Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 174 of 213
Found at i:52381198 original size:26 final size:24
Alignment explanation
Indices: 52381145--52381198 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
52381135 AGTATCAAGT
*
52381145 TATTTTAATTATGATTTTTTAAAA
1 TATTTTAATTATGATTTTGTAAAA
*
52381169 -ATTTTAATTATTATGTTTGTAAACA
1 TATTTTAATTATGAT-TTTGTAAA-A
52381194 TATTT
1 TATTT
52381199 ATTAACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 1 0.04
26 4 0.16
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (24 bp):
TATTTTAATTATGATTTTGTAAAA
Found at i:52393731 original size:20 final size:20
Alignment explanation
Indices: 52393687--52393724 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52393677 GCTATGTGGC
* *
52393687 TAGGCTATGTGGAATACCCT
1 TAGGCTGTGTAGAATACCCT
52393707 TAGGCTGTGTAGAATACC
1 TAGGCTGTGTAGAATACC
52393725 TTCAGGCCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (20 bp):
TAGGCTGTGTAGAATACCCT
Found at i:52393736 original size:20 final size:20
Alignment explanation
Indices: 52393698--52393736 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
52393688 AGGCTATGTG
*
52393698 GAATACCCTTAGGCTGTGTA
1 GAATACCCTTAGGCCGTGTA
52393718 GAATA-CCTTCAGGCCGTGT
1 GAATACCCTT-AGGCCGTGT
52393737 GACATTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (20 bp):
GAATACCCTTAGGCCGTGTA
Found at i:52394967 original size:21 final size:19
Alignment explanation
Indices: 52394943--52394985 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
52394933 GAAATTAAAG
52394943 TAAAACAAAAGAAAAAGGAAT
1 TAAAACAAAA-AAAAA-GAAT
* *
52394964 TAAAATAAAACAAAAGAAT
1 TAAAACAAAAAAAAAGAAT
52394983 TAA
1 TAA
52394986 TAAATGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 4 0.20
21 9 0.45
ACGTcount: A:0.72, C:0.05, G:0.09, T:0.14
Consensus pattern (19 bp):
TAAAACAAAAAAAAAGAAT
Found at i:52396554 original size:23 final size:24
Alignment explanation
Indices: 52396506--52396552 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
52396496 TGAGTATGTT
*
52396506 TGATTGTATTTTGAATAGGTTAAA
1 TGATTGTATTTTGAATAGCTTAAA
*
52396530 TGATTGGT-TTTTGAATTGCTTAA
1 TGATT-GTATTTTGAATAGCTTAA
52396553 TGCCCAAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (24 bp):
TGATTGTATTTTGAATAGCTTAAA
Found at i:52397109 original size:29 final size:29
Alignment explanation
Indices: 52397064--52397122 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
52397054 TTTGAAAAGG
* *
52397064 TAAAAGTCCCTAGGTTTGCCGTCTACTAT
1 TAAAAGTCCCTAAGTTTGCCGTCCACTAT
*
52397093 TAAAAGTCCCTAAGTTTGTCGTCCACTAT
1 TAAAAGTCCCTAAGTTTGCCGTCCACTAT
52397122 T
1 T
52397123 TTCTTCTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (29 bp):
TAAAAGTCCCTAAGTTTGCCGTCCACTAT
Found at i:52417477 original size:63 final size:63
Alignment explanation
Indices: 52417396--52417516 Score: 224
Period size: 63 Copynumber: 1.9 Consensus size: 63
52417386 TGTTAGGCTA
*
52417396 TGTAACTCACTGACTCTCATACAAAGGAACCTTCAGATGACACATGGCTGTGTCGCCAAACTG
1 TGTAACTCACTGACTCTCATACAAAGGAACCCTCAGATGACACATGGCTGTGTCGCCAAACTG
*
52417459 TGTAACTCACTGACTCTCATACAAAGGAACCCTCAGATGACACATGGTTGTGTCGCCA
1 TGTAACTCACTGACTCTCATACAAAGGAACCCTCAGATGACACATGGCTGTGTCGCCA
52417517 GGCCATGTGT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (63 bp):
TGTAACTCACTGACTCTCATACAAAGGAACCCTCAGATGACACATGGCTGTGTCGCCAAACTG
Found at i:52420558 original size:16 final size:16
Alignment explanation
Indices: 52420537--52420568 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52420527 GTTTTATTGC
*
52420537 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
52420553 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
52420569 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:52420854 original size:51 final size:52
Alignment explanation
Indices: 52420790--52420933 Score: 168
Period size: 51 Copynumber: 2.8 Consensus size: 52
52420780 GATACCGGTT
* *
52420790 CACAGAGTAGCCTGCACATAGTACTACACATGTGACCATCA-CTATCTGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCAGCTATCCGATA
* * * * *
52420841 CACGTAGTAGCCTGCATATAGTACTACACACGTGATCGA--AGCTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGA-CCATCAGCTATCCGATA
* *
52420892 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACC-ATCA
52420934 TTCTGGTAGC
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
50 2 0.03
51 70 0.93
52 2 0.03
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (52 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCAGCTATCCGATA
Found at i:52421223 original size:17 final size:16
Alignment explanation
Indices: 52421191--52421221 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52421181 CAATCTAGTC
52421191 GAAAAATCACATTTTG
1 GAAAAATCACATTTTG
*
52421207 GAAAAATTACATTTT
1 GAAAAATCACATTTT
52421222 TGCCCCTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (16 bp):
GAAAAATCACATTTTG
Found at i:52424801 original size:15 final size:16
Alignment explanation
Indices: 52424773--52424802 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52424763 GTTGGACTAA
52424773 ATTGAATGTGAGTTAT
1 ATTGAATGTGAGTTAT
52424789 ATTGAAT-TGAGTTA
1 ATTGAATGTGAGTTA
52424803 ATTCATTCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.43
Consensus pattern (16 bp):
ATTGAATGTGAGTTAT
Found at i:52425567 original size:16 final size:16
Alignment explanation
Indices: 52425528--52425568 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
52425518 TCTTTTTATG
*
52425528 ATTAAAACTAATTGTC
1 ATTAAAATTAATTGTC
*
52425544 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTC
52425560 ATTAAAATT
1 ATTAAAATT
52425569 CTATCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (16 bp):
ATTAAAATTAATTGTC
Found at i:52427076 original size:25 final size:26
Alignment explanation
Indices: 52427044--52427107 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 26
52427034 TTTAAACTAA
*
52427044 CCAG-AATACAGATTGAACATACAAT
1 CCAGAAATACAGATTAAACATACAAT
*
52427069 CCA-AAATACAAATTAAACATACAAT
1 CCAGAAATACAGATTAAACATACAAT
52427094 CCAGAAA-ACAGATT
1 CCAGAAATACAGATT
52427108 CCAAAATTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 31 0.91
26 3 0.09
ACGTcount: A:0.53, C:0.20, G:0.08, T:0.19
Consensus pattern (26 bp):
CCAGAAATACAGATTAAACATACAAT
Found at i:52428920 original size:9 final size:9
Alignment explanation
Indices: 52428906--52428935 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
52428896 CCATCGATTT
52428906 TATATTGTC
1 TATATTGTC
52428915 TATATTGTC
1 TATATTGTC
52428924 TATATTGTC
1 TATATTGTC
52428933 TAT
1 TAT
52428936 TTACCGCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.57
Consensus pattern (9 bp):
TATATTGTC
Found at i:52429194 original size:45 final size:45
Alignment explanation
Indices: 52429125--52429238 Score: 122
Period size: 45 Copynumber: 2.5 Consensus size: 45
52429115 AAACTTAGTG
* * * * *
52429125 AGACCACAGCTAAAAGTTGTTATGGCATAAGGA-CAACAATGAGTA
1 AGACCATAGCTAAAAGATGCTATGGCATAAGGACCAA-AATCAATA
* * *
52429170 AGACCATAGCAAAAAGATGCTATGGCATCATGACCAAAATCAATA
1 AGACCATAGCTAAAAGATGCTATGGCATAAGGACCAAAATCAATA
* *
52429215 AGACCATGGCTAAAAGACGCTATG
1 AGACCATAGCTAAAAGATGCTATG
52429239 ACATCATGGT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
45 54 0.95
46 3 0.05
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.18
Consensus pattern (45 bp):
AGACCATAGCTAAAAGATGCTATGGCATAAGGACCAAAATCAATA
Found at i:52429509 original size:56 final size:57
Alignment explanation
Indices: 52429400--52429525 Score: 193
Period size: 56 Copynumber: 2.2 Consensus size: 57
52429390 GTTATATTTT
* * *
52429400 GTAAGACCATAACTGAAAGATGTTGTGACAACAAGAGATGATTTGACAGTAAAACGA
1 GTAAGACCATAGCTAAAAGATGTTGTGACAACAAGAGATGATTTGACAATAAAACGA
*
52429457 GTAAGACCATAGCTAAAAGATGTATG-G-CAACAAGAGATGATTTGATAATAAAACGA
1 GTAAGACCATAGCTAAAAGATGT-TGTGACAACAAGAGATGATTTGACAATAAAACGA
52429513 GTAAGACCATAGC
1 GTAAGACCATAGC
52429526 ATCTTTCAGC
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
56 40 0.62
57 22 0.34
58 2 0.03
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (57 bp):
GTAAGACCATAGCTAAAAGATGTTGTGACAACAAGAGATGATTTGACAATAAAACGA
Found at i:52439331 original size:16 final size:16
Alignment explanation
Indices: 52439306--52439336 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52439296 TGATATATGT
*
52439306 TTGTTTGAATGATAAG
1 TTGTTGGAATGATAAG
52439322 TTGTTGGAATGATAA
1 TTGTTGGAATGATAA
52439337 AATTTATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (16 bp):
TTGTTGGAATGATAAG
Found at i:52452802 original size:23 final size:23
Alignment explanation
Indices: 52452778--52452828 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
52452768 GTAAATTAAT
*
52452778 TTTTTGTTA-AAAAAATTATCTA
1 TTTTTATTATAAAAAATTATCTA
*
52452800 TTTTTATTATAAAAAATTATC-C
1 TTTTTATTATAAAAAATTATCTA
52452822 TTTTTAT
1 TTTTTAT
52452829 GTTAGCATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTTTATTATAAAAAATTATCTA
