Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, whole genome shotgun sequence
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: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 17 of 84
Found at i:3056857 original size:23 final size:22
Alignment explanation
Indices: 3056827--3056869 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
3056817 GCTTCCAAAG
3056827 ATAGGATT-TTAAAGAAATTTGA
1 ATAGGATTCTT-AAGAAATTTGA
3056849 ATAGTGATTCTTAAGAAATTT
1 ATAG-GATTCTTAAGAAATTT
3056870 TTAGATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 13 0.68
24 2 0.11
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.40
Consensus pattern (22 bp):
ATAGGATTCTTAAGAAATTTGA
Found at i:3057023 original size:12 final size:12
Alignment explanation
Indices: 3056998--3057032 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
3056988 TTTTGTGAGG
3056998 AAAATGAAATATAA
1 AAAAT-AAA-ATAA
3057012 AAAATAAAATAA
1 AAAATAAAATAA
3057024 AAAATAAAA
1 AAAATAAAA
3057033 AGGCTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 13 0.62
13 3 0.14
14 5 0.24
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:3057221 original size:18 final size:18
Alignment explanation
Indices: 3057194--3057228 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3057184 TAATAAATGC
*
3057194 ATTTTAATTATTTAAAAT
1 ATTTTAATTACTTAAAAT
*
3057212 ATTTTTATTACTTAAAA
1 ATTTTAATTACTTAAAA
3057229 CATAATTAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTAATTACTTAAAAT
Found at i:3060670 original size:21 final size:21
Alignment explanation
Indices: 3060628--3060670 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3060618 ACAACAAATT
** * *
3060628 AATGACCAGGAGCAACGCCTC
1 AATGACCAACAGCAAAGACTC
3060649 AATGACCAACAGCAAAGACTC
1 AATGACCAACAGCAAAGACTC
3060670 A
1 A
3060671 CTGCTTTGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.30, G:0.19, T:0.09
Consensus pattern (21 bp):
AATGACCAACAGCAAAGACTC
Found at i:3064111 original size:2 final size:2
Alignment explanation
Indices: 3064104--3064129 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3064094 TTCAAACAAC
3064104 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
3064130 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3067590 original size:19 final size:19
Alignment explanation
Indices: 3067566--3067613 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
3067556 ATTTTCCATC
3067566 ATTTTTATTATT-TTTAATTA
1 ATTTTTATT-TTATTTAA-TA
3067586 ATTTTTATTTTATTTAATA
1 ATTTTTATTTTATTTAATA
3067605 ATTTTTATT
1 ATTTTTATT
3067614 CGATGGTCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTTATTTTATTTAATA
Found at i:3068318 original size:17 final size:17
Alignment explanation
Indices: 3068276--3068341 Score: 62
Period size: 16 Copynumber: 3.8 Consensus size: 17
3068266 ACAAAAATTC
3068276 CTCTTTTTTTTGGTTTTTG
1 CTCTTTTTTTT--TTTTTG
* *
3068295 GTTTTTTTTTTTTTTTG
1 CTCTTTTTTTTTTTTTG
**
3068312 CTC-TTTTCATTTTTTG
1 CTCTTTTTTTTTTTTTG
3068328 CTCCTTTTTTTTTT
1 CT-CTTTTTTTTTT
3068342 GGTTTGTTCG
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
16 13 0.35
17 8 0.22
18 7 0.19
19 9 0.24
ACGTcount: A:0.02, C:0.12, G:0.09, T:0.77
Consensus pattern (17 bp):
CTCTTTTTTTTTTTTTG
Found at i:3068851 original size:12 final size:13
Alignment explanation
Indices: 3068828--3068857 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
3068818 AATGATTTTT
3068828 TTATTCATTATCA
1 TTATTCATTATCA
3068841 TTATT-ATTATCA
1 TTATTCATTATCA
3068853 TTATT
1 TTATT
3068858 GTCTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATTCATTATCA
Found at i:3070242 original size:20 final size:19
Alignment explanation
Indices: 3070219--3070264 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
3070209 TTTTTTACAT
3070219 TTTTTCATTACTTTTATTTA
1 TTTTTCATTACTTTT-TTTA
**
3070239 TTTTTGGTTACTTTTTTTA
1 TTTTTCATTACTTTTTTTA
3070258 TTTTTCA
1 TTTTTCA
3070265 AATTTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.72
Consensus pattern (19 bp):
TTTTTCATTACTTTTTTTA
Found at i:3070543 original size:21 final size:21
Alignment explanation
Indices: 3070505--3070564 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
3070495 TAAAAATACA
**
3070505 TAAATAATAATAGTAATAAAAT
1 TAAA-AATAATAAAAATAAAAT
* *
3070527 TTAAAATAATAAAAATAATAT
1 TAAAAATAATAAAAATAAAAT
*
3070548 TAAAAATTAAAAAAAAT
1 TAAAAA-TAATAAAAAT
3070565 TTAACTTAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
TAAAAATAATAAAAATAAAAT
Found at i:3070543 original size:27 final size:27
Alignment explanation
Indices: 3070507--3070559 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3070497 AAAATACATA
* * *
3070507 AATAATAATAGTAATAAAATTTAAAAT
1 AATAAAAATAATAATAAAAATTAAAAT
*
3070534 AATAAAAATAATATTAAAAATTAAAA
1 AATAAAAATAATAATAAAAATTAAAA
3070560 AAAATTTAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (27 bp):
AATAAAAATAATAATAAAAATTAAAAT
Found at i:3073247 original size:4 final size:4
Alignment explanation
Indices: 3073238--3073263 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3073228 AATAGAGAAC
3073238 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
3073264 ATATATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:3077740 original size:2 final size:2
Alignment explanation
Indices: 3077733--3077779 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
3077723 TCAATCCTTA
3077733 AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
3077774 AT AT AT
1 AT AT AT
3077780 TGCCAAATCC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3078129 original size:3 final size:3
Alignment explanation
Indices: 3078121--3078157 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3078111 ATTTAAGACA
3078121 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3078158 AAAAGTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3080817 original size:11 final size:11
Alignment explanation
Indices: 3080801--3080826 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3080791 TCATTAACCG
3080801 TATTTATTTTA
1 TATTTATTTTA
3080812 TATTTATTTTA
1 TATTTATTTTA
3080823 TATT
1 TATT
3080827 ATATGCCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTTATTTTA
Found at i:3081805 original size:33 final size:33
Alignment explanation
Indices: 3081767--3081832 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3081757 ACAGACAAAC
* *
3081767 CCCCAACCCACGATATAAGCTCATTTAAACCCA
1 CCCCAACCCACGATATAAGCCCACTTAAACCCA
* *
3081800 CCCCAACCCATGATTTAAGCCCACTTAAACCCA
1 CCCCAACCCACGATATAAGCCCACTTAAACCCA
3081833 TTACTTCCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.41, G:0.06, T:0.18
Consensus pattern (33 bp):
CCCCAACCCACGATATAAGCCCACTTAAACCCA
Found at i:3088944 original size:19 final size:20
Alignment explanation
Indices: 3088908--3088948 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3088898 TACAACTAAT
*
3088908 AATTTTTATATAAGAATAAA
1 AATTTTGATATAAGAATAAA
*
3088928 AATTTTGATGTAA-AATAAA
1 AATTTTGATATAAGAATAAA
3088947 AA
1 AA
3088949 AATTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (20 bp):
AATTTTGATATAAGAATAAA
Found at i:3090097 original size:29 final size:24
Alignment explanation
Indices: 3090035--3090089 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
3090025 ATTGTCATAA
3090035 AAAAATTAATATAATTGTATGGAC
1 AAAAATTAATATAATTGTATGGAC
*
3090059 AAAAATTAATATAATTGTATTGAC
1 AAAAATTAATATAATTGTATGGAC
3090083 AAAAATT
1 AAAAATT
3090090 GACCTAATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.35
Consensus pattern (24 bp):
AAAAATTAATATAATTGTATGGAC
Found at i:3090882 original size:16 final size:16
Alignment explanation
Indices: 3090858--3090890 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3090848 ATGCTAATTG
*
3090858 TAAATACTTAATTTTA
1 TAAACACTTAATTTTA
3090874 TAAACACTTAATTTTA
1 TAAACACTTAATTTTA
3090890 T
1 T
3090891 CCATCGTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAACACTTAATTTTA
Found at i:3094332 original size:11 final size:11
Alignment explanation
Indices: 3094316--3094349 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3094306 GGGTAATTTC
3094316 TTATTATTTTT
1 TTATTATTTTT
3094327 TTATTATTTTCT
1 TTATTATTTT-T
3094339 TTA-TATTTTT
1 TTATTATTTTT
3094349 T
1 T
3094350 ATAAGTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.09
11 16 0.73
12 4 0.18
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (11 bp):
TTATTATTTTT
Found at i:3095117 original size:18 final size:18
Alignment explanation
Indices: 3095090--3095124 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3095080 TAATAAATGC
*
3095090 ATTTTAATTATTTAAAAT
1 ATTTTAATTACTTAAAAT
*
3095108 ATTTTTATTACTTAAAA
1 ATTTTAATTACTTAAAA
3095125 CATAATTAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTAATTACTTAAAAT
Found at i:3101781 original size:2 final size:2
Alignment explanation
Indices: 3101774--3101802 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3101764 TCAAACAATC
3101774 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 T
3101803 GTACGTATGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3102991 original size:57 final size:57
Alignment explanation
Indices: 3102928--3103422 Score: 731
