGTTTTTTGGA-AAGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATACTCAGAGCTTTAGCGTCG-TTTTTGAAGAAGC
*
3971513 GCCGCTAATGATCAGGGCTTTAGCGGCATTTTTG-GGAAAGCGCCGCTAATGA-TCAGGGC
65 GCCGCTAATGATCAGGGCTTTAGCGGCATTTTTGAAG-AAGCGCCGCTAAT-ACTCAGGGC
* * * * *
3971572 TTTAGAGGCGTTTTTGGGAAAGCGACACTAATACTGAGGGCTTTAGCGTCGTTTTTGAAGAAGCG
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATACTCAGAGCTTTAGCGTCGTTTTTGAAGAAGCG
*
3971637 CCGCTAAT-ACTTAGGGCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATACTCAGGGC
66 CCGCTAATGA-TCAGGGCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATACTCAGGGC
* * * *
3971695 TTTAGCGGCGTTTTT-GAAGAAGCGCCGCTAATACTTAGTGCTTTAGC-TACTTTTTTGAAGAAG
1 TTTAGCGGCGTTTTTGGGA-AAGCGCCGCTAATACTCAGAGCTTTAGCGT-CGTTTTTGAAGAAG
*
3971758 CGTCGCTAAT
64 CGCCGCTAAT
3971768 TCTCTATTTT
Statistics
Matches: 170, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
122 12 0.07
123 157 0.92
124 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (123 bp):
TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATACTCAGAGCTTTAGCGTCGTTTTTGAAGAAGCG
CCGCTAATGATCAGGGCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATACTCAGGGC
Found at i:3971750 original size:41 final size:41
Alignment explanation
Indices: 3971449--3971807 Score: 329
Period size: 41 Copynumber: 8.8 Consensus size: 41
3971439 CCTTCGGGAT
* ** * * *
3971449 TTTAGCGGCGTTTTTG-GGAAAGCGCCGCTAATGGTCAGAGA
1 TTTAGCGGCGTTTTTGAAG-AAGCGCCGCTAATACTTAGGGC
* *
3971490 TTTAGCGGCGTTTTTTGGA-AAGCGCCGCTAATGA-TCAGGGC
1 TTTAGCGGCG-TTTTTGAAGAAGCGCCGCTAAT-ACTTAGGGC
* * *
3971531 TTTAGCGGCATTTTTG-GGAAAGCGCCGCTAATGA-TCAGGGC
1 TTTAGCGGCGTTTTTGAAG-AAGCGCCGCTAAT-ACTTAGGGC
* * * * *
3971572 TTTAGAGGCGTTTTTG-GGAAAGCGACACTAATACTGAGGGC
1 TTTAGCGGCGTTTTTGAAG-AAGCGCCGCTAATACTTAGGGC
*
3971613 TTTAGCGTCGTTTTTGAAGAAGCGCCGCTAATACTTAGGGC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATACTTAGGGC
* *
3971654 TTTAGCGGCATTTTTGAAGAAGCGCCGCTAATACTCAGGGC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATACTTAGGGC
*
3971695 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATACTTAGTGC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATACTTAGGGC
** * * * **
3971736 TTTAGCTACTTTTTTGAAGAAGCGTCGCTAATTCTCTA--TT
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATACT-TAGGGC
* * *
3971776 TTTAGTGGCGTTTTTTAAAAAGCGCCGCTAAT
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAAT
3971808 GCTCAGGGAT
Statistics
Matches: 273, Mismatches: 37, Indels: 17
0.83 0.11 0.05
Matches are distributed among these distances:
40 32 0.12
41 232 0.85
42 9 0.03
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATACTTAGGGC
Done.