Found at i:52453553 original size:124 final size:124
Alignment explanation
Indices: 52453333--52453648 Score: 510
Period size: 124 Copynumber: 2.5 Consensus size: 124
52453323 GATAAAATCA
**
52453333 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAGCCGCGCTCA-CGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGC-CATCGTGGACGCGCTTTTGCTACAG
52453397 TAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAA-ACTTC
65 TAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACA-TTC
* * *
52453457 AAGCAGGATGCTTTATTAGAAGAATTTCTAAAATCGCGCCATCGTGGATGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCATCGTGGACGCGCTTTTGCTACAGT
*
52453522 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGTAAATAGTATAAAAAACGATTC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAC-ATTC
* * *
52453582 AAGTAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCATCGTGGACGCGCTTTTGCTACAGT
52453647 AG
66 AG
52453649 CATGTTTGGG
Statistics
Matches: 177, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
123 2 0.01
124 110 0.62
125 64 0.36
126 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (124 bp):
AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCATCGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACATTC
Found at i:52456755 original size:53 final size:53
Alignment explanation
Indices: 52456696--52456798 Score: 179
Period size: 53 Copynumber: 1.9 Consensus size: 53
52456686 ATTTTTAGTA
* *
52456696 AAATTATCAATTGTTAATTGTATTAATTTTTAGTAAATTTATCAAATTATATC
1 AAATTATCAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATTATATC
*
52456749 AAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATTAT
1 AAATTATCAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATTAT
52456799 TAATTGTTAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.49
Consensus pattern (53 bp):
AAATTATCAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATTATATC
Found at i:52456996 original size:27 final size:28
Alignment explanation
Indices: 52456962--52457016 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
52456952 TGGATAGTTA
*
52456962 AGGGTTTTTAAGGTAAGGG-TTATGGTT
1 AGGGTTTTAAAGGTAAGGGTTTATGGTT
*
52456989 AGGGTTTTAAAGTTAAGGGTTTATGGTT
1 AGGGTTTTAAAGGTAAGGGTTTATGGTT
52457017 TTAAGTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.42
Consensus pattern (28 bp):
AGGGTTTTAAAGGTAAGGGTTTATGGTT
Found at i:52457009 original size:15 final size:15
Alignment explanation
Indices: 52456957--52457010 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
52456947 AGGCTTGGAT
*
52456957 AGTTAAGGGTTTTTA
1 AGTTAAGGGTTTTAA
* *
52456972 AGGTAAGGG--TTAT
1 AGTTAAGGGTTTTAA
*
52456985 GGTT-AGGGTTTTAA
1 AGTTAAGGGTTTTAA
52456999 AGTTAAGGGTTT
1 AGTTAAGGGTTT
52457011 ATGGTTTTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
12 4 0.14
13 4 0.14
14 6 0.21
15 15 0.52
ACGTcount: A:0.26, C:0.00, G:0.33, T:0.41
Consensus pattern (15 bp):
AGTTAAGGGTTTTAA
Found at i:52457009 original size:21 final size:21
Alignment explanation
Indices: 52456985--52457349 Score: 453
Period size: 21 Copynumber: 17.5 Consensus size: 21
52456975 TAAGGGTTAT
*
52456985 GGTTAGGGTTTTAAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAG
*
52457006 GGTTTATGG-TTTTAAGTTAAG
1 GG-TTAGGGTTTTTAAGTTAAG
* *
52457027 GGTTATGGTATTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAG
52457048 GGTTTAGGGTTTTTAAGTTAAG
1 GG-TTAGGGTTTTTAAGTTAAG
52457070 GGTTAGGGTTTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAG
*
52457091 GGTTAGGGTATTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAG
52457112 GGTTTAGGGTTTTTAAGTTAAG
1 GG-TTAGGGTTTTTAAGTTAAG
*
52457134 GGTTCGGGTTTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAG
*
52457155 GGTTTAGGGTTTTTAAGTTAAT
1 GG-TTAGGGTTTTTAAGTTAAG
* *
52457177 GATTAGAGTTTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAG
*
52457198 GGTTTAGGATTTTTAAGTTAAG
1 GG-TTAGGGTTTTTAAGTTAAG
*
52457220 GGTTTAGGGTTTTTAAGTTAAT
1 GG-TTAGGGTTTTTAAGTTAAG
52457242 GGTTAGGGTTTTTAAG----G
1 GGTTAGGGTTTTTAAGTTAAG
* *
52457259 GTTTAAGGTTTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAG
* *
52457280 AGTTTAAGG-TTTTAAGTTAAG
1 -GGTTAGGGTTTTTAAGTTAAG
52457301 GGTTAGGGTTTTTAA--T--G
1 GGTTAGGGTTTTTAAGTTAAG
*
52457318 GTTTAGGGTTTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAG
52457339 GGTTAGGGTTT
1 GGTTAGGGTTT
52457350 AGGGTTAGGG
Statistics
Matches: 303, Mismatches: 25, Indels: 32
0.84 0.07 0.09
Matches are distributed among these distances:
17 29 0.10
19 2 0.01
20 12 0.04
21 151 0.50
22 109 0.36
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (21 bp):
GGTTAGGGTTTTTAAGTTAAG
Found at i:52457063 original size:43 final size:42
Alignment explanation
Indices: 52456985--52457349 Score: 453
Period size: 43 Copynumber: 8.8 Consensus size: 42
52456975 TAAGGGTTAT
* *
52456985 GGTTAGGGTTTTAAAGTTAAGGGTTTATGG-TTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAG
* *
52457027 GGTTATGGTATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAG
*
52457070 GGTTAGGGTTTTTAAGTTAAGGGTTAGGGTATTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAG
*
52457112 GGTTTAGGGTTTTTAAGTTAAGGGTTCGGGTTTTTAAGTTAAG
1 GG-TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAG
* * *
52457155 GGTTTAGGGTTTTTAAGTTAATGATTAGAGTTTTTAAGTTAAG
1 GG-TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAG
* *
52457198 GGTTTAGGATTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAT
1 GG-TTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAG
* *
52457242 GGTTAGGGTTTTTAAG----GGTTTAAGGTTTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAG
* *
52457280 AGTTTAAGG-TTTTAAGTTAAGGGTTAGGGTTTTTAA--T--G
1 -GGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAG
*
52457318 GTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTT
1 GGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTT
52457350 AGGGTTAGGG
Statistics
Matches: 287, Mismatches: 27, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
37 7 0.02
38 48 0.17
39 8 0.03
40 1 0.00
42 60 0.21
43 144 0.50
44 19 0.07
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (42 bp):
GGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAG
Found at i:52457261 original size:16 final size:17
Alignment explanation
Indices: 52457248--52457333 Score: 57
Period size: 17 Copynumber: 4.6 Consensus size: 17
52457238 TAATGGTTAG
52457248 GGTTTTTAAGGGTTTAA
1 GGTTTTTAAGGGTTTAA
52457265 GGTTTTTAAGTTAAGAGTTTAA
1 GGTTTTTAAG----G-GTTTAA
*
52457287 GGTTTTAAGTTAAGGG-TTAG
1 GG-TTT---TTAAGGGTTTAA
* *
52457307 GGTTTTTAATGGTTTAG
1 GGTTTTTAAGGGTTTAA
52457324 GGTTTTTAAG
1 GGTTTTTAAG
52457334 TTAAGGGTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
16 6 0.11
17 23 0.41
19 3 0.05
20 5 0.09
21 2 0.04
22 9 0.16
23 3 0.05
26 5 0.09
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (17 bp):
GGTTTTTAAGGGTTTAA
Found at i:52457286 original size:51 final size:50
Alignment explanation
Indices: 52457231--52457364 Score: 124
Period size: 59 Copynumber: 2.5 Consensus size: 50
52457221 GTTTAGGGTT
52457231 TTTAAGTTAATGGTTAGGGTTTTTAAGGGTTTAAGGTTTTTAAGTTAAGAG
1 TTTAAGTTAATGGTTAGGGTTTTTAAGGGTTTAAGGTTTTTAAGTTAAG-G
* *
52457282 TTTAAGGTTTTAAGTTAAGGGTTAGGGTTTTTAATGGTTTAGGGTTTTTAAGTTAAGG
1 TTTAA-G--TTAA--T---GGTTAGGGTTTTTAAGGGTTTAAGGTTTTTAAGTTAAGG
* * * *
52457340 GTTAGGGTTTAGGGTTAGGGTTTTT
1 TTTA-AGTTAATGGTTAGGGTTTTT
52457365 GTTAGGGTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
51 18 0.26
52 1 0.01
54 4 0.06
56 4 0.06
58 5 0.07
59 36 0.53
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (50 bp):
TTTAAGTTAATGGTTAGGGTTTTTAAGGGTTTAAGGTTTTTAAGTTAAGG
Found at i:52457342 original size:15 final size:16
Alignment explanation
Indices: 52457296--52457342 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
52457286 AGGTTTTAAG
52457296 TTAAGGGTT-AGGGTTT
1 TTAA-GGTTAAGGGTTT
*
52457312 TTAATGGTTTAGGGTTT
1 TTAA-GGTTAAGGGTTT
52457329 TTAA-GTTAAGGGTT
1 TTAAGGTTAAGGGTT
52457343 AGGGTTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 9 0.32
16 8 0.29
17 11 0.39
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (16 bp):
TTAAGGTTAAGGGTTT
Found at i:52457355 original size:13 final size:13
Alignment explanation
Indices: 52457337--52457362 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52457327 TTTTAAGTTA
52457337 AGGGTTAGGGTTT
1 AGGGTTAGGGTTT
52457350 AGGGTTAGGGTTT
1 AGGGTTAGGGTTT
52457363 TTGTTAGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (13 bp):
AGGGTTAGGGTTT
Found at i:52457393 original size:7 final size:7
Alignment explanation
Indices: 52457381--52457419 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
52457371 GTTTGTCAAT
52457381 TAAATTA
1 TAAATTA
52457388 TAAATT-
1 TAAATTA
52457394 T-AATTA
1 TAAATTA
52457400 TAAATTA
1 TAAATTA
*
52457407 TAAATTT
1 TAAATTA
52457414 TAAATT