Period size: 57 Copynumber: 8.5 Consensus size: 57
3102918 TTGTGTAGGA
* *
3102928 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGGAAATTTATTCTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAATTTATTTTTAAGG
* *
3102985 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTAGAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATA---TTTTTTGGAAATTTATTTTTAAGG
* * *
3103045 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTGTTTATAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAA-TTTATTTTTAAGG
* *
3103103 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAATTTATTTTTAAGG
*
3103160 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAATTTATTTTTAAGG
* *
3103217 AAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTGGAAACTTTGATTTTCAAAG
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTGGAAA-TTT-ATTTTTAAGG
* *
3103276 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAATTTATTTTTAAGG
** * * *
3103333 AAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTGAAAAATTTGATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTG-GAAATTT-ATTTTTAAGG
3103392 AAAATTGATACTTTCAACTTTTCCTCAAAAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA
3103423 CCCCTTATTT
Statistics
Matches: 399, Mismatches: 29, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
57 187 0.47
58 77 0.19
59 81 0.20
60 54 0.14
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAATTTATTTTTAAGG
Found at i:3103308 original size:116 final size:115
Alignment explanation
Indices: 3102928--3103422 Score: 742
Period size: 116 Copynumber: 4.3 Consensus size: 115
3102918 TTGTGTAGGA
* *
3102928 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGGAAATTTATTCTTAAGGAAAATTGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAATTTATTTTTAAGGAAAATTGA
* ** * *
3102993 TACTTTCAACTTTTCCCCAAAAATATTTTTTTTTAGAAATTTATTTTTAAGG
66 TACTTTCAACTTTTTCCCAAAAATA-TTTTTTGGA-AAATTTATTTTCAAAG
* * *
3103045 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTGTTTATAAGAAAAATTG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAA-TTTATTTTTAAGGAAAATTG
* * *
3103110 ATACTTTCAACTTTTTCTCAAAAATATTTTTT-GAAAATTTATTTTTAAGG
65 ATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAAATTTATTTTCAAAG
*
3103160 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTTTAAGGAAAATTGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAATTTATTTTTAAGGAAAATTGA
*
3103225 TACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAACTTTGATTTTCAAAG
66 TACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAAATTT-ATTTTCAAAG
* *
3103276 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAAGGAAAATTGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAATTTATTTTTAAGGAAAATTGA
** *
3103341 TACTTTCAACTTTTTTTCAAAAATATTTTTTGAAAAATTTGATTTTC-AAG
66 TACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAAATTT-ATTTTCAAAG
3103391 AAAAATTGATACTTTCAACTTTTCCTCAAAAA
1 -AAAATTGATACTTTCAACTTTTCCTCAAAAA
3103423 CCCCTTATTT
Statistics
Matches: 352, Mismatches: 22, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
114 48 0.14
115 69 0.20
116 146 0.41
117 49 0.14
118 40 0.11
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (115 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAATTTATTTTTAAGGAAAATTGA
TACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAAATTTATTTTCAAAG
Found at i:3103498 original size:6 final size:6
Alignment explanation
Indices: 3103470--3103542 Score: 58
Period size: 6 Copynumber: 11.5 Consensus size: 6
3103460 AAAAGAAATT
* **
3103470 AAATAA TAAATTAA AAGAAAA AAATAA AAATAAA AAAGTAA AACCAA AAATAA
1 AAATAA -AAA-TAA AA-ATAA AAATAA AAAT-AA AAA-TAA AAATAA AAATAA
*
3103523 AAAT-A AAATAA AGATAA AAA
1 AAATAA AAATAA AAATAA AAA
3103543 AACATTAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
5 5 0.09
6 25 0.47
7 18 0.34
8 5 0.09
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:3103500 original size:27 final size:26
Alignment explanation
Indices: 3103454--3103530 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 26
3103444 TAGATTTTTT
* *
3103454 TTAAAAAAAAGAAAT-TAAATAATAAA
1 TTAAAAAAAA-AAATAAAAATAAAAAA
3103480 TTAAAAGAAAAAAATAAAAATAAAAAA
1 TTAAAA-AAAAAAATAAAAATAAAAAA
* **
3103507 GTAAAACCAAAAATAAAAATAAAA
1 TTAAAAAAAAAAATAAAAATAAAA
3103531 TAAAGATAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
26 26 0.59
27 18 0.41
ACGTcount: A:0.77, C:0.03, G:0.04, T:0.17
Consensus pattern (26 bp):
TTAAAAAAAAAAATAAAAATAAAAAA
Found at i:3103504 original size:13 final size:13
Alignment explanation
Indices: 3103470--3103543 Score: 57
Period size: 13 Copynumber: 5.8 Consensus size: 13
3103460 AAAAGAAATT
*
3103470 AAATAATAAATTAA
1 AAATAA-AAAATAA
3103484 AAGA-AAAAAATAA
1 AA-ATAAAAAATAA
3103497 AAATAAAAAAGT-A
1 AAATAAAAAA-TAA
**
3103510 AAACCAAAAATAA
1 AAATAAAAAATAA
3103523 AAAT--AAAATAA
1 AAATAAAAAATAA
*
3103534 AGATAAAAAA
1 AAATAAAAAA
3103544 ACATTAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
11 10 0.20
12 2 0.04
13 31 0.63
14 5 0.10
15 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.15
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:3104547 original size:6 final size:6
Alignment explanation
Indices: 3104532--3104619 Score: 92
Period size: 6 Copynumber: 14.8 Consensus size: 6
3104522 AAATATATAT
*
3104532 ATAAATA ATAAAA ATAAAA ATAAAA ATAGAA AT-AAA AT-AAA ATAAAA
1 ATAAA-A ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
* * * *
3104579 ATGTAAA ATACAA TTAAAA ATAAAA ATAAGA AT-AAA ATAAA
1 AT-AAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
3104620 GAAAAAAGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
5 13 0.19
6 45 0.66
7 10 0.15
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.20
Consensus pattern (6 bp):
ATAAAA
Found at i:3104621 original size:12 final size:11
Alignment explanation
Indices: 3104538--3104633 Score: 81
Period size: 11 Copynumber: 8.4 Consensus size: 11
3104528 ATATATAAAT
3104538 AATAAAAATAAA
1 AATAAAAAT-AA
3104550 AATAAAAATAGA
1 AATAAAAATA-A
3104562 AAT-AAAATAA
1 AATAAAAATAA
3104572 AATAAAAATGTAA
1 AATAAAAA--TAA
* *
3104585 AATACAATTAAA
1 AATAAAAAT-AA
3104597 AATAAAAATAA
1 AATAAAAATAA
3104608 GAAT-AAAATAA
1 -AATAAAAATAA
*
3104619 AGA-AAAAAGAA
1 A-ATAAAAATAA
3104630 AATA
1 AATA
3104634 GACTTACCCA
Statistics
Matches: 70, Mismatches: 5, Indels: 19
0.74 0.05 0.20
Matches are distributed among these distances:
10 6 0.09
11 30 0.43
12 25 0.36
13 9 0.13
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:3104626 original size:47 final size:45
Alignment explanation
Indices: 3104546--3104633 Score: 126
Period size: 47 Copynumber: 1.9 Consensus size: 45
3104536 ATAATAAAAA
3104546 TAAAAATAAAAATAGAAATAAAATAAAATAAAAATGTAAAATACAAT
1 TAAAAATAAAAATAGAAATAAAATAAAATAAAAA-G-AAAATACAAT
3104593 TAAAAATAAAAATA-AGAATAAAATAAAGA-AAAAAGAAAATA
1 TAAAAATAAAAATAGA-AATAAAATAAA-ATAAAAAGAAAATA
3104634 GACTTACCCA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
45 6 0.15
46 2 0.05
47 30 0.77
48 1 0.03
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (45 bp):
TAAAAATAAAAATAGAAATAAAATAAAATAAAAAGAAAATACAAT
Found at i:3104787 original size:1 final size:1
Alignment explanation
Indices: 3104783--3104821 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
3104773 TTACTTTTCA
* * *
3104783 TTTTTTTTGTTTTTTTTGTTTTTTTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3104822 GATCAAAGCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (1 bp):
T
Found at i:3104795 original size:9 final size:9
Alignment explanation
Indices: 3104783--3104821 Score: 64
Period size: 8 Copynumber: 4.6 Consensus size: 9
3104773 TTACTTTTCA
3104783 TTTTTTTTG
1 TTTTTTTTG
3104792 TTTTTTTTG
1 TTTTTTTTG
3104801 -TTTTTTT-
1 TTTTTTTTG
3104808 TTTTTTTTG
1 TTTTTTTTG
3104817 TTTTT
1 TTTTT
3104822 GATCAAAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 14 0.50
9 14 0.50
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:3104886 original size:41 final size:41
Alignment explanation
Indices: 3104829--3105053 Score: 206
Period size: 42 Copynumber: 5.7 Consensus size: 41
3104819 TTTGATCAAA
* * *
3104829 GCTCCTCTAAACAGAGGCTCAACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
3104870 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAATAAATT
3104912 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAATAAA--
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAAATAAATT
* * * * * ** *
3104952 ------C-AGA-GGCA-CCACGAC--TTTGAGAAAGTAAATT
1 GCTCCTCTAAACAG-AGGCACCACGACTTTGGAAAATAAATT
* *
3104983 GCTCCTCTAAACAGAGGCACCAAGACTTTGGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GGAAAATAAATT
3105025 GCTCCTCTAAACAGAGGCACCACGACTTT
1 GCTCCTCTAAACAGAGGCACCACGACTTT
3105054 ACAGAGGCAC
Statistics
Matches: 147, Mismatches: 20, Indels: 33
0.74 0.10 0.17
Matches are distributed among these distances:
29 8 0.05
30 2 0.01
32 6 0.04
33 3 0.02
34 1 0.01
37 1 0.01
38 3 0.02
39 5 0.03
41 31 0.21
42 86 0.59
43 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
Found at i:3104961 original size:29 final size:29
Alignment explanation
Indices: 3104919--3104980 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
3104909 ATTGCTCCTC
3104919 TAAACAGAGGCACCACGACTTTGAGAAAA
1 TAAACAGAGGCACCACGACTTTGAGAAAA
*
3104948 TAAACAGAGGCACCACGACTTTGAGAAAG
1 TAAACAGAGGCACCACGACTTTGAGAAAA
3104977 TAAA
1 TAAA
3104981 TTGCTCCTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (29 bp):
TAAACAGAGGCACCACGACTTTGAGAAAA
Found at i:3104993 original size:71 final size:71
Alignment explanation
Indices: 3104877--3105022 Score: 240
Period size: 71 Copynumber: 2.1 Consensus size: 71
3104867 ATTGCTCCTC
*
3104877 TAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG
1 TAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCACCAAGACTTTG
3104942 AGAAAA
66 AGAAAA
*
3104948 TAAACAGAGGCACCACGACTTT-GAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAAGACTTT
1 TAAACAGAGGCACCACGACTTTGGA-AAAATAAATTGCTCCTCTAAACAGAGGCACCAAGACTTT
* *
3105012 GGGAAAG
65 GAGAAAA
3105019 TAAA
1 TAAA
3105023 TTGCTCCTCT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
70 2 0.03
71 68 0.97
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.18
Consensus pattern (71 bp):
TAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCACCAAGACTTTG
AGAAAA
Found at i:3105059 original size:19 final size:19
Alignment explanation
Indices: 3105035--3105072 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3105025 GCTCCTCTAA
3105035 ACAGAGGCACCACGACTTT
1 ACAGAGGCACCACGACTTT
3105054 ACAGAGGCACCACGACTTT
1 ACAGAGGCACCACGACTTT
3105073 TGGAAAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.16
Consensus pattern (19 bp):
ACAGAGGCACCACGACTTT
Found at i:3105088 original size:61 final size:61
Alignment explanation
Indices: 3104993--3105114 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
3104983 GCTCCTCTAA
3104993 ACAGAGGCACCAAGACTTTGGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT
1 ACAGAGGCACCAAGACTTTGGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT
* *
3105054 ACAGAGGCACCACGACTTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT
1 ACAGAGGCACCAAGACTTTGGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT
3105115 GGAAAGTAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (61 bp):
ACAGAGGCACCAAGACTTTGGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT
Found at i:3105128 original size:41 final size:41
Alignment explanation
Indices: 3105054--3105256 Score: 320
Period size: 41 Copynumber: 4.9 Consensus size: 41
3105044 CCACGACTTT
3105054 ACAGAGGCACCACGACTTTTGGAAAGTAAATTGCTCCTCTAA
1 ACAGAGGCACCACGAC-TTTGGAAAGTAAATTGCTCCTCTAA
3105096 ACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAA
1 ACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAA
*
3105137 ACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTCCTCTAA
1 ACAGAGGCACCACGACTTTG-GAAAGTAAATTGCTCCTCTAA
3105179 ACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAA
1 ACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAA
* * *
3105220 ATAGAGGCA--ATGAAACTTTGGAAAATAAATTGCTCCT
1 ACAGAGGCACCACG--ACTTTGGAAAGTAAATTGCTCCT
3105257 TGACAATCAT
Statistics
Matches: 153, Mismatches: 5, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
39 2 0.01
41 95 0.62
42 56 0.37
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (41 bp):
ACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAA
Found at i:3105193 original size:83 final size:83
Alignment explanation
Indices: 3105054--3105228 Score: 316
Period size: 83 Copynumber: 2.1 Consensus size: 83
3105044 CCACGACTTT
*
3105054 ACAGAGGCACCACGACTTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAA
1 ACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAA
3105119 AGTAAATTGCTCCTCTAA
66 AGTAAATTGCTCCTCTAA
3105137 ACAGAGGCACCACGAC-TTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGA
1 ACAGAGGCACCACGACTTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGA
3105201 AAGTAAATTGCTCCTCTAA
65 AAGTAAATTGCTCCTCTAA
*
3105220 ATAGAGGCA
1 ACAGAGGCA
3105229 ATGAAACTTT
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
82 4 0.04
83 85 0.96
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.22
Consensus pattern (83 bp):
ACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAA
AGTAAATTGCTCCTCTAA
Found at i:3105238 original size:83 final size:82
Alignment explanation
Indices: 3105054--3105256 Score: 304
Period size: 83 Copynumber: 2.5 Consensus size: 82
3105044 CCACGACTTT
*
3105054 ACAGAGGCACCACGACTTTTG-GAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGA
1 ACAGAGGCA-CACGAC-TTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGA
3105118 AAGTAAATTGCTCCTCTAA
64 AAGTAAATTGCTCCTCTAA
3105137 ACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAA
1 ACAGAGGCA-CACGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAA
3105202 AGTAAATTGCTCCTCTAA
65 AGTAAATTGCTCCTCTAA
* * *
3105220 ATAGAGGCA-ATGAAACTTTGGAAAA-TAAATTGCTCCT
1 ACAGAGGCACACG--ACTTTGAAAAAGTAAATTGCTCCT
3105257 TGACAATCAT
Statistics
Matches: 113, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
81 2 0.02
82 16 0.14
83 95 0.84
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (82 bp):
ACAGAGGCACACGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAA
GTAAATTGCTCCTCTAA
Found at i:3106262 original size:7 final size:8
Alignment explanation
Indices: 3106244--3106299 Score: 69
Period size: 8 Copynumber: 6.9 Consensus size: 8
3106234 TGAGTCCTCA
*
3106244 TTTTTCAC
1 TTTTTCAT
3106252 TTTTTC-T
1 TTTTTCAT
3106259 TTTTTCAT
1 TTTTTCAT
*
3106267 TTTTTTAT
1 TTTTTCAT
3106275 TTTTTCCAT
1 TTTTT-CAT
3106284 TTTTTCAT
1 TTTTTCAT
3106292 TGTTTTCA
1 T-TTTTCA
3106300 AGCATAGTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
7 6 0.14
8 23 0.55
9 13 0.31
ACGTcount: A:0.11, C:0.14, G:0.02, T:0.73
Consensus pattern (8 bp):
TTTTTCAT
Found at i:3106278 original size:17 final size:17
Alignment explanation
Indices: 3106244--3106299 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
3106234 TGAGTCCTCA
*
3106244 TTTTTCACTTTTTC--T
1 TTTTTCATTTTTTCATT
*
3106259 TTTTTCATTTTTTTATT
1 TTTTTCATTTTTTCATT
*
3106276 TTTTCCATTTTTTCATT
1 TTTTTCATTTTTTCATT
*
3106293 GTTTTCA
1 TTTTTCA
3106300 AGCATAGTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 12 0.36
17 21 0.64
ACGTcount: A:0.11, C:0.14, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTTTCATTTTTTCATT
Found at i:3112429 original size:23 final size:23
Alignment explanation
Indices: 3112399--3112449 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
3112389 TTAGCTTACC
3112399 ATTCTTGATAGCACTCTCAATGA
1 ATTCTTGATAGCACTCTCAATGA
3112422 ATTCTTGATAGCACTCTCAATGA
1 ATTCTTGATAGCACTCTCAATGA
*
3112445 TTTCT
1 ATTCT
3112450 CTTGAGATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (23 bp):
ATTCTTGATAGCACTCTCAATGA
Found at i:3116797 original size:57 final size:58
Alignment explanation
Indices: 3116731--3116872 Score: 223
Period size: 60 Copynumber: 2.4 Consensus size: 58
3116721 TTTTGTGTAG
*
3116731 GAAAAATTGATACTTTCAACTTTTCTCCAAAAATA-TTTTTTGGAAATTTATTCTTAA
1 GAAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTAGAAATTTATTCTTAA
* *
3116788 GAAAAATTGATACTTTCAACTTTTATCCAAAAATATTTTTTTTTAGAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCTCCAAAAATA--TTTTTTTAGAAATTTATTCTTAA
*
3116848 GGAAAATTGATACTTTCAACTTTTC
1 GAAAAATTGATACTTTCAACTTTTC
3116873 CCTTTAAAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
57 34 0.44
60 43 0.56
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (58 bp):
GAAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTAGAAATTTATTCTTAA
Found at i:3116946 original size:58 final size:57
Alignment explanation
Indices: 3116878--3117082 Score: 306
Period size: 58 Copynumber: 3.5 Consensus size: 57
3116868 TTTTCCCTTT
3116878 AAAATTGATACTTTCAACTTTT-CTCCAAAAATATTTTTTGGAAACTTTGTTTCTAAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTTGGAAACTTTGTTT-TAAGG
* * *
3116936 AAAATTGATACTTTAAACTTTTCCTCAAAAATATTTTTTGGAAA-TTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTT-GTTTTAAGG
* *
3116993 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTG-TTTT-AAGG
3117052 AAAATTGATACTTTCAACTTTTCCTCAAAAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA
3117083 CTTCTTTTTT
Statistics
Matches: 133, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
57 48 0.36
58 50 0.38
59 35 0.26
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.42
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTGTTTTAAGG
Found at i:3117005 original size:57 final size:58
Alignment explanation
Indices: 3116878--3117082 Score: 315
Period size: 57 Copynumber: 3.5 Consensus size: 58
3116868 TTTTCCCTTT
* *
3116878 AAAATTGATACTTTCAACTTTT-CTCCAAAAATATTTTTTGGAAACTTTGTTTCTAAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTTGGAAACTTTATTTTTAAGG
* *
3116936 AAAATTGATACTTTAAACTTTTCCTCAAAAATATTTTTTGGAAA-TTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTATTTTTAAGG
* * *
3116993 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTT-ATTTTTAAGG
3117052 AAAATTGATACTTTCAACTTTTCCTCAAAAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA
3117083 CTTCTTTTTT