1 TAAATT
52457420 TTTAAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 4 0.14
6 2 0.07
7 23 0.79
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (7 bp):
TAAATTA
Found at i:52457420 original size:7 final size:7
Alignment explanation
Indices: 52457380--52457429 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
52457370 GGTTTGTCAA
52457380 TTAAATT
1 TTAAATT
*
52457387 ATAAA-T
1 TTAAATT
52457393 TT-AATT
1 TTAAATT
*
52457399 ATAAATT
1 TTAAATT
*
52457406 ATAAATT
1 TTAAATT
52457413 TTAAATTT
1 TTAAA-TT
52457421 TTAAATT
1 TTAAATT
52457428 TT
1 TT
52457430 TAATAAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 2 0.06
6 4 0.11
7 23 0.64
8 7 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TTAAATT
Found at i:52457648 original size:21 final size:21
Alignment explanation
Indices: 52457624--52457664 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52457614 CCAACTTCCG
* * *
52457624 GCGGGGGTTGTGGTTGCTCTA
1 GCGGGGATTATGGTTCCTCTA
52457645 GCGGGGATTATGGTTCCTCT
1 GCGGGGATTATGGTTCCTCT
52457665 GGTAGGGCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.17, G:0.41, T:0.34
Consensus pattern (21 bp):
GCGGGGATTATGGTTCCTCTA
Found at i:52457948 original size:18 final size:18
Alignment explanation
Indices: 52457922--52457964 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
52457912 GACTCGGAAA
* * *
52457922 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
52457940 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
52457958 AGGATAC
1 AGGATAC
52457965 GTACCTAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:52458622 original size:7 final size:7
Alignment explanation
Indices: 52458612--52458637 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52458602 TTATATACAT
52458612 AATACTA
1 AATACTA
52458619 AATACTA
1 AATACTA
52458626 AATACTA
1 AATACTA
52458633 AATAC
1 AATAC
52458638 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:52461176 original size:61 final size:58
Alignment explanation
Indices: 52461069--52461184 Score: 169
Period size: 61 Copynumber: 1.9 Consensus size: 58
52461059 ATCAATTTAA
*
52461069 TATTAAATTAATATAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATG
1 TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATG
* * *
52461127 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTTAATTTAATTTAATATTAA
1 TATTAAATTAATAGAATACTTA--T-CAAGATAAATATTAAATTAAATTTAATATTAA
52461185 GATAATCACT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 20 0.39
60 1 0.02
61 30 0.59
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (58 bp):
TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATG
Found at i:52461220 original size:30 final size:30
Alignment explanation
Indices: 52461164--52461222 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
52461154 AAGATAAATA
* *
52461164 TTTAATTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAAGTTAATATAAAGATAATCAC
*
52461194 TTTAATATTAAGTTAATA-AAATATAATCA
1 TTTAAT-TTAAGTTAATATAAAGATAATCA
52461223 AGATAAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (30 bp):
TTTAATTTAAGTTAATATAAAGATAATCAC
Found at i:52462530 original size:15 final size:15
Alignment explanation
Indices: 52462512--52462541 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52462502 AATCACTTTA
52462512 ATATTAAATTAATAT
1 ATATTAAATTAATAT
*
52462527 ATATTAATTTAATAT
1 ATATTAAATTAATAT
52462542 TAAATCTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTAAATTAATAT
Found at i:52462558 original size:26 final size:26
Alignment explanation
Indices: 52462508--52462560 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
52462498 ACTTAATCAC
*
52462508 TTTAATATTAAATTAATATATATTAA
1 TTTAATATTAAATTAATATAAATTAA
*
52462534 TTTAATATTAAATCTTATA-AAATTAA
1 TTTAATATTAAAT-TAATATAAATTAA
52462560 T
1 T
52462561 AGAATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
TTTAATATTAAATTAATATAAATTAA
Found at i:52462566 original size:26 final size:26
Alignment explanation
Indices: 52462511--52462568 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
52462501 TAATCACTTT
* **
52462511 AATATTAAATTAATATATATTAATTT
1 AATATTAAATTAATATAAATTAATAG
*
52462537 AATATTAAATCTTATA-AAATTAATAG
1 AATATTAAAT-TAATATAAATTAATAG
52462563 AATATT
1 AATATT
52462569 TATCTACAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
AATATTAAATTAATATAAATTAATAG
Found at i:52468873 original size:19 final size:18
Alignment explanation
Indices: 52468831--52468873 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
52468821 ATGCAAGTAG
*
52468831 TTTGGTTTGTAATGTGGA
1 TTTGGTTTGTAATGTGAA
52468849 TTTGGTTTGATAAT-TGAA
1 TTTGGTTTG-TAATGTGAA
52468867 TTGTGGT
1 TT-TGGT
52468874 GTTAATGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (18 bp):
TTTGGTTTGTAATGTGAA
Found at i:52470148 original size:20 final size:20
Alignment explanation
Indices: 52470120--52470177 Score: 53
Period size: 25 Copynumber: 2.6 Consensus size: 20
52470110 TAGCTCCCAT
*
52470120 CTCCAATCCACAACGAGAAC
1 CTCCTATCCACAACGAGAAC
52470140 CTCCTATCCAATCCACAACGAGAAC
1 CTCC--T---ATCCACAACGAGAAC
52470165 CTCCTATCACACA
1 CTCCTATC-CACA
52470178 GGCTTCTCGT
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
20 7 0.23
21 4 0.13
23 1 0.03
25 19 0.61
ACGTcount: A:0.36, C:0.41, G:0.07, T:0.16
Consensus pattern (20 bp):
CTCCTATCCACAACGAGAAC
Found at i:52470149 original size:25 final size:25
Alignment explanation
Indices: 52470121--52470172 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
52470111 AGCTCCCATC
52470121 TCCAATCCACAACGAGAACCTCCTA
1 TCCAATCCACAACGAGAACCTCCTA
52470146 TCCAATCCACAACGAGAACCTCCTA
1 TCCAATCCACAACGAGAACCTCCTA
52470171 TC
1 TC
52470173 ACACAGGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.40, G:0.08, T:0.17
Consensus pattern (25 bp):
TCCAATCCACAACGAGAACCTCCTA
Found at i:52472175 original size:24 final size:22
Alignment explanation
Indices: 52472144--52472203 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
52472134 ATATATATAT
52472144 CAAA-ATTATAACATTACATAAAA
1 CAAATATTATAACATT--ATAAAA
*
52472167 TAAATATTATAAACTATTATAAAA
1 CAAATATTAT-AAC-ATTATAAAA
52472191 CAAATA-TATAACA
1 CAAATATTATAACA
52472204 GGATAGGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 1 0.03
22 3 0.09
23 6 0.19
24 16 0.50
25 3 0.09
26 3 0.09
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (22 bp):
CAAATATTATAACATTATAAAA
Found at i:52473191 original size:69 final size:68
Alignment explanation
Indices: 52473108--52473242 Score: 180
Period size: 68 Copynumber: 2.0 Consensus size: 68
52473098 TAATTAAACT
* * * *
52473108 TAATCACTTTAATATTAAATTAATATAATATTTATCAAGATAAATATTAGATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAATAAAAGA-CTATCAAGATAAATATTAAATTAAATTTAATATT
52473173 AAGA
65 AAGA
* * * * *
52473177 TAATCATTTTAATATTAAATTAATAAAAGACTATTACGATAAGTATTAAATTTAATTTAATATTA
1 TAATCACTTTAATATTAAATTAATAAAAGACTATCAAGATAAATATTAAATTAAATTTAATATTA
52473242 A
66 A
52473243 ATTTATTAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
68 30 0.53
69 27 0.47
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (68 bp):
TAATCACTTTAATATTAAATTAATAAAAGACTATCAAGATAAATATTAAATTAAATTTAATATTA
AGA
Found at i:52473255 original size:17 final size:17
Alignment explanation
Indices: 52473220--52473252 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52473210 TTACGATAAG
*
52473220 TATTAAATTTAATTTAA
1 TATTAAATTTAATTAAA
52473237 TATTAAATTT-ATTAAA
1 TATTAAATTTAATTAAA
52473253 ATAATATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAAATTTAATTAAA
Found at i:52478252 original size:56 final size:53
Alignment explanation
Indices: 52478123--52478286 Score: 165
Period size: 50 Copynumber: 3.0 Consensus size: 53
52478113 TACATCGGAG
* ***
52478123 TTCTCATATTGGTGCCCATGCCATGTCCCAAACATGGTCTTATGGGGGACCTCTCA
1 TTCTCA-A-TGGTGCCAATGCCATGT-CCAAACATGGTCTTACATGGGACCTCTCA
* *
52478179 -TCTCAA---TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCAAA
1 TTCTCAATGGTGCCAATGCCATGTCC-AAACATGGTCTTACATGGGACCTCTC--A
*
52478231 TTCTCAATGGTGCCAATGCCATGTTCCAAACATGGTCTTACATGGGATCTCATCA
1 TTCTCAATGGTGCCAATGCCATG-TCCAAACATGGTCTTACATGGGACCTC-TCA
52478286 T
1 T
52478287 CCAAATGTCA
Statistics
Matches: 90, Mismatches: 9, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
49 2 0.02
50 34 0.38
52 1 0.01
53 6 0.07
54 1 0.01
55 7 0.08
56 34 0.38
57 5 0.06
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (53 bp):
TTCTCAATGGTGCCAATGCCATGTCCAAACATGGTCTTACATGGGACCTCTCA
Found at i:52483411 original size:21 final size:23
Alignment explanation
Indices: 52483350--52483418 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
52483340 TACGGAACAG
*
52483350 AATAGAACACCGTC-GAAGCAGAT
1 AATAGAACACCG-CAGAAGCGGAT
*
52483373 AATAGAACACCGCTGAAGCGGAT
1 AATAGAACACCGCAGAAGCGGAT
*
52483396 AATA-AA-ACCGCAGAAGCGAAT
1 AATAGAACACCGCAGAAGCGGAT
52483417 AA
1 AA
52483419 ACAGATAGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 15 0.36
22 3 0.07
23 24 0.57
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (23 bp):
AATAGAACACCGCAGAAGCGGAT
Found at i:52487232 original size:18 final size:17
Alignment explanation
Indices: 52487209--52487247 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
52487199 TTTTCATCAA
52487209 ACATATATACATTATTTC
1 ACATATAT-CATTATTTC
52487227 AC--ATATCATTATTTC
1 ACATATATCATTATTTC
52487242 ACATAT
1 ACATAT
52487248 TTCTCATCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
15 11 0.58
16 4 0.21
17 2 0.11
18 2 0.11
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (17 bp):
ACATATATCATTATTTC
Found at i:52487238 original size:15 final size:16
Alignment explanation
Indices: 52487213--52487247 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
52487203 CATCAAACAT
52487213 ATATACATTATTTCAC
1 ATATACATTATTTCAC
52487229 ATAT-CATTATTTCAC
1 ATATACATTATTTCAC
52487244 ATAT
1 ATAT
52487248 TTCTCATCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATACATTATTTCAC
Found at i:52488701 original size:22 final size:24
Alignment explanation
Indices: 52488673--52488716 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
52488663 ATTTTGTTTA
52488673 ATTTTAACTT-TTAT-TCAAAAAC
1 ATTTTAACTTGTTATATCAAAAAC
*
52488695 ATTTTAATTTGTTATATCAAAA
1 ATTTTAACTTGTTATATCAAAA
52488717 CATATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (24 bp):
ATTTTAACTTGTTATATCAAAAAC
Found at i:52492908 original size:17 final size:15
Alignment explanation
Indices: 52492896--52492936 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
52492886 ACAATTAATG
52492896 ATTTTTAAAAATTTAT
1 ATTTTTAAAAA-TTAT
* *
52492912 ATTTTTAATAATTTT
1 ATTTTTAAAAATTAT
52492927 ATTTTTAAAA
1 ATTTTTAAAA
52492937 TAATTTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTTAAAAATTAT
Found at i:52492929 original size:15 final size:16
Alignment explanation
Indices: 52492896--52492936 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
52492886 ACAATTAATG
52492896 ATTTTTAAAAATTTAT
1 ATTTTTAAAAATTTAT
*
52492912 ATTTTTAATAATTT-T
1 ATTTTTAAAAATTTAT
52492927 ATTTTTAAAA
1 ATTTTTAAAA
52492937 TAATTTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTTAAAAATTTAT
Found at i:52492938 original size:17 final size:16
Alignment explanation
Indices: 52492896--52492943 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
52492886 ACAATTAATG
52492896 ATTTTTAAA-AATTTAT
1 ATTTTTAAATAATTT-T
52492912 ATTTTT-AATAATTTT
1 ATTTTTAAATAATTTT
52492927 ATTTTTAAAATAATTTT
1 ATTTTT-AAATAATTTT
52492944 TGTATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.31
16 11 0.38
17 9 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTTAAATAATTTT
Found at i:52493418 original size:16 final size:16
Alignment explanation
Indices: 52493393--52493451 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
52493383 ATTCGTCCTC
52493393 TTTATAATAATTATTT
1 TTTATAATAATTATTT
*
52493409 TTTATGATAA-TATTT
1 TTTATAATAATTATTT
52493424 TATTATAATAATTAAATTT
1 T-TTATAATAATT--ATTT
*
52493443 GTTATAATA
1 TTTATAATA
52493452 TTGAGTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 6 0.17
16 17 0.47
17 1 0.03
18 8 0.22
19 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTTATAATAATTATTT
Found at i:52497609 original size:5 final size:5
Alignment explanation
Indices: 52497595--52497627 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
52497585 TGCTTCTAAA
*
52497595 ATGA- ATGAT ATGAT ATGGT ATGAT ATGAT ATGA
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGA
52497628 ATTGATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.36
Consensus pattern (5 bp):
ATGAT
Found at i:52505181 original size:98 final size:98
Alignment explanation
Indices: 52505004--52505198 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
52504994 ACAATAAAAT
*
52505004 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
*
52505069 TCTAGAATCCCAAACTCGGAATATTTCCTTTAC
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
52505102 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
* *
52505167 TTTAAAATCTCAAACTCGGAATATTTCCTTTA
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTA
52505199 TTATTTTTTA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
Found at i:52505491 original size:9 final size:9
Alignment explanation
Indices: 52505477--52505501 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52505467 TGCAAATGTT
52505477 ATAATAACA
1 ATAATAACA
52505486 ATAATAACA
1 ATAATAACA
52505495 ATAATAA
1 ATAATAA
52505502 ATACATCATC
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAATAACA
Found at i:52506135 original size:3 final size:3
Alignment explanation
Indices: 52506129--52506163 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
52506119 TTACAATACC
*
52506129 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
52506164 ATTTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:52506144 original size:18 final size:18
Alignment explanation
Indices: 52506111--52506162 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
52506101 TGTACATGAA
* *
52506111 AATAATAATTACAATACC
1 AATAATAATAATAATACC
**
52506129 AATAATAATAATAATAGT
1 AATAATAATAATAATACC
52506147 AATAATAATAATAATA
1 AATAATAATAATAATA
52506163 AATTTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (18 bp):
AATAATAATAATAATACC
Found at i:52508899 original size:22 final size:23
Alignment explanation
Indices: 52508850--52508894 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
52508840 GGGTATCTAC
*
52508850 AAATTAAATC-TCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
52508872 AAATCAAATCTTCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
52508895 TATCATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTACA
Found at i:52508907 original size:19 final size:19
Alignment explanation
Indices: 52508883--52508936 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
52508873 AATCAAATCT
52508883 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
*
52508902 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
52508921 TCTAATATTACATATC
1 TCTAAGATTACATATC
52508937 CTCGAAGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:52509607 original size:17 final size:16
Alignment explanation
Indices: 52509585--52509652 Score: 63
Period size: 17 Copynumber: 4.3 Consensus size: 16
52509575 AAAAAGTATT
52509585 TTAAAAACATTTTAAAA
1 TTAAAAA-ATTTTAAAA
52509602 TTAAAAAA---TAAAA
1 TTAAAAAATTTTAAAA
*
52509615 -TAAAAGTATTTTAAAA
1 TTAAAA-AATTTTAAAA
52509631 TTAAAAAATTTTTAAAA
1 TTAAAAAA-TTTTAAAA
*
52509648 ATAAA
1 TTAAA
52509653 TATATTTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
12 5 0.12
13 6 0.14
16 7 0.17
17 24 0.57
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (16 bp):
TTAAAAAATTTTAAAA
Found at i:52509648 original size:29 final size:28
Alignment explanation
Indices: 52509560--52509650 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 28
52509550 ACCAAAAATT
52509560 TATTTTAAAATTTTAAAAAAGTATTTTAAAAA
1 TATTTTAAAA--TTAAAAAA-T-TTTTAAAAA
* *** *
52509592 CATTTTAAAATTAAAAAATAAAATAAAAG
1 TATTTTAAAATTAAAAAAT-TTTTAAAAA
52509621 TATTTTAAAATTAAAAAATTTTTAAAAA
1 TATTTTAAAATTAAAAAATTTTTAAAAA
52509649 TA
1 TA
52509651 AATATATTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
28 7 0.14
29 25 0.51
30 8 0.16
32 9 0.18
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (28 bp):
TATTTTAAAATTAAAAAATTTTTAAAAA
Found at i:52522380 original size:49 final size:49
Alignment explanation
Indices: 52522218--52522381 Score: 147
Period size: 49 Copynumber: 3.4 Consensus size: 49
52522208 CCAGCTTGTA
* *
52522218 TTGAACTACATCAATTATGGTATTATGCTTAGATGCTTGTATTAAACAT
1 TTGAACTGCATCAATTATGGTATTATGCTTAGATGCTTGTATTGAACAT
* * * * * * * *
52522267 TTGAACTGCATTAATTATGTTTTTTTTACTTAGATCCTT-TGTGGTAAC--
1 TTGAACTGCATCAATTATG-GTATTATGCTTAGATGCTTGTATTG-AACAT
* ** *
52522315 -TCATTTGCATCGATTATGGTATTATGCTTAGATGCTTGTATTGAACAT
1 TTGAACTGCATCAATTATGGTATTATGCTTAGATGCTTGTATTGAACAT
*
52522363 TTGAACTGCATCCATTATG
1 TTGAACTGCATCAATTATG
52522382 TTCTTTTTAC
Statistics
Matches: 83, Mismatches: 26, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
46 17 0.20
47 16 0.19
49 33 0.40
50 17 0.20
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (49 bp):
TTGAACTGCATCAATTATGGTATTATGCTTAGATGCTTGTATTGAACAT
Found at i:52522395 original size:96 final size:97
Alignment explanation
Indices: 52522226--52522419 Score: 336
Period size: 96 Copynumber: 2.0 Consensus size: 97
52522216 TATTGAACTA
* *
52522226 CATCAATTATGGTATTATGCTTAGATGCTTGTATTAAACATTTGAACTGCATTAATTATGTTTTT
1 CATCAATTATGGTATTATGCTTAGATGCTTGTATTAAACATTTGAACTGCATCAATTATGTTCTT
52522291 TTTACTTAGAT-CCTTTGTGGTAACTCATTTG
66 TTTACTTAGATACCTTTGTGGTAACTCATTTG
* * *
52522322 CATCGATTATGGTATTATGCTTAGATGCTTGTATTGAACATTTGAACTGCATCCATTATGTTCTT