Statistics
Matches: 134, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
57 51 0.38
58 43 0.32
59 40 0.30
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.42
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTATTTTTAAGG
Found at i:3117211 original size:4 final size:4
Alignment explanation
Indices: 3117202--3117241 Score: 62
Period size: 4 Copynumber: 9.5 Consensus size: 4
3117192 ATCCTAATTT
3117202 AATA AATA AATA CAATA AATA CAATA AATA AATA AATA AA
1 AATA AATA AATA -AATA AATA -AATA AATA AATA AATA AA
3117242 AAAAAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 26 0.76
5 8 0.24
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:3117220 original size:9 final size:8
Alignment explanation
Indices: 3117202--3117241 Score: 62
Period size: 9 Copynumber: 4.8 Consensus size: 8
3117192 ATCCTAATTT
3117202 AATAAATA
1 AATAAATA
3117210 AATACAATA
1 AATA-AATA
3117219 AATACAATA
1 AATA-AATA
3117228 AATAAATA
1 AATAAATA
3117236 AATAAA
1 AATAAA
3117242 AAAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 14 0.45
9 17 0.55
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (8 bp):
AATAAATA
Found at i:3117220 original size:13 final size:12
Alignment explanation
Indices: 3117202--3117241 Score: 62
Period size: 13 Copynumber: 3.2 Consensus size: 12
3117192 ATCCTAATTT
3117202 AATAAATAAATA
1 AATAAATAAATA
3117214 CAATAAATACAATA
1 -AATAAATA-AATA
3117228 AATAAATAAATA
1 AATAAATAAATA
3117240 AA
1 AA
3117242 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.23
13 16 0.62
14 4 0.15
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (12 bp):
AATAAATAAATA
Found at i:3119233 original size:19 final size:19
Alignment explanation
Indices: 3119209--3119256 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
3119199 ATTTTCCATC
3119209 ATTTTTATTATT-TTTAATTA
1 ATTTTTATT-TTATTTAA-TA
3119229 ATTTTTATTTTATTTAATA
1 ATTTTTATTTTATTTAATA
3119248 ATTTTTATT
1 ATTTTTATT
3119257 CGATGGTCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTTATTTTATTTAATA
Found at i:3119719 original size:20 final size:20
Alignment explanation
Indices: 3119696--3119750 Score: 101
Period size: 20 Copynumber: 2.7 Consensus size: 20
3119686 TGGTTTATGC
3119696 AAAAGAGAAAGAAAAAGAGCA
1 AAAAG-GAAAGAAAAAGAGCA
3119717 AAAAGGAAAGAAAAAGAGCA
1 AAAAGGAAAGAAAAAGAGCA
3119737 AAAAGGAAAGAAAA
1 AAAAGGAAAGAAAA
3119751 TCGAGTTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 29 0.85
21 5 0.15
ACGTcount: A:0.73, C:0.04, G:0.24, T:0.00
Consensus pattern (20 bp):
AAAAGGAAAGAAAAAGAGCA
Found at i:3120493 original size:12 final size:13
Alignment explanation
Indices: 3120470--3120499 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
3120460 AATGATTTTT
3120470 TTATTCATTATCA
1 TTATTCATTATCA
3120483 TTATT-ATTATCA
1 TTATTCATTATCA
3120495 TTATT
1 TTATT
3120500 GTCTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATTCATTATCA
Found at i:3121537 original size:20 final size:21
Alignment explanation
Indices: 3121512--3121559 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
3121502 AGTTAATTTT
3121512 TATTTTTATTTA-ATAAAAAA
1 TATTTTTATTTATATAAAAAA
*
3121532 TATTTTTA-TTATATTAAAAA
1 TATTTTTATTTATATAAAAAA
3121552 T-TTTTTAT
1 TATTTTTAT
3121560 AAATATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTTTTATTTATATAAAAAA
Found at i:3121565 original size:20 final size:20
Alignment explanation
Indices: 3121527--3121566 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3121517 TTATTTAATA
*
3121527 AAAAATATTTTTATTATATT
1 AAAAATATTTTTATAATATT
3121547 AAAAAT-TTTTTATAAATATT
1 AAAAATATTTTTAT-AATATT
3121567 TTAATGTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAAAATATTTTTATAATATT
Found at i:3122018 original size:22 final size:22
Alignment explanation
Indices: 3121974--3122020 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3121964 CATAAATAAT
* **
3121974 AATAATATTAAAATTTATTAAA
1 AATAATATTAAAAATTAAAAAA
3121996 AATAATATTAAAAATTAAAAAA
1 AATAATATTAAAAATTAAAAAA
3122018 AAT
1 AAT
3122021 TTAAACTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AATAATATTAAAAATTAAAAAA
Found at i:3122566 original size:16 final size:18
Alignment explanation
Indices: 3122540--3122581 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
3122530 ACCACATCCC
* *
3122540 TCTTTTCTTTGGTTT-TT
1 TCTTTTTTTTGATTTGTT
3122557 T-TTTTTTTTGATTTGTT
1 TCTTTTTTTTGATTTGTT
3122574 TCTTTTTT
1 TCTTTTTT
3122582 CTGGGGTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 11 0.52
17 4 0.19
18 6 0.29
ACGTcount: A:0.02, C:0.07, G:0.10, T:0.81
Consensus pattern (18 bp):
TCTTTTTTTTGATTTGTT
Found at i:3123040 original size:3 final size:3
Alignment explanation
Indices: 3123032--3123059 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3123022 TAATTAATTA
3123032 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3123060 GTCAAAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3123413 original size:4 final size:4
Alignment explanation
Indices: 3123400--3123436 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
3123390 AGAAAAGAAA
*
3123400 TATT TA-T TATT TATT TATT AATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TA
3123437 AACTATTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:3134465 original size:15 final size:15
Alignment explanation
Indices: 3134423--3134471 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
3134413 TTTTTTCCTC
*
3134423 CTTTTCTGTTCCTTCT
1 CTTTTCT-TTCCTTTT
3134439 -TTTTC-TTCCTTTT
1 CTTTTCTTTCCTTTT
*
3134452 CTTTTCTTTCCTTTC
1 CTTTTCTTTCCTTTT
3134467 CTTTT
1 CTTTT
3134472 TCCTTCCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 7 0.24
14 5 0.17
15 17 0.59
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (15 bp):
CTTTTCTTTCCTTTT
Found at i:3137832 original size:2 final size:2
Alignment explanation
Indices: 3137816--3137850 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3137806 AAAGTTATTT
* *
3137816 TA TA TA AA TA AA 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 TA T
3137851 TTGTTTTGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3153635 original size:24 final size:24
Alignment explanation
Indices: 3153599--3153650 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3153589 AAATTATATT
* *
3153599 TTAAATTTCAAATTTAAAATTAAA
1 TTAAAATTAAAATTTAAAATTAAA
* *
3153623 TTAAAATTAAAATTTAATATTATA
1 TTAAAATTAAAATTTAAAATTAAA
3153647 TTAA
1 TTAA
3153651 TTCAAATTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TTAAAATTAAAATTTAAAATTAAA
Found at i:3160474 original size:5 final size:5
Alignment explanation
Indices: 3160416--3160454 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
3160406 AAATATTAAT
* * *
3160416 AAAGG AAAGG AAAGG AAAGG AAAGA AAAAG AAAAG AAAG
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAG
3160455 TTTTTTAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:3163995 original size:2 final size:2
Alignment explanation
Indices: 3163988--3164014 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3163978 TCAACGGGAG
3163988 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
3164015 GATGAAACTA
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:3166999 original size:30 final size:30
Alignment explanation
Indices: 3166958--3167016 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
3166948 GCATAAGGAA
*
3166958 TTGTTTTGAATATGATGTGGAAGAGTGATT
1 TTGTTTCGAATATGATGTGGAAGAGTGATT
3166988 TTGTTTCGAATATGATGTGGAAGAGTGAT
1 TTGTTTCGAATATGATGTGGAAGAGTGAT
3167017 AATTCTAGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.02, G:0.31, T:0.41
Consensus pattern (30 bp):
TTGTTTCGAATATGATGTGGAAGAGTGATT
Found at i:3168549 original size:2 final size:2
Alignment explanation
Indices: 3168536--3168577 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
3168526 TTGTATCAAT
* *
3168536 TA TA TT TA TA TA TA TA TA AA 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
3168578 CTTCTAAGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3169820 original size:10 final size:9
Alignment explanation
Indices: 3169795--3169819 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3169785 TTAGTGAAAC
3169795 AAAAAAATA
1 AAAAAAATA
3169804 AAAAAAATA
1 AAAAAAATA
3169813 AAAAAAA
1 AAAAAAA
3169820 AGTTAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATA
Found at i:3174451 original size:2 final size:2
Alignment explanation
Indices: 3174444--3174473 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3174434 CCTCACTTCT
3174444 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3174474 GTGATTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3175042 original size:14 final size:13
Alignment explanation
Indices: 3175023--3175053 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
3175013 TTAATATTAA
3175023 AAAATATAAAATGT
1 AAAATATAAAAT-T
3175037 AAAATATAAAATT
1 AAAATATAAAATT
3175050 AAAA
1 AAAA
3175054 AAACACTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (13 bp):
AAAATATAAAATT
Found at i:3178296 original size:2 final size:2
Alignment explanation
Indices: 3178289--3178320 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3178279 AAATTTAGTA
3178289 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
3178321 GAAAAGATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3185377 original size:2 final size:2
Alignment explanation
Indices: 3185370--3185422 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3185360 TCCAATATTA
3185370 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3185412 AG AG AG AG AG A
1 AG AG AG AG AG A
3185423 ACCATTACCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3189639 original size:23 final size:22
Alignment explanation
Indices: 3189595--3189656 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
3189585 TTGTGTGGAA
*
3189595 TTTTTTATTTGTTTTTAGATTTT
1 TTTTTTATTTGTTTTTA-ATTTC
3189618 TTTTTTATGTTGTTGTTT-ATTTC
1 TTTTTTAT-TTGTT-TTTAATTTC
* *
3189641 TTTTTTCTTTTTTTTT
1 TTTTTTATTTGTTTTT
3189657 TTTAATATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 3 0.09
22 4 0.12
23 19 0.56
24 5 0.15
25 3 0.09
ACGTcount: A:0.08, C:0.03, G:0.08, T:0.81
Consensus pattern (22 bp):
TTTTTTATTTGTTTTTAATTTC
Found at i:3189644 original size:24 final size:22
Alignment explanation
Indices: 3189595--3189662 Score: 64
Period size: 25 Copynumber: 2.9 Consensus size: 22
3189585 TTGTGTGGAA
3189595 TTTTTTATTTGTTTTTAGATTTT
1 TTTTTTATTTGTTTTTA-ATTTT
*
3189618 TTTTTTATGTTGTTGTTTATTTCTT
1 TTTTTTAT-TTGTT-TTTAATT-TT
* *
3189643 TTTTCTTTTTTTTTTTTAAT
1 TTTT-TTATTTGTTTTTAAT
3189663 ATAAATTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 8 0.22
24 12 0.32
25 14 0.38
26 3 0.08
ACGTcount: A:0.10, C:0.03, G:0.07, T:0.79
Consensus pattern (22 bp):
TTTTTTATTTGTTTTTAATTTT
Found at i:3211163 original size:14 final size:14
Alignment explanation
Indices: 3211137--3211175 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3211127 TGTAGTTGTT
*
3211137 AGAAAAAATAAATA
1 AGAAAAAAGAAATA
*
3211151 AGATAAAAGAAATA
1 AGAAAAAAGAAATA
*
3211165 ATAAAAAAGAA
1 AGAAAAAAGAA
3211176 TTTTGGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (14 bp):
AGAAAAAAGAAATA
Found at i:3217408 original size:20 final size:20
Alignment explanation
Indices: 3217365--3217405 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
3217355 ACTCTCTCCC
*
3217365 TCTTGATTTTTCTGATTGAT
1 TCTTGATTTTTCTAATTGAT
*
3217385 TCTTGATTGTTTTTAATTGAT
1 TCTTGATT-TTTCTAATTGAT
3217406 CTTAATGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.17, C:0.07, G:0.15, T:0.61
Consensus pattern (20 bp):
TCTTGATTTTTCTAATTGAT
Found at i:3219297 original size:23 final size:23
Alignment explanation
Indices: 3219265--3219310 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
3219255 TGAAACCAAG
3219265 GCCTTATGATCAGAGCGTGATTA
1 GCCTTATGATCAGAGCGTGATTA
*
3219288 GCCTTGTGATCAGAGCGTGATTA
1 GCCTTATGATCAGAGCGTGATTA
3219311 ACCGCTTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (23 bp):
GCCTTATGATCAGAGCGTGATTA
Found at i:3221548 original size:20 final size:21
Alignment explanation
Indices: 3221523--3221563 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3221513 TCTCTCTCTC
3221523 TCTTGATT-TTTCTAATTGAT
1 TCTTGATTATTTCTAATTGAT
*
3221543 TCTTGATTATTTTTAATTGAT
1 TCTTGATTATTTCTAATTGAT
3221564 CTTCATGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.22, C:0.07, G:0.10, T:0.61
Consensus pattern (21 bp):
TCTTGATTATTTCTAATTGAT
Found at i:3228126 original size:62 final size:62
Alignment explanation
Indices: 3228029--3228152 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
3228019 ATTTTATAAC
3228029 CCTAAAACCATTGGATTTGCTAATAAGAATGCCACAATTGTTAAAATTCCAAACTAAATTGG
1 CCTAAAACCATTGGATTTGCTAATAAGAATGCCACAATTGTTAAAATTCCAAACTAAATTGG
3228091 CCTAAAACCATTGGATTTGCTAATAAGAATGCCACAATTGTTAAAATTCCAAACTAAATTGG
1 CCTAAAACCATTGGATTTGCTAATAAGAATGCCACAATTGTTAAAATTCCAAACTAAATTGG
3228153 AAAGGGAAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (62 bp):
CCTAAAACCATTGGATTTGCTAATAAGAATGCCACAATTGTTAAAATTCCAAACTAAATTGG
Found at i:3237016 original size:13 final size:13
Alignment explanation
Indices: 3236994--3237027 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3236984 TTAAAAATGA
3236994 TTTAAT-AAAAAT
1 TTTAATAAAAAAT
3237006 TTTAATAAAAAAT
1 TTTAATAAAAAAT
*
3237019 TTAAATAAA
1 TTTAATAAA
3237028 TATATTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTAATAAAAAAT
Found at i:3238586 original size:44 final size:43
Alignment explanation
Indices: 3238536--3238704 Score: 234
Period size: 43 Copynumber: 3.9 Consensus size: 43
3238526 CACTCAATTC
3238536 TAGTTTCAAGTTCTTATTTAGAAAGCCCAGTATGGGTATTTGAG
1 TAGTTTCAAGTTCTTATTTAGAAAG-CCAGTATGGGTATTTGAG
* * *
3238580 TAGTTTCAAGTTTTTATTTATAAAGCCAGTATGGGTATTAGAG
1 TAGTTTCAAGTTCTTATTTAGAAAGCCAGTATGGGTATTTGAG
* *
3238623 TTAG-TGC-AGTTCTTATTTAGAAAGCCCAGTATGGGTGTTTGAG
1 -TAGTTTCAAGTTCTTATTTAGAAAG-CCAGTATGGGTATTTGAG
* *
3238666 TAGTTTCAAGTTTTTATTTATAAAGCCAGTATGGGTATT
1 TAGTTTCAAGTTCTTATTTAGAAAGCCAGTATGGGTATT
3238705 AAAGTTAGTG
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
42 18 0.17
43 50 0.46
44 41 0.38
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.41
Consensus pattern (43 bp):
TAGTTTCAAGTTCTTATTTAGAAAGCCAGTATGGGTATTTGAG
Found at i:3238689 original size:86 final size:86
Alignment explanation
Indices: 3238544--3238717 Score: 330
Period size: 86 Copynumber: 2.0 Consensus size: 86
3238534 TCTAGTTTCA
3238544 AGTTCTTATTTAGAAAGCCCAGTATGGGTATTTGAGTAGTTTCAAGTTTTTATTTATAAAGCCAG
1 AGTTCTTATTTAGAAAGCCCAGTATGGGTATTTGAGTAGTTTCAAGTTTTTATTTATAAAGCCAG
*
3238609 TATGGGTATTAGAGTTAGTGC
66 TATGGGTATTAAAGTTAGTGC
*
3238630 AGTTCTTATTTAGAAAGCCCAGTATGGGTGTTTGAGTAGTTTCAAGTTTTTATTTATAAAGCCAG
1 AGTTCTTATTTAGAAAGCCCAGTATGGGTATTTGAGTAGTTTCAAGTTTTTATTTATAAAGCCAG
3238695 TATGGGTATTAAAGTTAGTGC
66 TATGGGTATTAAAGTTAGTGC
3238716 AG
1 AG
3238718 AAAAATGATC
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (86 bp):
AGTTCTTATTTAGAAAGCCCAGTATGGGTATTTGAGTAGTTTCAAGTTTTTATTTATAAAGCCAG
TATGGGTATTAAAGTTAGTGC
Found at i:3240012 original size:30 final size:31
Alignment explanation
Indices: 3239978--3240039 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
3239968 TCTCTAAAAG
3239978 TTAATTTCTATTTT-TTTTTATTCTACCAAA
1 TTAATTTCTATTTTGTTTTTATTCTACCAAA
3240008 TTAATTTCTATTTTGTTTTTATTCTACCAAA
1 TTAATTTCTATTTTGTTTTTATTCTACCAAA
3240039 T
1 T
3240040 CGAACAAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 14 0.45
31 17 0.55
ACGTcount: A:0.26, C:0.13, G:0.02, T:0.60
Consensus pattern (31 bp):
TTAATTTCTATTTTGTTTTTATTCTACCAAA
Found at i:3240642 original size:85 final size:86
Alignment explanation
Indices: 3240488--3240657 Score: 256
Period size: 85 Copynumber: 2.0 Consensus size: 86
3240478 ATCCATTTCT
* *
3240488 AAGTTCCCTCATATCTTTAGGCTTTGGGTAAATAACGAGATAATGAATCTTCTTTTTGCCACTGG
1 AAGTTCCCTCATATCTTTAGGCTTTGGGTAAATAACAAGATAATGAATCTTCTTTTTGCCACTGA
3240553 ATTTTCCAATCAAATTCGTCC
66 ATTTTCCAATCAAATTCGTCC
* * *
3240574 AAGTT-CCTCATA-CATTTAGGCTTTGGGTAAATAGCAAGCTAATGAGTCTTCTTTTTGCCA-TA
1 AAGTTCCCTCATATC-TTTAGGCTTTGGGTAAATAACAAGATAATGAATCTTCTTTTTGCCACT-
3240636 GAATTTTCCAATCAAATTCGTC
64 GAATTTTCCAATCAAATTCGTC
3240658 GTAACACTCG
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
84 2 0.03
85 70 0.91
86 5 0.06
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (86 bp):
AAGTTCCCTCATATCTTTAGGCTTTGGGTAAATAACAAGATAATGAATCTTCTTTTTGCCACTGA
ATTTTCCAATCAAATTCGTCC
Found at i:3243480 original size:18 final size:19
Alignment explanation
Indices: 3243459--3243495 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3243449 AAAAATGTTC
*
3243459 ATATTTTA-ATTTTTAAAA
1 ATATTTTAGATTTTGAAAA
3243477 ATATTTTAGATTTTGAAAA
1 ATATTTTAGATTTTGAAAA
3243496 TTTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
ATATTTTAGATTTTGAAAA
Found at i:3244160 original size:24 final size:22
Alignment explanation
Indices: 3244133--3244183 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
3244123 TTTTTAAAAG
*
3244133 AAAATTCATATTTTAAAATTTAA
1 AAAATTCAGATTTTAAAA-TTAA
* *
3244156 TAAAATTTAGATTTTGAAATTAA
1 -AAAATTCAGATTTTAAAATTAA
3244179 AAAAT
1 AAAAT
3244184 AAAATTTCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 4 0.17
24 15 0.62
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (22 bp):
AAAATTCAGATTTTAAAATTAA
Found at i:3245363 original size:23 final size:23
Alignment explanation
Indices: 3245333--3245379 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
3245323 GCGCGGCTCC
3245333 TATCCAATTTCAAGTATAAAGGT
1 TATCCAATTTCAAGTATAAAGGT
*
3245356 TATCCAATTTCAAGTATAATGGT
1 TATCCAATTTCAAGTATAAAGGT
3245379 T
1 T
3245380 CGTCTATGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (23 bp):
TATCCAATTTCAAGTATAAAGGT
Found at i:3247217 original size:97 final size:97
Alignment explanation
Indices: 3247102--3247295 Score: 370
Period size: 97 Copynumber: 2.0 Consensus size: 97
3247092 ACTACAGTAC
3247102 AGGCGTGGCACACCCCACCAATTCTAGTTCACTAATTGATAGAGGTGGAGAGTAGCTAATTGGGC
1 AGGCGTGGCACACCCCACCAATTCTAGTTCACTAATTGATAGAGGTGGAGAGTAGCTAATTGGGC
*
3247167 AAAAACCAAATTCAGCAGCTTATCAATTAGGT
66 AAAAACCAAATTCAGCAACTTATCAATTAGGT
*
3247199 AGGCGTGGCACACCCCACCAATTCTAGTTCACTAATTGATAGAGGTGGAGGGTAGCTAATTGGGC