1 CATCAATTATGGTATTATGCTTAGATGCTTGTATTAAACATTTGAACTGCATCAATTATGTTCTT
52522387 TTTACTTAGATACCTTTGTGGTAACTCATTTG
66 TTTACTTAGATACCTTTGTGGTAACTCATTTG
52522419 C
1 C
52522420 CTCTTTTTAA
Statistics
Matches: 92, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
96 71 0.77
97 21 0.23
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.45
Consensus pattern (97 bp):
CATCAATTATGGTATTATGCTTAGATGCTTGTATTAAACATTTGAACTGCATCAATTATGTTCTT
TTTACTTAGATACCTTTGTGGTAACTCATTTG
Found at i:52522943 original size:19 final size:19
Alignment explanation
Indices: 52522919--52522980 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
52522909 AAAACTTTGA
52522919 TCTTAACATTAATTTTAAT
1 TCTTAACATTAATTTTAAT
* ** * *
52522938 TCTTAATAAAAACTTTGA-
1 TCTTAACATTAATTTTAAT
*
52522956 TCTCAACATTAATTTTAAT
1 TCTTAACATTAATTTTAAT
52522975 TCTTAA
1 TCTTAA
52522981 TCTTGGATTT
Statistics
Matches: 30, Mismatches: 12, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
18 12 0.40
19 18 0.60
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.47
Consensus pattern (19 bp):
TCTTAACATTAATTTTAAT
Found at i:52522948 original size:37 final size:37
Alignment explanation
Indices: 52522907--52522981 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
52522897 TCGACGATGG
*
52522907 TAAAAACTTTGATCTTAACATTAATTTTAATTCTTAA
1 TAAAAACTTTGATCTCAACATTAATTTTAATTCTTAA
52522944 TAAAAACTTTGATCTCAACATTAATTTTAATTCTTAA
1 TAAAAACTTTGATCTCAACATTAATTTTAATTCTTAA
52522981 T
1 T
52522982 CTTGGATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (37 bp):
TAAAAACTTTGATCTCAACATTAATTTTAATTCTTAA
Found at i:52523117 original size:28 final size:30
Alignment explanation
Indices: 52523085--52523148 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 30
52523075 CTAATCTAAT
*
52523085 TATTAA-GAAAGAT-TTTTAATATGTAGTA
1 TATTAATGAAAAATATTTTAATATGTAGTA
*
52523113 TATTAATGAAAAATGATTTTCATATGTAGTA
1 TATTAATGAAAAAT-ATTTTAATATGTAGTA
52523144 TATTA
1 TATTA
52523149 TTGTCAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 6 0.19
29 6 0.19
31 19 0.61
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (30 bp):
TATTAATGAAAAATATTTTAATATGTAGTA
Found at i:52523139 original size:31 final size:31
Alignment explanation
Indices: 52523098--52523164 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
52523088 TAAGAAAGAT
*
52523098 TTTTAATATGTAGTATATTAATGAAAAATGA
1 TTTTCATATGTAGTATATTAATGAAAAATGA
* **
52523129 TTTTCATATGTAGTATATTATTGTCAAATGA
1 TTTTCATATGTAGTATATTAATGAAAAATGA
52523160 TTTTC
1 TTTTC
52523165 TAATGTCTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (31 bp):
TTTTCATATGTAGTATATTAATGAAAAATGA
Found at i:52523352 original size:76 final size:76
Alignment explanation
Indices: 52523229--52523456 Score: 408
Period size: 76 Copynumber: 3.0 Consensus size: 76
52523219 TATCAAATTT
*
52523229 TATTTGTTTAAATATATA---TAATTGCCCACGAAAAGATAAGCTTTTGTGATATTGGTTCTCTT
1 TATTTGTTTAAATATATATGTTAATTGCCGACGAAAAGATAAGCTTTTGTGATATTGGTTCTCTT
52523291 TAAATAAAGAA
66 TAAATAAAGAA
*
52523302 TATTTGTTTAAATATATATGTTAATTGCCGATGAAAAGATAAGCTTTTGTGATATTGGTTCTCTT
1 TATTTGTTTAAATATATATGTTAATTGCCGACGAAAAGATAAGCTTTTGTGATATTGGTTCTCTT
52523367 TAAATAAAGAA
66 TAAATAAAGAA
*
52523378 TATTTGTTTAAATATATATGTTAATTGCCGACGAAAAGATAAGCTTTTGTGATATTGGTTCTTTT
1 TATTTGTTTAAATATATATGTTAATTGCCGACGAAAAGATAAGCTTTTGTGATATTGGTTCTCTT
52523443 TAAATAAAGAA
66 TAAATAAAGAA
52523454 TAT
1 TAT
52523457 ATTGGAACGT
Statistics
Matches: 148, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
73 18 0.12
76 130 0.88
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (76 bp):
TATTTGTTTAAATATATATGTTAATTGCCGACGAAAAGATAAGCTTTTGTGATATTGGTTCTCTT
TAAATAAAGAA
Found at i:52523892 original size:44 final size:44
Alignment explanation
Indices: 52523829--52523916 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
52523819 ATTAACGCAA
* * * *
52523829 TATTTGGTAGTACAAAATTATTTGAAAGCTCTAGAAGAGCTAAT
1 TATTTGGTAGTACAAAATTAATTAAAAGCTCCAGAAAAGCTAAT
52523873 TATTTGGTCA-TACAAAATTAATTAAAAGCTCCAGAAAAGCTAAT
1 TATTTGGT-AGTACAAAATTAATTAAAAGCTCCAGAAAAGCTAAT
52523917 ATATCAATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 38 0.97
45 1 0.03
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (44 bp):
TATTTGGTAGTACAAAATTAATTAAAAGCTCCAGAAAAGCTAAT
Found at i:52525918 original size:27 final size:27
Alignment explanation
Indices: 52525808--52525944 Score: 91
Period size: 27 Copynumber: 5.1 Consensus size: 27
52525798 AGCCTACTAG
* * **
52525808 GACAATAAACAC-AAGGTAGTCTGTCGG
1 GACAATAAACACGGA-GTAGTCTGCCAA
* *
52525835 GACAATAAACGCGGTGTAGTCTGCCAA
1 GACAATAAACACGGAGTAGTCTGCCAA
* * * *
52525862 GACAATAAACATAGG-GTAATCCGCTAA
1 GACAATAAACA-CGGAGTAGTCTGCCAA
* ***
52525889 GACAATAAACATGGAGTAGTCTGTTGA
1 GACAATAAACACGGAGTAGTCTGCCAA
*
52525916 GACAGTAAACACGGAGTAG-CTTGCCAA
1 GACAATAAACACGGAGTAGTC-TGCCAA
52525943 GA
1 GA
52525945 TAGTAATGAC
Statistics
Matches: 85, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
26 3 0.04
27 80 0.94
28 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (27 bp):
GACAATAAACACGGAGTAGTCTGCCAA
Found at i:52529770 original size:11 final size:12
Alignment explanation
Indices: 52529756--52529785 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
52529746 AAAATTTTTA
52529756 TAAACTA-TAAT
1 TAAACTATTAAT
52529767 TAAACTATTAAT
1 TAAACTATTAAT
52529779 TAAACTA
1 TAAACTA
52529786 ACTAAGCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (12 bp):
TAAACTATTAAT
Found at i:52531851 original size:23 final size:24
Alignment explanation
Indices: 52531807--52531851 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
52531797 AACAGTGATA
*
52531807 ATTTATTTTCTAATTATAAATTCT
1 ATTTATTTTCTAAATATAAATTCT
* *
52531831 ATTTTTTTTC-AAATATCAATT
1 ATTTATTTTCTAAATATAAATT
52531852 TTAGTTGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTATTTTCTAAATATAAATTCT
Found at i:52540990 original size:41 final size:40
Alignment explanation
Indices: 52540908--52541009 Score: 127
Period size: 41 Copynumber: 2.6 Consensus size: 40
52540898 GAAATCCTTG
*
52540908 TTATAATTATTGTAATTATAA--TTTACGGTCGAATATTA
1 TTATAATTATTGTAATTATAATTTTTACGGTCAAATATTA
* * *
52540946 TTATAATTATTGTAATTGTAATTTTTTTCGGTCAAATGTTA
1 TTATAATTATTGTAATTATAA-TTTTTACGGTCAAATATTA
* *
52540987 TTATTATTATGGTAATTATAATT
1 TTATAATTATTGTAATTATAATT
52541010 ATTATATTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
38 20 0.37
40 2 0.04
41 32 0.59
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.52
Consensus pattern (40 bp):
TTATAATTATTGTAATTATAATTTTTACGGTCAAATATTA
Found at i:52543075 original size:58 final size:56
Alignment explanation
Indices: 52543012--52543128 Score: 144
Period size: 57 Copynumber: 2.1 Consensus size: 56
52543002 ATAGAAATGG
* * * *
52543012 TGAAATGGAGAAATAGAAAACATTTGGAATTGATTATGGTGTTCTCCAAAAATGAAAA
1 TGAAATGGAGAAAT-GAAAACATTAGGAAATGAATATAGTGTTCTCC-AAAATGAAAA
* * * *
52543070 TGAAATGGAGAAATGGAATCATTAGGAAATGAATCTAGTTTTCTCCAAAATGAAAA
1 TGAAATGGAGAAATGAAAACATTAGGAAATGAATATAGTGTTCTCCAAAATGAAAA
52543126 TGA
1 TGA
52543129 CCTGAAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
56 13 0.25
57 24 0.47
58 14 0.27
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.27
Consensus pattern (56 bp):
TGAAATGGAGAAATGAAAACATTAGGAAATGAATATAGTGTTCTCCAAAATGAAAA
Found at i:52544453 original size:35 final size:37
Alignment explanation
Indices: 52544407--52544481 Score: 109
Period size: 35 Copynumber: 2.1 Consensus size: 37
52544397 CACTAGTGTA
*
52544407 TTAAATAATAGTATATTT-A-TAGATCATCTATATAT
1 TTAAATAATAGTATATTTAAGCAGATCATCTATATAT
*
52544442 TTAAATGATAGTATATTTAAAGCAGATCATCTATATAT
1 TTAAATAATAGTATATTT-AAGCAGATCATCTATATAT
52544480 TT
1 TT
52544482 TATCATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
35 17 0.49
37 1 0.03
38 17 0.49
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (37 bp):
TTAAATAATAGTATATTTAAGCAGATCATCTATATAT
Found at i:52544690 original size:21 final size:20
Alignment explanation
Indices: 52544658--52544696 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
52544648 TTGAATCTTG
*
52544658 AAACCTATACCCCAAACCCC
1 AAACCTAAACCCCAAACCCC
52544678 AAACTCTAAACCCCAAACC
1 AAAC-CTAAACCCCAAACC
52544697 TTGATTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.44, C:0.46, G:0.00, T:0.10
Consensus pattern (20 bp):
AAACCTAAACCCCAAACCCC
Found at i:52547038 original size:22 final size:21
Alignment explanation
Indices: 52547013--52547055 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
52547003 GAAGGAATAA
52547013 TTATATAAAATTTTAAATTAGT
1 TTAT-TAAAATTTTAAATTAGT
*
52547035 TTATTTAAATTTTAAATTAGT
1 TTATTAAAATTTTAAATTAGT
52547056 AATTGTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TTATTAAAATTTTAAATTAGT
Found at i:52547218 original size:15 final size:16
Alignment explanation
Indices: 52547183--52547226 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
52547173 CATTTTAGAA
52547183 ATAATA-AATT-TA-T
1 ATAATATAATTATATT
52547196 ATAATATAA-TATATT
1 ATAATATAATTATATT
*
52547211 ATATTATAATTATATT
1 ATAATATAATTATATT
52547227 GATCATGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 7 0.27
14 4 0.15
15 9 0.35
16 6 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATAATATAATTATATT
Found at i:52574402 original size:754 final size:754
Alignment explanation
Indices: 52572955--52574456 Score: 2995
Period size: 754 Copynumber: 2.0 Consensus size: 754
52572945 GGTCAGCCAC
52572955 CTTGAGGAGCACTTTGCGAAGGAACAAACATGATAATTGAAGGAAGCTATTATGATTGATTCCCA
1 CTTGAGGAGCACTTTGCGAAGGAACAAACATGATAATTGAAGGAAGCTATTATGATTGATTCCCA
52573020 GAGAACTGTCGAATCAATTAGAGCTTATTATTCTTTATATTTATTTTATTTTGATATTAATCATG
66 GAGAACTGTCGAATCAATTAGAGCTTATTATTCTTTATATTTATTTTATTTTGATATTAATCATG
52573085 TTCACAATTTGTTTTGTTGTTTTTCTATCAACAATGGTAGCTTAATTCTGTTTTGCTAGAATGAT
131 TTCACAATTTGTTTTGTTGTTTTTCTATCAACAATGGTAGCTTAATTCTGTTTTGCTAGAATGAT
52573150 TACATTAATTTGATGAAGTACATTTGATTTATGTTCATAATGTTTTATACCTCAATCAATCATAC
196 TACATTAATTTGATGAAGTACATTTGATTTATGTTCATAATGTTTTATACCTCAATCAATCATAC
52573215 TTTCAATTAAAATCATGCATGTATTTCATCCATTAAAATGTGATTGAATGCATTAGAATTAGTTG
261 TTTCAATTAAAATCATGCATGTATTTCATCCATTAAAATGTGATTGAATGCATTAGAATTAGTTG
52573280 ACCGATCCTATCTAAACAATGATTAATGGACGGAATAATTGAAAGCTGCATGCTTAATTTAGATC
326 ACCGATCCTATCTAAACAATGATTAATGGACGGAATAATTGAAAGCTGCATGCTTAATTTAGATC
52573345 CTAGCCCGATTAAATTAAAGGTTCGTAATAACTCGGGAGAGCTCTATTACCTTGCATAACTTTTA
391 CTAGCCCGATTAAATTAAAGGTTCGTAATAACTCGGGAGAGCTCTATTACCTTGCATAACTTTTA
52573410 GATTTGTGTGATTAAATTGTTTCAAACCTAATTCATCCTTGTTACTTCATATGAATTCTAAGACA
456 GATTTGTGTGATTAAATTGTTTCAAACCTAATTCATCCTTGTTACTTCATATGAATTCTAAGACA
52573475 CCCTTAGTTAAATATGATCATGGTAGTATGCATGTTTTTCTAAGTAAAAGATTCCAAAATGACAA
521 CCCTTAGTTAAATATGATCATGGTAGTATGCATGTTTTTCTAAGTAAAAGATTCCAAAATGACAA
52573540 TATTGGTTTTAAAAAGAGTTCATGAAAGATCGAGTTGCTATGGAATATTTTTCGGAACATTATGA
586 TATTGGTTTTAAAAAGAGTTCATGAAAGATCGAGTTGCTATGGAATATTTTTCGGAACATTATGA
52573605 GCATGATAAAAATGAATTAAGTCAATTGATGTGATTATTCTAGCCTAAACATGTTATTGTTGTTG
651 GCATGATAAAAATGAATTAAGTCAATTGATGTGATTATTCTAGCCTAAACATGTTATTGTTGTTG
52573670 AAATCTTGTGAATTTTGCTGCTAAATCCATCTTGTGAAT
716 AAATCTTGTGAATTTTGCTGCTAAATCCATCTTGTGAAT
52573709 CTTGAGGAGCACTTTGCGAAGGAACAAACATGATAATTGAAGGAAGCTATTATGATTGATTCCCA
1 CTTGAGGAGCACTTTGCGAAGGAACAAACATGATAATTGAAGGAAGCTATTATGATTGATTCCCA
52573774 GAGAACTGTCGAATCAATTAGAGCTTATTATTCTTTATATTTATTTTATTTTGATATTAATCATG
66 GAGAACTGTCGAATCAATTAGAGCTTATTATTCTTTATATTTATTTTATTTTGATATTAATCATG
*
52573839 TTCACAATTTGTTTTGTTGTTTTTCTATCAACAATGGTTGCTTAATTCTGTTTTGCTAGAATGAT
131 TTCACAATTTGTTTTGTTGTTTTTCTATCAACAATGGTAGCTTAATTCTGTTTTGCTAGAATGAT
52573904 TACATTAATTTGATGAAGTACATTTGATTTATGTTCATAATGTTTTATACCTCAATCAATCATAC
196 TACATTAATTTGATGAAGTACATTTGATTTATGTTCATAATGTTTTATACCTCAATCAATCATAC
52573969 TTTCAATTAAAATCATGCATGTATTTCATCCATTAAAATGTGATTGAATGCATTAGAATTAGTTG
261 TTTCAATTAAAATCATGCATGTATTTCATCCATTAAAATGTGATTGAATGCATTAGAATTAGTTG
52574034 ACCGATCCTATCTAAACAATGATTAATGGACGGAATAATTGAAAGCTGCATGCTTAATTTAGATC
326 ACCGATCCTATCTAAACAATGATTAATGGACGGAATAATTGAAAGCTGCATGCTTAATTTAGATC
52574099 CTAGCCCGATTAAATTAAAGGTTCGTAATAACTCGGGAGAGCTCTATTACCTTGCATAACTTTTA
391 CTAGCCCGATTAAATTAAAGGTTCGTAATAACTCGGGAGAGCTCTATTACCTTGCATAACTTTTA
52574164 GATTTGTGTGATTAAATTGTTTCAAACCTAATTCATCCTTGTTACTTCATATGAATTCTAAGACA
456 GATTTGTGTGATTAAATTGTTTCAAACCTAATTCATCCTTGTTACTTCATATGAATTCTAAGACA
52574229 CCCTTAGTTAAATATGATCATGGTAGTATGCATGTTTTTCTAAGTAAAAGATTCCAAAATGACAA
521 CCCTTAGTTAAATATGATCATGGTAGTATGCATGTTTTTCTAAGTAAAAGATTCCAAAATGACAA
52574294 TATTGGTTTTAAAAAGAGTTCATGAAAGATCGAGTTGCTATGGAATATTTTTCGGAACATTATGA
586 TATTGGTTTTAAAAAGAGTTCATGAAAGATCGAGTTGCTATGGAATATTTTTCGGAACATTATGA
52574359 GCATGATAAAAATGAATTAAGTCAATTGATGTGATTATTCTAGCCTAAACATGTTATTGTTGTTG
651 GCATGATAAAAATGAATTAAGTCAATTGATGTGATTATTCTAGCCTAAACATGTTATTGTTGTTG
52574424 AAATCTTGTGAATTTTGCTGCTAAATCCATCTT
716 AAATCTTGTGAATTTTGCTGCTAAATCCATCTT
52574457 TCATTTTATT
Statistics
Matches: 747, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
754 747 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (754 bp):
CTTGAGGAGCACTTTGCGAAGGAACAAACATGATAATTGAAGGAAGCTATTATGATTGATTCCCA
GAGAACTGTCGAATCAATTAGAGCTTATTATTCTTTATATTTATTTTATTTTGATATTAATCATG
TTCACAATTTGTTTTGTTGTTTTTCTATCAACAATGGTAGCTTAATTCTGTTTTGCTAGAATGAT
TACATTAATTTGATGAAGTACATTTGATTTATGTTCATAATGTTTTATACCTCAATCAATCATAC
TTTCAATTAAAATCATGCATGTATTTCATCCATTAAAATGTGATTGAATGCATTAGAATTAGTTG
ACCGATCCTATCTAAACAATGATTAATGGACGGAATAATTGAAAGCTGCATGCTTAATTTAGATC
CTAGCCCGATTAAATTAAAGGTTCGTAATAACTCGGGAGAGCTCTATTACCTTGCATAACTTTTA
GATTTGTGTGATTAAATTGTTTCAAACCTAATTCATCCTTGTTACTTCATATGAATTCTAAGACA
CCCTTAGTTAAATATGATCATGGTAGTATGCATGTTTTTCTAAGTAAAAGATTCCAAAATGACAA
TATTGGTTTTAAAAAGAGTTCATGAAAGATCGAGTTGCTATGGAATATTTTTCGGAACATTATGA
GCATGATAAAAATGAATTAAGTCAATTGATGTGATTATTCTAGCCTAAACATGTTATTGTTGTTG
AAATCTTGTGAATTTTGCTGCTAAATCCATCTTGTGAAT
Found at i:52582379 original size:19 final size:19
Alignment explanation
Indices: 52582355--52582465 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
52582345 AATCTTCAGG
*
52582355 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
52582374 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
* *
52582393 AATATATAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
52582412 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
52582431 GATATATAATCTTAGATAT
1 GATATACAATCTTAGATAT
52582450 GATATACAATCTTAGA
1 GATATACAATCTTAGA
52582466 AGATATGATT
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 83 1.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.38
Consensus pattern (19 bp):
GATATACAATCTTAGATAT
Found at i:52582405 original size:38 final size:38
Alignment explanation
Indices: 52582362--52582465 Score: 190
Period size: 38 Copynumber: 2.7 Consensus size: 38
52582352 AGGGATATGC
52582362 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
52582400 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
52582438 AATCTTAGATATGATATACAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
52582466 AGATATGATT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:52585351 original size:24 final size:24
Alignment explanation
Indices: 52585323--52585368 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
52585313 ATCAAAGGAT
*
52585323 GGAAAAGCTA-GAGCAGTTTCAAAA
1 GGAAAAGC-AGGAGCAGCTTCAAAA
*
52585347 GGAAATGCAGGAGCAGCTTCAA
1 GGAAAAGCAGGAGCAGCTTCAA
52585369 CGACAAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.41, C:0.15, G:0.28, T:0.15
Consensus pattern (24 bp):
GGAAAAGCAGGAGCAGCTTCAAAA
Found at i:52589497 original size:132 final size:132
Alignment explanation
Indices: 52589323--52590216 Score: 1411
Period size: 132 Copynumber: 6.8 Consensus size: 132
52589313 TTGACAGCGA
*
52589323 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* * *
52589388 TCTTCTTCCCTGGACAACAGCGGAATAGATTGAAGATTTCAGATCTTATCTTCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
*
52589453 GG
131 AG
* * *
52589455 AGCAGATTGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTCAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* *
52589520 TCTACTTCCCTGAACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
52589585 AG
131 AG
* *
52589587 AGCAAATCGAAGATGGCGGATTTTACCTCCCTTTGG-TATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
*
52589651 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
*
52589716 AA
131 AG
* * *
52589718 AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTATATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* * *
52589783 TCTACTTCCTTGGACAACAGTGGAATAGATTGAAGATTTCAGGTATTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
52589848 AG
131 AG
*
52589850 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
52589915 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
52589980 AG
131 AG
*
52589982 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTAGTTATAGTGGAGTACATTGAAGCCAGTAA-
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
** * *
52590046 TCATA-TATCCCTGGTTAGCAGTGGAATAGGTTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
66 TC-TACT-TCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
*
52590110 GTGG
129 GTAG
* * * *
52590114 AGCAAATCGAAGATGGTGGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA-
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* * *
52590178 TCATA-TATCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
66 TC-TACT-TCCCTGGACAACAGTGGAATAGATTGAAGATT
52590217 GTAAGTCCTA
Statistics
Matches: 716, Mismatches: 43, Indels: 6
0.94 0.06 0.01
Matches are distributed among these distances:
131 126 0.18
132 590 0.82
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (132 bp):
AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
AG
Found at i:52590565 original size:19 final size:19