1 AGGCGTGGCACACCCCACCAATTCTAGTTCACTAATTGATAGAGGTGGAGAGTAGCTAATTGGGC
3247264 AAAAACCAAATTCAGCAACTTATCAATTAGGT
66 AAAAACCAAATTCAGCAACTTATCAATTAGGT
3247296 TTTACTAGCA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (97 bp):
AGGCGTGGCACACCCCACCAATTCTAGTTCACTAATTGATAGAGGTGGAGAGTAGCTAATTGGGC
AAAAACCAAATTCAGCAACTTATCAATTAGGT
Found at i:3247354 original size:15 final size:16
Alignment explanation
Indices: 3247315--3247356 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
3247305 ATATAGATAG
3247315 GAAGAA-GAAAGTGTA
1 GAAGAATGAAAGTGTA
**
3247330 GAAGCCTGAAAGTG-A
1 GAAGAATGAAAGTGTA
3247345 GAAGAATGAAAG
1 GAAGAATGAAAG
3247357 AAAATGGAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.50, C:0.05, G:0.33, T:0.12
Consensus pattern (16 bp):
GAAGAATGAAAGTGTA
Found at i:3250438 original size:21 final size:21
Alignment explanation
Indices: 3250409--3250449 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3250399 ATAATAACTC
3250409 TAAACTAAATATAATACAAAAA
1 TAAACTAAATA-AATACAAAAA
*
3250431 TAAA-TAAATAAATTCAAAA
1 TAAACTAAATAAATACAAAA
3250450 CTTTATCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAACTAAATAAATACAAAAA
Found at i:3250841 original size:24 final size:26
Alignment explanation
Indices: 3250796--3250847 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 26
3250786 CGTTCTATTT
3250796 TATTCTTTTGGTTTAAAAATATT-TTA
1 TATTCTTTT-GTTTAAAAATATTGTTA
**
3250822 TATTCTTTT-TTTAATTATATTGTTA
1 TATTCTTTTGTTTAAAAATATTGTTA
3250847 T
1 T
3250848 CATTTCTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 10 0.43
25 4 0.17
26 9 0.39
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (26 bp):
TATTCTTTTGTTTAAAAATATTGTTA
Found at i:3254612 original size:12 final size:12
Alignment explanation
Indices: 3254594--3254623 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3254584 CTTAAAATTG
3254594 ATTTAATAAAAA
1 ATTTAATAAAAA
*
3254606 CTTTAATAAAAA
1 ATTTAATAAAAA
3254618 ATTTAA
1 ATTTAA
3254624 ATCGATAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (12 bp):
ATTTAATAAAAA
Found at i:3257415 original size:17 final size:17
Alignment explanation
Indices: 3257393--3257425 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3257383 GTGCCAGATT
*
3257393 CAGTATTACGAGTGAAA
1 CAGTATTACAAGTGAAA
3257410 CAGTATTACAAGTGAA
1 CAGTATTACAAGTGAA
3257426 TTTCTTCTGA
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:0.42, C:0.12, G:0.21, T:0.24
Consensus pattern (17 bp):
CAGTATTACAAGTGAAA
Found at i:3260233 original size:20 final size:21
Alignment explanation
Indices: 3260208--3260248 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3260198 TCTCTCTCTC
*
3260208 TCTTGATT-TTTTTGATTGAT
1 TCTTGATTGTTTTTAATTGAT
3260228 TCTTGATTGTTTTTAATTGAT
1 TCTTGATTGTTTTTAATTGAT
3260249 CTTAATGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.17, C:0.05, G:0.15, T:0.63
Consensus pattern (21 bp):
TCTTGATTGTTTTTAATTGAT
Found at i:3263080 original size:48 final size:48
Alignment explanation
Indices: 3263004--3263099 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
3262994 TTAGGACTTG
*
3263004 AGCATGCACTCATCTGGCATCTTAGATTAGACTACTTGCCACGGTTCA
1 AGCAAGCACTCATCTGGCATCTTAGATTAGACTACTTGCCACGGTTCA
* *
3263052 AGCAAGCACTTATCTTGCATCTTAGATTAGACTACTTGCCACGGTTCA
1 AGCAAGCACTCATCTGGCATCTTAGATTAGACTACTTGCCACGGTTCA
3263100 CACCCTTGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (48 bp):
AGCAAGCACTCATCTGGCATCTTAGATTAGACTACTTGCCACGGTTCA
Found at i:3265060 original size:693 final size:693
Alignment explanation
Indices: 3263032--3266497 Score: 6299
Period size: 693 Copynumber: 5.0 Consensus size: 693
3263022 ATCTTAGATT
* *
3263032 AGACTACTTGCCACGGTTCAAGCAAGCACTTATCTTGCATCTTAGATTAGACTACTTGCCACGGT
1 AGACTACTTGCCACGGTTCAAGCATGCACTTATCTTGCATCTTAGATTAGACTACTTACCACGGT
* *
3263097 TCACACCCTTGTGAAGTGTTATCCACTCTAGCCCTTCTGGCATCATAGTTTTGTCCCATAAACTT
66 TCACACCCTTGTGAAGTATTATCCACTCTAGCCCTTCTGGCATCATAGTTTTGTCCCATAAACTC
* * *
3263162 AACCTCCAGGCTTGCACTGTTTTAGGACTCGAGCATGCACTCATTTGGC--ATCTTAAATTAGAT
131 AACCTCCAGGCTTGCACTGTTTTAGGACTCGAGCATGCACTCATCTGGCATATCTTAGATTAGAC
* * *
3263225 TACTTATCACGGTTCACACCCTTGTAAAGTATTATCCACTTTGACCCTTCTGGGCTTATAGTTTT
196 TACTTGTCACGGTTCACACCCTTGTGAAGTATTATCCACTTTGGCCCTTCTGGGCTTATAGTTTT
* *
3263290 GTCCCATAAATGGTGCCTCACAAGGAAGACGAAGACTCACTGTCCTCAGTGGCACATCGCTTGTA
261 GTCCCATAAATGGTGCATCACAAGGAAGATGAAGACTCACTGTCCTCAGTGGCACATCGCTTGTA
*
3263355 CCCTCAGAGCTGGTTCCGATGCACCTCACAAGGGAATGTGTGAATGCTTATATCTCAAAAACAAC
326 CCCTCAGAGCTGGTTTCGATGCACCTCACAAGGGAATGTGTGAATGCTTATATCTCAAAAACAAC
3263420 TCTAGTACACAGTCGATGTGGGATTCATGACTTTTCTTTAGGATCGTGACATTCTTTCCCACTCC
391 TCTAGTACACAGTCGATGTGGGATTCATGACTTTTCTTTAGGATCGTGACATTCTTTCCCACTCC
3263485 AACGGAGACCCATCGTCTTTAGTTGCCCATCGCTTGTACCCTTAGAGTTGGTTTTGATATCACTT
456 AACGGAGACCCATCGTCTTTAGTTGCCCATCGCTTGTACCCTTAGAGTTGGTTTTGATATCACTT
3263550 ATCATGGCTTGAAACACGAACTCTAGACTTGCGTAGCTCTAAGACCCAGATATGGGTTCATCCGA
521 ATCATGGCTTGAAACACGAACTCTAGACTTGCGTAGCTCTAAGACCCAGATATGGGTTCATCCGA
3263615 CATTTTAGATCAATCTACCTACTAGGGTTAACACTTTTGTGAGGTATTATCCACTTTAACCTCTC
586 CATTTTAGATCAATCTACCTACTAGGGTTAACACTTTTGTGAGGTATTATCCACTTTAACCTCTC
3263680 TGGCTCTACGATTTTGTCCCACAAAAGGTACCTTACAAGAAAG
651 TGGCTCTACGATTTTGTCCCACAAAAGGTACCTTACAAGAAAG
* * *
3263723 AGACTACTTGCCATGGTTCAAGCATGCACTTATCTTGCATCGTAGATTAGACTACTTATCACGGT
1 AGACTACTTGCCACGGTTCAAGCATGCACTTATCTTGCATCTTAGATTAGACTACTTACCACGGT
3263788 TCACACCCTTGTGAAGTATTATCCACTCTAGCCCTTCTGGCATCATAGTTTTGTCCCATAAACTC
66 TCACACCCTTGTGAAGTATTATCCACTCTAGCCCTTCTGGCATCATAGTTTTGTCCCATAAACTC
*
3263853 AACCTTCAGGCTTGCACTGTTTTAGGACTCGAGCATGCACTCATCTGGCATATCTTAGATTAGAC
131 AACCTCCAGGCTTGCACTGTTTTAGGACTCGAGCATGCACTCATCTGGCATATCTTAGATTAGAC
*
3263918 TACTTGTCACGGTTCACA-CCTTGTGAAGTATTATCCATTTTGGCCCTTCTGGGCTTATAGTTTT
196 TACTTGTCACGGTTCACACCCTTGTGAAGTATTATCCACTTTGGCCCTTCTGGGCTTATAGTTTT
3263982 GTCCCATAAATGGTGCATCACAAGGAAGATGAAGACTCACTGTCCTCAGTGGCACATCGCTTGTA
261 GTCCCATAAATGGTGCATCACAAGGAAGATGAAGACTCACTGTCCTCAGTGGCACATCGCTTGTA
* * * *
3264047 CCCTCAGAGGTGGTTTTGATGCACCTCACAATGGAATGTGCGAATGCTTATATCTCAAAAACAAC
326 CCCTCAGAGCTGGTTTCGATGCACCTCACAAGGGAATGTGTGAATGCTTATATCTCAAAAACAAC
* *
3264112 TCTAGTACATAGTCGATGTGGGATTCATGACTTTTCTTTAGGACCGTGACATTCTTTCCCACTCC
391 TCTAGTACACAGTCGATGTGGGATTCATGACTTTTCTTTAGGATCGTGACATTCTTTCCCACTCC
*
3264177 AACGGAGACCCATCGTCTTTAGTTACCCATCGCTTGTACCCTTAGAGTTGGTTTTGATATCACTT
456 AACGGAGACCCATCGTCTTTAGTTGCCCATCGCTTGTACCCTTAGAGTTGGTTTTGATATCACTT
3264242 ATCATGGCTTGAAACACGAACTCTAGACTTGCGTAGCTCTAAGACCCAGATATGGGTTCATCCGA
521 ATCATGGCTTGAAACACGAACTCTAGACTTGCGTAGCTCTAAGACCCAGATATGGGTTCATCCGA
* *
3264307 CATTTTAGATCAATCTACCTACTAGGGTTAACACTTTTGTGAGGTATTATCCACTTTAACCTTTT
586 CATTTTAGATCAATCTACCTACTAGGGTTAACACTTTTGTGAGGTATTATCCACTTTAACCTCTC
*
3264372 TGGCTCTACGATTTTATCCCACAAAAGGTACCTTACAAGAAAG
651 TGGCTCTACGATTTTGTCCCACAAAAGGTACCTTACAAGAAAG
3264415 AGACTACTTGCCACGGTTCAAGCATGCACTTATCTTGCATCTTAGATTAGACTACTTACCACGGT
1 AGACTACTTGCCACGGTTCAAGCATGCACTTATCTTGCATCTTAGATTAGACTACTTACCACGGT
*
3264480 TCACACCCTTGTGAAGTATTATCCACTCTAGCCCTTCTGGCATCATAATTTTGTCCCATAAACTC
66 TCACACCCTTGTGAAGTATTATCCACTCTAGCCCTTCTGGCATCATAGTTTTGTCCCATAAACTC
3264545 AACCTCCAGGCTTGCACTGTTTTAGGACTCGAGCATGCACTCATCTGGCATATCTTAGATTAGAC
131 AACCTCCAGGCTTGCACTGTTTTAGGACTCGAGCATGCACTCATCTGGCATATCTTAGATTAGAC
* *
3264610 TACTTGTCACGGTTCACACCCTTGTGAAGTATTATTCACTTTAGCCCTTCTGGGCTTATAGTTTT
196 TACTTGTCACGGTTCACACCCTTGTGAAGTATTATCCACTTTGGCCCTTCTGGGCTTATAGTTTT
* * * *
3264675 GTCCCATAAATAGTGCCTCACAAGGAAGATGAAGACTCACTGTCTTCAGTGACACATCGCTTGTA
261 GTCCCATAAATGGTGCATCACAAGGAAGATGAAGACTCACTGTCCTCAGTGGCACATCGCTTGTA
* * * * *
3264740 CCCTTAGAGATGGTTTCGATGTACCTCACAAGGGAATGCGTGAATGCTTATATCTCAAAAACAAT
326 CCCTCAGAGCTGGTTTCGATGCACCTCACAAGGGAATGTGTGAATGCTTATATCTCAAAAACAAC
*
3264805 TCTAGTACACAGTCGATGTGGGAGTCATGACTTTTCTTTAGGATCGTGACATTCTTTCCCACTCC
391 TCTAGTACACAGTCGATGTGGGATTCATGACTTTTCTTTAGGATCGTGACATTCTTTCCCACTCC
*
3264870 AACGGAGATCCATCGTCTTTAGTTGCCCATCGCTTGTACCCTTAGAGTTGGTTTTGATATCACTT
456 AACGGAGACCCATCGTCTTTAGTTGCCCATCGCTTGTACCCTTAGAGTTGGTTTTGATATCACTT
3264935 ATCATGGCTTGAAACACGAACTCTAGACTTGCGTAGCTCTAAGACCCAGATATGGGTTCATCCGA
521 ATCATGGCTTGAAACACGAACTCTAGACTTGCGTAGCTCTAAGACCCAGATATGGGTTCATCCGA
3265000 CATTTTAGATCAATCTACCTACTAGGGTTAACACTTTTGTGAGGTATTATCCACTTTAACCTCTC
586 CATTTTAGATCAATCTACCTACTAGGGTTAACACTTTTGTGAGGTATTATCCACTTTAACCTCTC
*
3265065 TGGCTCTACGATTTTGTCCCACAAAAGATACCTTACAAGAAAG
651 TGGCTCTACGATTTTGTCCCACAAAAGGTACCTTACAAGAAAG
* * *
3265108 AGACTACTTGCCATGGTTCAAGCATGCACTTATCTTGCATCGTAGATTAGACTACTTATCACGGT
1 AGACTACTTGCCACGGTTCAAGCATGCACTTATCTTGCATCTTAGATTAGACTACTTACCACGGT
3265173 TCACACCCTTGTGAAGTATTATCCACTCTAGCCCTTCTGGCATCATAGTTTTGTCCCATAAACTC
66 TCACACCCTTGTGAAGTATTATCCACTCTAGCCCTTCTGGCATCATAGTTTTGTCCCATAAACTC
3265238 AACCTTCCAGGCTTGCACTGTTTTAGGACTCGAGCATGCACTCATCTGGCATATCTTAGATTAGA
131 AACC-TCCAGGCTTGCACTGTTTTAGGACTCGAGCATGCACTCATCTGGCATATCTTAGATTAGA
3265303 CTACTTGTCACGGTTCACACCCTTGTGAAGTATTATCCACTTTGGCCCTTCTGGGCTTATAGTTT
195 CTACTTGTCACGGTTCACACCCTTGTGAAGTATTATCCACTTTGGCCCTTCTGGGCTTATAGTTT