Alignment explanation
Indices: 52590541--52590651 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
52590531 AATCTTCAGG
52590541 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
52590560 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
52590579 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
52590598 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
52590617 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
52590636 GATATGCAATTTTAGA
1 GATATGCAATCTTAGA
52590652 AGATATGATT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 81 1.00
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:52590591 original size:38 final size:38
Alignment explanation
Indices: 52590548--52590651 Score: 190
Period size: 38 Copynumber: 2.7 Consensus size: 38
52590538 AGGGATATGC
52590548 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
52590586 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
52590624 AATCTTAGATATGATATGCAATTTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
52590652 AGATATGATT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.39
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:52594679 original size:132 final size:132
Alignment explanation
Indices: 52594505--52595399 Score: 1411
Period size: 132 Copynumber: 6.8 Consensus size: 132
52594495 TTGACAGCGA
*
52594505 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* * *
52594570 TCTTCTTCCCTGGACAACAGCGGAATAGATTGAAGATTTCAGATCTTATCTTCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
*
52594635 GG
131 AG
* * *
52594637 AGCAGATTGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTCAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* *
52594702 TCTACTTCCCTGAACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
52594767 AG
131 AG
* * *
52594769 AGCAAATCGAAGATGGCGGATTTTACCTCCCTTTGGGTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
*
52594834 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
*
52594899 AA
131 AG
* * *
52594901 AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTATATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* * *
52594966 TCTACTTCCTTGGACAACAGTGGAATAGATTGAAGATTTCAGGTATTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
52595031 AG
131 AG
*
52595033 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
52595098 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
52595163 AG
131 AG
*
52595165 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTAGTTATAGTGGAGTACATTGAAGCCAGTAA-
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
** * *
52595229 TCATA-TATCCCTGGTTAGCAGTGGAATAGGTTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
66 TC-TACT-TCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
*
52595293 GTGG
129 GTAG
* * * *
52595297 AGCAAATCGAAGATGGTGGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA-
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* * *
52595361 TCATA-TATCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
66 TC-TACT-TCCCTGGACAACAGTGGAATAGATTGAAGATT
52595400 GTAAGTCCTA
Statistics
Matches: 716, Mismatches: 45, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
131 3 0.00
132 713 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (132 bp):
AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
AG
Found at i:52595749 original size:19 final size:19
Alignment explanation
Indices: 52595725--52595835 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
52595715 AATCTTCAGG
52595725 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
52595744 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
52595763 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
52595782 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
52595801 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
52595820 GATATGCAATTTTAGA
1 GATATGCAATCTTAGA
52595836 AGATATGATT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 81 1.00
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:52595775 original size:38 final size:38
Alignment explanation
Indices: 52595732--52595835 Score: 190
Period size: 38 Copynumber: 2.7 Consensus size: 38
52595722 AGGGATATGC
52595732 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
52595770 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
52595808 AATCTTAGATATGATATGCAATTTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
52595836 AGATATGATT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.39
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:52599861 original size:132 final size:132
Alignment explanation
Indices: 52599687--52600579 Score: 1393
Period size: 132 Copynumber: 6.8 Consensus size: 132
52599677 TTGACAGCGA
*
52599687 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* * *
52599752 TCTTCTTCCCTGGACAACAGCGGAATAGATTGAAGATTTCAGATCTTATCTTCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
*
52599817 GG
131 AG
* * *
52599819 AGCAGATTGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTCAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* *
52599884 TCTACTTCCCTGAACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
52599949 AG
131 AG
* * *
52599951 AGCAAATCGAAGATGGCGGATTTTACCTCCCTTTGGGTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
*
52600016 TCTACTT-CCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
*
52600080 AA
131 AG
* * *
52600082 AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTATATTGAAGCCAGT-AT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* * *
52600146 TCTACTTCCTTGGACAACAGTGGAATAGATTGAAGATTTCAGGTATTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
52600211 AG
131 AG
*
52600213 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
52600278 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
52600343 AG
131 AG
*
52600345 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTAGTTATAGTGGAGTACATTGAAGCCAGTAA-
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
** * *
52600409 TCATA-TATCCCTGGTTAGCAGTGGAATAGGTTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
66 TC-TACT-TCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
*
52600473 GTGG
129 GTAG
* * * *
52600477 AGCAAATCGAAGATGGTGGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA-
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* * *
52600541 TCATA-TATCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
66 TC-TACT-TCCCTGGACAACAGTGGAATAGATTGAAGATT
52600580 GTAAGTCCTA
Statistics
Matches: 712, Mismatches: 45, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
130 9 0.01
131 230 0.32
132 473 0.66
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (132 bp):
AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
AG
Found at i:52600927 original size:19 final size:19
Alignment explanation
Indices: 52600903--52601013 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
52600893 AATCTTCAGG
52600903 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
52600922 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
52600941 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
52600960 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
52600979 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
52600998 GATATGCAATTTTAGA
1 GATATGCAATCTTAGA
52601014 AGATATGATT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 81 1.00
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:52600953 original size:38 final size:38
Alignment explanation
Indices: 52600910--52601013 Score: 190
Period size: 38 Copynumber: 2.7 Consensus size: 38
52600900 AGGGATATGC
52600910 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
52600948 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
52600986 AATCTTAGATATGATATGCAATTTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
52601014 AGATATGATT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.39
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:52612200 original size:103 final size:102
Alignment explanation
Indices: 52612030--52612236 Score: 378
Period size: 103 Copynumber: 2.0 Consensus size: 102
52612020 TAGATAAGAA
* * *
52612030 TACTAAAAAATGAGTCTGATTTAACACTAATAATATATAATTAACTAAAACATGAGTAAAATAAA
1 TACTAAAAAATGAGTCTAATTTAACACTAATAATATATAATTAACTAAAACATAAATAAAATAAA
52612095 ATTCCTAAAATCTACTAAAATTAACTTATAGAATAAAC
66 ATTCCT-AAATCTACTAAAATTAACTTATAGAATAAAC
52612133 TACTAAAAAATGAGTCTAATTTAACACTAATAATATATAATTAACTAAAACATAAATAAAATAAA
1 TACTAAAAAATGAGTCTAATTTAACACTAATAATATATAATTAACTAAAACATAAATAAAATAAA
52612198 ATTCCTAAATCTACTAAAATTAACTTATAGAATAAAC
66 ATTCCTAAATCTACTAAAATTAACTTATAGAATAAAC
52612235 TA
1 TA
52612237 AAATAAAATA
Statistics
Matches: 101, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
102 33 0.33
103 68 0.67
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.30
Consensus pattern (102 bp):