3265368 TGTCCCATAAATGGTGCATCACAAGGAAGATGAAGACTCACTGTCCTCAGTGGCACATCGCTTGT
260 TGTCCCATAAATGGTGCATCACAAGGAAGATGAAGACTCACTGTCCTCAGTGGCACATCGCTTGT
* * * *
3265433 ACCCTCAGAGGTGGTTTTGATGCACCTCACAATGGAATGTGTGAATGGTTATATCTCAAAAACAA
325 ACCCTCAGAGCTGGTTTCGATGCACCTCACAAGGGAATGTGTGAATGCTTATATCTCAAAAACAA
* * * *
3265498 CTCTAGTACATAGTCGATGTGGGATTCATGACTTTTCTTTAGGACCGTGACATTCTTTTCGACTC
390 CTCTAGTACACAGTCGATGTGGGATTCATGACTTTTCTTTAGGATCGTGACATTCTTTCCCACTC
*
3265563 CAACGGAGATCCATCGTCTTTAGTTGCCCATCGCTTGTACCCTTAGAGTTGGTTTTGATATCACT
455 CAACGGAGACCCATCGTCTTTAGTTGCCCATCGCTTGTACCCTTAGAGTTGGTTTTGATATCACT
*
3265628 TATCATGGCCTGAAACACGAACTCTAGACTTGCGTAGCTCTAAGACCCAGATATGGGTTCATCCG
520 TATCATGGCTTGAAACACGAACTCTAGACTTGCGTAGCTCTAAGACCCAGATATGGGTTCATCCG
3265693 ACATTTTAGATCAATCTACCTACTAGGGTTAACACTTTTGTGAGGTATTATCCACTTTAACCTCT
585 ACATTTTAGATCAATCTACCTACTAGGGTTAACACTTTTGTGAGGTATTATCCACTTTAACCTCT
* * *
3265758 CTGGCTCTACGATTTTATCCCACAAAACGTACCGTACAAGAAAG
650 CTGGCTCTACGATTTTGTCCCACAAAAGGTACCTTACAAGAAAG
3265802 AGACTACTTGCCACGGTTCAAGCATGCACTTATCTTGCATCTTAGATTAGACTACTTACCACGGT
1 AGACTACTTGCCACGGTTCAAGCATGCACTTATCTTGCATCTTAGATTAGACTACTTACCACGGT
*
3265867 TCACACCCTTGTGAAGTATTATCCACTCTAGCCTTTCTGGCATCATAGTTTTGTCCCATAAACTC
66 TCACACCCTTGTGAAGTATTATCCACTCTAGCCCTTCTGGCATCATAGTTTTGTCCCATAAACTC
*
3265932 AACCTCCAGGCTTGCACTGTTTTAGGACTCAAGCATGCACTCATCTGGCATATCTTAGATTAGAC
131 AACCTCCAGGCTTGCACTGTTTTAGGACTCGAGCATGCACTCATCTGGCATATCTTAGATTAGAC
*
3265997 TACTTGTCACGGTTCACACCTTTGTGAAGTATTATCCACTTTGGCCCTTCTGGGCTTATAGTTTT
196 TACTTGTCACGGTTCACACCCTTGTGAAGTATTATCCACTTTGGCCCTTCTGGGCTTATAGTTTT
*
3266062 GTCCCATAAATGGTGCATCACAAGGAAGACGAAGACTCACTGTCCTCAGTGGCACATCGCTTGTA
261 GTCCCATAAATGGTGCATCACAAGGAAGATGAAGACTCACTGTCCTCAGTGGCACATCGCTTGTA
*
3266127 CCCTCAGAGCTGGTTCCGATGCACCTCACAAGGGAATGTGTGAATGCTTATATCTCAAAAACAAC
326 CCCTCAGAGCTGGTTTCGATGCACCTCACAAGGGAATGTGTGAATGCTTATATCTCAAAAACAAC
*
3266192 TCTAGTACACAGTTGATGTGGGATTCATGACTTTTCTTTAGGATCGTGACATTCTTTCCCACTCC
391 TCTAGTACACAGTCGATGTGGGATTCATGACTTTTCTTTAGGATCGTGACATTCTTTCCCACTCC
3266257 AACGGAGACCCATCGTCTTTAGTTGCCCATCGCTTGTACCCTTAGAGTTGGTTTTGATATCACTT
456 AACGGAGACCCATCGTCTTTAGTTGCCCATCGCTTGTACCCTTAGAGTTGGTTTTGATATCACTT
3266322 ATCATGGCTTGAAACACGAACTCTAGACTTGCGTAGCTCTAAGACCCAGATATGGGTTCATCCGA
521 ATCATGGCTTGAAACACGAACTCTAGACTTGCGTAGCTCTAAGACCCAGATATGGGTTCATCCGA
*
3266387 CATTTTAGATCAATCTACCTACTAGGATTAACACTTTTGTGAGGTATTATCCACTTTAACCTCTC
586 CATTTTAGATCAATCTACCTACTAGGGTTAACACTTTTGTGAGGTATTATCCACTTTAACCTCTC
*
3266452 TGGCTCTACGATTTTGTCCCACAAAAGATACCTTACAAGAAAG
651 TGGCTCTACGATTTTGTCCCACAAAAGGTACCTTACAAGAAAG
3266495 AGA
1 AGA
3266498 ATGTGTTAAC
Statistics
Matches: 2662, Mismatches: 109, Indels: 6
0.96 0.04 0.00
Matches are distributed among these distances:
691 170 0.06
692 671 0.25
693 1156 0.43
694 665 0.25
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (693 bp):
AGACTACTTGCCACGGTTCAAGCATGCACTTATCTTGCATCTTAGATTAGACTACTTACCACGGT
TCACACCCTTGTGAAGTATTATCCACTCTAGCCCTTCTGGCATCATAGTTTTGTCCCATAAACTC
AACCTCCAGGCTTGCACTGTTTTAGGACTCGAGCATGCACTCATCTGGCATATCTTAGATTAGAC
TACTTGTCACGGTTCACACCCTTGTGAAGTATTATCCACTTTGGCCCTTCTGGGCTTATAGTTTT
GTCCCATAAATGGTGCATCACAAGGAAGATGAAGACTCACTGTCCTCAGTGGCACATCGCTTGTA
CCCTCAGAGCTGGTTTCGATGCACCTCACAAGGGAATGTGTGAATGCTTATATCTCAAAAACAAC
TCTAGTACACAGTCGATGTGGGATTCATGACTTTTCTTTAGGATCGTGACATTCTTTCCCACTCC
AACGGAGACCCATCGTCTTTAGTTGCCCATCGCTTGTACCCTTAGAGTTGGTTTTGATATCACTT
ATCATGGCTTGAAACACGAACTCTAGACTTGCGTAGCTCTAAGACCCAGATATGGGTTCATCCGA
CATTTTAGATCAATCTACCTACTAGGGTTAACACTTTTGTGAGGTATTATCCACTTTAACCTCTC
TGGCTCTACGATTTTGTCCCACAAAAGGTACCTTACAAGAAAG
Found at i:3267561 original size:20 final size:21
Alignment explanation
Indices: 3267538--3267580 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3267528 ACAATCAATC
*
3267538 AATAAATT-AAAATATAATTA
1 AATAAATTCAAAATAAAATTA
*
3267558 AATAAATTCAATATAAAATTA
1 AATAAATTCAAAATAAAATTA
3267579 AA
1 AA
3267581 ATCAACTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAAATTCAAAATAAAATTA
Found at i:3268948 original size:59 final size:59
Alignment explanation
Indices: 3268801--3268969 Score: 202
Period size: 59 Copynumber: 2.9 Consensus size: 59
3268791 AGATTTTTGG
* * *
3268801 ACTTTCAATGTAGTTTAATA-GTGGTGAGTTGATAGTCTAGGCTTCAAATATATTTTTAA
1 ACTTTCAATGTAGTTTAGTAGGT-GTGAGTTGGTAGTCTGGGCTTCAAATATATTTTTAA
* * * *
3268860 ACTTTTAACT-TAGTTTCGTAGAG-GCGAGTTGGTAGTTTGGGCTTCAAATATATTTTT-A
1 ACTTTCAA-TGTAGTTTAGTAG-GTGTGAGTTGGTAGTCTGGGCTTCAAATATATTTTTAA
*
3268918 ACTTTCATTGTAGTTTAGTAGGTGTTGAGTTGGTAGTCTGGGCTTCAAATAT
1 ACTTTCAATGTAGTTTAGTAGGTG-TGAGTTGGTAGTCTGGGCTTCAAATAT
3268970 TGAAAAAGCA
Statistics
Matches: 92, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
57 2 0.02
58 18 0.20
59 70 0.76
60 1 0.01
61 1 0.01
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.43
Consensus pattern (59 bp):
ACTTTCAATGTAGTTTAGTAGGTGTGAGTTGGTAGTCTGGGCTTCAAATATATTTTTAA
Found at i:3271797 original size:15 final size:16
Alignment explanation
Indices: 3271761--3271790 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3271751 AGATAGGAGG
3271761 AAGAAAGTGTAGAAGC
1 AAGAAAGTGTAGAAGC
3271777 AAGAAAGTG-AGAAG
1 AAGAAAGTGTAGAAG
3271791 AATGAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.03, G:0.33, T:0.10
Consensus pattern (16 bp):
AAGAAAGTGTAGAAGC
Found at i:3277507 original size:5 final size:5
Alignment explanation
Indices: 3277497--3277611 Score: 70
Period size: 6 Copynumber: 20.8 Consensus size: 5
3277487 TATATTTTTG
*
3277497 TTATA TTATA TTATA GTATAGTA TTATTA TCATA TTATA TTATCA TTATCA
1 TTATA TTATA TTATA -T-TA-TA TTA-TA TTATA TTATA TTAT-A TTAT-A
* ** *
3277548 -TATTA TTATTA TTATTA GTATA TTATA TGGTA TTATA TCATA TTACTA
1 TTA-TA TTA-TA TTA-TA TTATA TTATA TTATA TTATA TTATA TTA-TA
3277596 TTATTA TTATTA TTAT
1 TTA-TA TTA-TA TTAT
3277612 TACTACTACT
Statistics
Matches: 91, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
5 42 0.46
6 44 0.48
7 3 0.03
8 2 0.02
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (5 bp):
TTATA
Found at i:3277526 original size:3 final size:3
Alignment explanation
Indices: 3277518--3277651 Score: 79
Period size: 3 Copynumber: 46.7 Consensus size: 3
3277508 TATAGTATAG
* * *
3277518 TAT TAT TAT CA- TAT TA- TAT TAT CAT TAT CA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
3277563 TAG TA- TAT TA- TAT GGTAT TA- TAT CA- TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT --TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
3277606 TAT TAT TAC TAC TAC TAC TAC TAT TAT TAT T-T T-T GTAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
3277650 TA
1 TA
3277652 CTTTTTTTTT
Statistics
Matches: 107, Mismatches: 13, Indels: 22
0.75 0.09 0.15
Matches are distributed among these distances:
2 14 0.13
3 89 0.83
4 1 0.01
5 3 0.03
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:3277571 original size:14 final size:13
Alignment explanation
Indices: 3277503--3277651 Score: 74
Period size: 14 Copynumber: 11.0 Consensus size: 13
3277493 TTTGTTATAT
*
3277503 TATATTA-TAGTA
1 TATATTATTATTA
3277515 TAGTATTATTATCATA
1 TA-TATTATTAT--TA
*
3277531 TTATATTATCATTA
1 -TATATTATTATTA
3277545 TCATATTATTATTA
1 T-ATATTATTATTA
3277559 T-TATTAGTATATTA
1 TATATTA-T-TATTA
**
3277573 TATGGTATTA-TA
1 TATATTATTATTA
*
3277585 TCATATTACTATTA
1 T-ATATTATTATTA
3277599 T-TATTATTATTA
1 TATATTATTATTA
* * *
3277611 T-TACTACTACTA
1 TATATTATTATTA
*
3277623 CTACTATTATTATTTT
1 -TA-TATTATTA-TTA
*
3277639 TGTATTATTATTA
1 TATATTATTATTA
3277652 CTTTTTTTTT
Statistics
Matches: 104, Mismatches: 18, Indels: 29
0.69 0.12 0.19
Matches are distributed among these distances:
12 29 0.28
13 18 0.17
14 34 0.33
15 10 0.10
16 11 0.11
17 2 0.02
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.55
Consensus pattern (13 bp):
TATATTATTATTA
Found at i:3277631 original size:49 final size:49
Alignment explanation
Indices: 3277529--3277632 Score: 115
Period size: 46 Copynumber: 2.1 Consensus size: 49
3277519 ATTATTATCA
* * **
3277529 TATTATATTATCATTATCATATTATTATTATTATTAGTATATTATATGG
1 TATTATATCATCATTATCATATTATTATTATTATTAGTATACTATATAC
*
3277578 TATTATATCAT-ATTA-C-TATTATTATTATTATTATTACTACTACTACTAC
1 TATTATATCATCATTATCATATTATTATTATTATTAGTA-TACTA-TA-TAC
3277627 TATTAT
1 TATTAT
3277633 TATTTTTGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
46 19 0.40
47 5 0.11
48 6 0.13
49 17 0.36
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.54
Consensus pattern (49 bp):
TATTATATCATCATTATCATATTATTATTATTATTAGTATACTATATAC
Found at i:3278055 original size:21 final size:20
Alignment explanation
Indices: 3278027--3278074 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
3278017 ATACTGGGAA
*
3278027 TTCTGGATATAGATTTGGGT
1 TTCTGGATATAGATTTAGGT
* *
3278047 TTCTAGGATCTAGTTTTAGGT
1 TTCT-GGATATAGATTTAGGT
*
3278068 TTTTGGA
1 TTCTGGA
3278075 GCTGGGATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.19, C:0.06, G:0.27, T:0.48
Consensus pattern (20 bp):
TTCTGGATATAGATTTAGGT
Found at i:3278286 original size:12 final size:12
Alignment explanation
Indices: 3278264--3278288 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3278254 CCAATTTTCA
3278264 GTTAAATTTTTG
1 GTTAAATTTTTG
3278276 GTTAAATTTTTG
1 GTTAAATTTTTG
3278288 G
1 G
3278289 AAGAAATTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (12 bp):
GTTAAATTTTTG
Found at i:3278547 original size:24 final size:22
Alignment explanation
Indices: 3278483--3278550 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 22
3278473 TAGGTTTTAC
3278483 TTTT-CTCATTTTATTTTTA-T
1 TTTTACTCATTTTATTTTTATT
*
3278503 TTTT--TGATTTTA-TTTTATT
1 TTTTACTCATTTTATTTTTATT
3278522 TTTTAACTCATTTTATTTTTAGTT
1 TTTT-ACTCATTTTATTTTTA-TT
3278546 TTTTA
1 TTTTA
3278551 TTATTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 5 0.12
19 12 0.30
20 4 0.10
22 7 0.17
23 6 0.15
24 6 0.15
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (22 bp):
TTTTACTCATTTTATTTTTATT
Found at i:3295375 original size:12 final size:13
Alignment explanation
Indices: 3295360--3295390 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
3295350 TAGAAAATGA
3295360 TTTAATAAAA-AT
1 TTTAATAAAATAT
3295372 TTTAATAAAATAT
1 TTTAATAAAATAT
3295385 TTTAAT
1 TTTAAT
3295391 CGATAGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAATAAAATAT
Found at i:3296911 original size:19 final size:19
Alignment explanation
Indices: 3296887--3296924 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3296877 CATAGTCCAA
3296887 CTTATAATTTCAATCTTTT
1 CTTATAATTTCAATCTTTT
*
3296906 CTTATAATTTCGATCTTTT
1 CTTATAATTTCAATCTTTT
3296925 TAATCAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.03, T:0.58
Consensus pattern (19 bp):
CTTATAATTTCAATCTTTT
Found at i:3297253 original size:26 final size:28
Alignment explanation
Indices: 3297224--3297280 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
3297214 TTTTTATTCC
*
3297224 TTTTTTTAC-TTTGAATT-TTTAAAAAA
1 TTTTTTCACATTTGAATTGTTTAAAAAA
* *
3297250 -TTTTTCACATTTTAATTGTTTAAAATA
1 TTTTTTCACATTTGAATTGTTTAAAAAA
3297277 TTTT
1 TTTT
3297281 AGATTTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
25 7 0.28
26 7 0.28
27 8 0.32
28 3 0.12
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (28 bp):
TTTTTTCACATTTGAATTGTTTAAAAAA
Found at i:3302663 original size:26 final size:25
Alignment explanation
Indices: 3302602--3302677 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 25
3302592 ACTTTGAATT
*
3302602 TTTTAAAAAAATTTT-CATATTTAAA
1 TTTTAAAAAAATTTTAGAT-TTTAAA
**
3302627 TATTTTTAAAAATTTTAGATTTTGAAA
1 T-TTTAAAAAAATTTTAGATTTT-AAA
3302654 TTTTAAAAAAATTTTCTAGATTTT
1 TTTTAAAAAAA-TTT-TAGATTTT
3302678 TAAAAAGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
25 1 0.02
26 23 0.56
27 9 0.22
28 8 0.20
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (25 bp):
TTTTAAAAAAATTTTAGATTTTAAA
Found at i:3304898 original size:20 final size:21
Alignment explanation
Indices: 3304875--3304914 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3304865 ACACACTTTC
*
3304875 TCTTGATT-TTTTTAATTGAT
1 TCTTAATTCTTTTTAATTGAT
3304895 TCTTAATTCTTTTTAATTGA
1 TCTTAATTCTTTTTAATTGA
3304915 ACTTAGTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.62
Consensus pattern (21 bp):
TCTTAATTCTTTTTAATTGAT
Found at i:3309512 original size:12 final size:13
Alignment explanation
Indices: 3309497--3309527 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
3309487 TAGAAAATGA
3309497 TTTAATAAAA-AT
1 TTTAATAAAATAT
3309509 TTTAATAAAATAT
1 TTTAATAAAATAT
3309522 TTTAAT
1 TTTAAT
3309528 CGATAGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAATAAAATAT
Found at i:3312831 original size:36 final size:33
Alignment explanation
Indices: 3312743--3312832 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 33
3312733 TTCAATTCAA
* * *
3312743 TTTTTTCTTTTGTTTAAAAATATT-TTATATTTC
1 TTTTTT-TTTTGTTTATAATTTTTGTTATATTTC
*
3312776 TTTTTTTTTTGTTTGTAATTTTTGTTATCATTTC
1 TTTTTTTTTTGTTTATAATTTTTGTTAT-ATTTC
3312810 TCTTTTTTTTAT-TCTTATAATTT
1 T-TTTTTTTT-TGT-TTATAATTT
3312833 GTAATTTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
32 13 0.28
33 10 0.21
34 6 0.13
35 9 0.19
36 9 0.19
ACGTcount: A:0.18, C:0.07, G:0.04, T:0.71
Consensus pattern (33 bp):
TTTTTTTTTTGTTTATAATTTTTGTTATATTTC
Found at i:3314923 original size:3 final size:3
Alignment explanation
Indices: 3314915--3315025 Score: 92
Period size: 3 Copynumber: 38.7 Consensus size: 3
3314905 TATAGTATAG
* * *
3314915 TAT TAT TAT CA- TAT TA- TAT TAT CAT TAT CA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
3314960 TAG TA- TAT TA- TAT GGTAT TA- TAT CA- TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT --TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
3315003 TAT TGT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
3315026 CTACTACTAC
Statistics
Matches: 86, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
2 11 0.13
3 72 0.84
5 3 0.03
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:3314981 original size:49 final size:44
Alignment explanation
Indices: 3314926--3315014 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 44
3314916 ATTATTATCA
*
3314926 TATTATATTATCATTATCATATTATTATTATTATTAGTATATTATATGG
1 TATTATATCAT-ATTA-C-TATTATTATTATTATT-GT-TATTATATGG
3314975 TATTATATCATATTACTATTATTATTATTATTGTTATTAT
1 TATTATATCATATTACTATTATTATTATTATTGTTATTAT
3315015 TATTATTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
44 6 0.15
45 2 0.05
46 16 0.41
47 1 0.03
48 4 0.10
49 10 0.26
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (44 bp):
TATTATATCATATTACTATTATTATTATTATTGTTATTATATGG
Found at i:3315030 original size:3 final size:3
Alignment explanation
Indices: 3315024--3315076 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
3315014 TTATTATTAT
* *
3315024 TAC TAC TAC TAC TAC TAT TAC TAC TAC TAC TAC TAT TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
3315072 TAC TA
1 TAC TA
3315077 TTATTATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (3 bp):
TAC
Found at i:3315042 original size:18 final size:18
Alignment explanation
Indices: 3315021--3315079 Score: 118
Period size: 18 Copynumber: 3.3 Consensus size: 18
3315011 TTATTATTAT
3315021 TATTACTACTACTACTAC
1 TATTACTACTACTACTAC
3315039 TATTACTACTACTACTAC
1 TATTACTACTACTACTAC
3315057 TATTACTACTACTACTAC
1 TATTACTACTACTACTAC
3315075 TATTA
1 TATTA
3315080 TTATTTTTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.34, C:0.25, G:0.00, T:0.41
Consensus pattern (18 bp):
TATTACTACTACTACTAC
Found at i:3315504 original size:21 final size:20
Alignment explanation
Indices: 3315476--3315523 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
3315466 ATACTGGGAA
*
3315476 TTCTGGATATAGATTTGGGT
1 TTCTGGATATAGATTTAGGT
* *
3315496 TTCTAGGATCTAGTTTTAGGT
1 TTCT-GGATATAGATTTAGGT
*
3315517 TTTTGGA
1 TTCTGGA
3315524 GCTGGGATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.19, C:0.06, G:0.27, T:0.48
Consensus pattern (20 bp):
TTCTGGATATAGATTTAGGT
Found at i:3315736 original size:12 final size:12
Alignment explanation
Indices: 3315714--3315738 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3315704 CCAATTTTCA
3315714 GTTAAATTTTTG
1 GTTAAATTTTTG
3315726 GTTAAATTTTTG
1 GTTAAATTTTTG
3315738 G
1 G
3315739 AAGAAATTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (12 bp):
GTTAAATTTTTG
Found at i:3315997 original size:24 final size:22
Alignment explanation
Indices: 3315933--3316000 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 22
3315923 TAGGTTTTCC
3315933 TTTT-CTCATTTTATTTTTA-T
1 TTTTACTCATTTTATTTTTATT
*
3315953 TTTT--TGATTTTA-TTTTATT
1 TTTTACTCATTTTATTTTTATT
3315972 TTTTAACTCATTTTATTTTTAGTT
1 TTTT-ACTCATTTTATTTTTA-TT
3315996 TTTTA
1 TTTTA
3316001 TTATTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 5 0.12
19 12 0.30
20 4 0.10
22 7 0.17
23 6 0.15
24 6 0.15
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (22 bp):
TTTTACTCATTTTATTTTTATT
Found at i:3319763 original size:24 final size:24
Alignment explanation
Indices: 3319716--3319763 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3319706 AATAGAAAAA
*
3319716 CTCTTAATTTTTTTTACTTTTTCT
1 CTCTTAATTTTTTTTACTTATTCT
*
3319740 CTCTTTATTTTTTTTA-TTGATTCT
1 CTCTTAATTTTTTTTACTT-ATTCT
3319764 TCATTGTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.12, C:0.15, G:0.02, T:0.71
Consensus pattern (24 bp):
CTCTTAATTTTTTTTACTTATTCT
Found at i:3329368 original size:81 final size:78
Alignment explanation
Indices: 3329260--3329407 Score: 215
Period size: 81 Copynumber: 1.9 Consensus size: 78
3329250 ATTATTAAAT
* * * *
3329260 AATCAATTAATCAACCAATCAATAAATTAAAATATAATTATACAAATTCAACATACAAACTTAAA
1 AATCAAATAAACAACCAATCAACAAATTAAAATATAATTAAACAAATTCAACATA-AAA-TTAAA
3329325 TATAATGATACTTGAA
64 -ATAATGATACTTGAA
* *
3329341 AATCAAATAAACAATCAATCAACAAATTAAAATATAATTAAATAAATTCAACATAAAATTAAAAT
1 AATCAAATAAACAACCAATCAACAAATTAAAATATAATTAAACAAATTCAACATAAAATTAAAAT
3329406 AA
66 AA
3329408 ACTCATACGT
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
78 4 0.07
79 5 0.08
80 3 0.05
81 49 0.80
ACGTcount: A:0.59, C:0.12, G:0.01, T:0.28
Consensus pattern (78 bp):
AATCAAATAAACAACCAATCAACAAATTAAAATATAATTAAACAAATTCAACATAAAATTAAAAT
AATGATACTTGAA
Done.