TACTAAAAAATGAGTCTAATTTAACACTAATAATATATAATTAACTAAAACATAAATAAAATAAA
ATTCCTAAATCTACTAAAATTAACTTATAGAATAAAC
Found at i:52618623 original size:32 final size:33
Alignment explanation
Indices: 52618582--52618649 Score: 120
Period size: 32 Copynumber: 2.1 Consensus size: 33
52618572 GATTTAATCC
52618582 AACCTAATATATGTTTTTCTATTTCCCAAAATA
1 AACCTAATATATGTTTTTCTATTTCCCAAAATA
*
52618615 AACC-AATATATGTTTTTCTATTTCTCAAAATA
1 AACCTAATATATGTTTTTCTATTTCCCAAAATA
52618647 AAC
1 AAC
52618650 ATTATTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 30 0.88
33 4 0.12
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (33 bp):
AACCTAATATATGTTTTTCTATTTCCCAAAATA
Found at i:52627670 original size:20 final size:21
Alignment explanation
Indices: 52627638--52627676 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
52627628 CTTCCCCCTT
52627638 TTTTCCTTATTTT-ATTTTAA
1 TTTTCCTTATTTTAATTTTAA
52627658 TTTTCCTGT-TTTTAATTTT
1 TTTTCCT-TATTTTAATTTT
52627677 GGGGTAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.15, C:0.10, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTTCCTTATTTTAATTTTAA
Found at i:52640149 original size:16 final size:16
Alignment explanation
Indices: 52640128--52640173 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
52640118 TTATTAAATT
52640128 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
52640144 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
52640159 AT-TATGTTAAATTAT
1 ATATAT-TTTAATTAT
52640174 CTTTTATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:52640247 original size:120 final size:120
Alignment explanation
Indices: 52640034--52640291 Score: 507
Period size: 120 Copynumber: 2.1 Consensus size: 120
52640024 GGCAGTTGTC
52640034 TAATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGA
1 TAATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGA
52640099 ATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAA
66 ATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAA
52640154 TAATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGA
1 TAATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGA
52640219 ATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAA
66 ATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAA
52640274 TAATAATTATGTTTAAAT
1 TAATAATTATG-TTAAAT
52640292 ATGATTAAAT
Statistics
Matches: 137, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
120 131 0.96
121 6 0.04
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
TAATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGA
ATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAA
Found at i:52640269 original size:16 final size:16
Alignment explanation
Indices: 52640248--52640289 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
52640238 TTATTAAATT
*
52640248 ATATATTTTAATTATA
1 ATATATTTTAATAATA
52640264 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
52640279 AT-TATGTTTAA
1 ATATAT-TTTAA
52640290 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:52640274 original size:15 final size:15
Alignment explanation
Indices: 52640239--52640280 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
52640229 TTAAGAATTT
*
52640239 TATTAAATTAT-ATA
1 TATTTAATTATAATA
52640253 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
52640267 TATTTAATAATAAT
1 TATTTAATTATAAT
52640281 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:52640460 original size:39 final size:40
Alignment explanation
Indices: 52640417--52640521 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
52640407 TTCCATTATG
52640417 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
52640456 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
52640501 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
52640522 ACACCTCTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:52640515 original size:45 final size:44
Alignment explanation
Indices: 52640415--52640524 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
52640405 TTTTCCATTA
52640415 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
52640454 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
52640499 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
52640525 CCTCTATTCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:52640524 original size:16 final size:16
Alignment explanation
Indices: 52640503--52640572 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
52640493 TTGATTTGCT
*
52640503 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
52640519 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
52640535 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
52640551 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
52640567 AATACA
1 ATTACA
52640573 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:52640949 original size:31 final size:30
Alignment explanation
Indices: 52640884--52640955 Score: 99
Period size: 31 Copynumber: 2.4 Consensus size: 30
52640874 TGTATATATG
*
52640884 AACTTTAATTTGGTGCAATTATACACGTGA
1 AACTTTAATTTGGTGCAAATATACACGTGA
* * *
52640914 AACTTTAATTGTGGTTCAAATATATACTTGA
1 AACTTTAATT-TGGTGCAAATATACACGTGA
52640945 AACTTTAATTT
1 AACTTTAATTT
52640956 TGATTTAATC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 11 0.30
31 26 0.70
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (30 bp):
AACTTTAATTTGGTGCAAATATACACGTGA
Found at i:52641026 original size:29 final size:29
Alignment explanation
Indices: 52640994--52641049 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
52640984 AAATACATCA
*
52640994 ATTTAGTTT-TATATTAGATAAATATAATT
1 ATTTA-TTTATATAATAGATAAATATAATT
*
52641023 ATTTATTTATGTAATAGATAAATATAA
1 ATTTATTTATATAATAGATAAATATAA
52641050 AATGATGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (29 bp):
ATTTATTTATATAATAGATAAATATAATT
Found at i:52646150 original size:33 final size:33
Alignment explanation
Indices: 52646113--52646176 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
52646103 GTCCCAGTGG
* *
52646113 ACTATATTTGTTCTGTGCT-TATTGTCCTAGCGA
1 ACTATATCTGTTCTATG-TATATTGTCCTAGCGA
*
52646146 ACTATCTCTGTTCTATGTATATTGTCCTAGC
1 ACTATATCTGTTCTATGTATATTGTCCTAGC
52646177 AGACTATCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 26 0.96
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.45
Consensus pattern (33 bp):
ACTATATCTGTTCTATGTATATTGTCCTAGCGA
Found at i:52650446 original size:19 final size:19
Alignment explanation
Indices: 52650422--52650461 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
52650412 AGTTGAATGA
*
52650422 AGAAAGTTGCTTACAATTC
1 AGAAAGTTGCCTACAATTC
52650441 AGAAAGTTGCCTACAATTC
1 AGAAAGTTGCCTACAATTC
52650460 AG
1 AG
52650462 GTATTTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (19 bp):
AGAAAGTTGCCTACAATTC
Found at i:52652502 original size:13 final size:13
Alignment explanation
Indices: 52652484--52652518 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
52652474 AAAACTTAAT
52652484 GTCATGCAATCAA
1 GTCATGCAATCAA
52652497 GTCATGCAATCAA
1 GTCATGCAATCAA
52652510 GTCATGCAA
1 GTCATGCAA
52652519 ACCAGAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (13 bp):
GTCATGCAATCAA
Found at i:52656926 original size:31 final size:31
Alignment explanation
Indices: 52656824--52656938 Score: 106
Period size: 31 Copynumber: 3.6 Consensus size: 31
52656814 CCAGCGAACT
*** *
52656824 TTATGTGTATTTACTATCCCAATGGACTATATA
1 TTATGTG--TTTACTATCCCAGCAGACTATTTA
* * *
52656857 TTTTGTGCTTACTATCCCTA-CAGACTATTTG
1 TTATGTGTTTACTATCCC-AGCAGACTATTTA
*
52656888 TTTTGTGTTTACTATCCCAGCAGACTATTTA
1 TTATGTGTTTACTATCCCAGCAGACTATTTA
* *
52656919 TTATGTGTTTATTGTCCCAG
1 TTATGTGTTTACTATCCCAG
52656939 GAGGCTATCT
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
30 1 0.01
31 61 0.88
32 1 0.01
33 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (31 bp):
TTATGTGTTTACTATCCCAGCAGACTATTTA
Found at i:52661971 original size:14 final size:15
Alignment explanation
Indices: 52661952--52661981 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
52661942 CATTTCTTGG
52661952 TCGGTTCAGTT-AAC
1 TCGGTTCAGTTCAAC
52661966 TCGGTTCAGTTCAAC
1 TCGGTTCAGTTCAAC
52661981 T
1 T
52661982 GGACCACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (15 bp):
TCGGTTCAGTTCAAC
Found at i:52672842 original size:19 final size:18
Alignment explanation
Indices: 52672820--52672859 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
52672810 GAAATTTTGG
52672820 AATGGAAAAGAAGAGAGAA
1 AATGG-AAAGAAGAGAGAA
* *
52672839 AATGGAGAGAAGAGAGGA
1 AATGGAAAGAAGAGAGAA
52672857 AAT
1 AAT
52672860 ATGTGAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.35, T:0.07
Consensus pattern (18 bp):
AATGGAAAGAAGAGAGAA
Found at i:52679054 original size:24 final size:22
Alignment explanation
Indices: 52679027--52679082 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 22
52679017 AAATATTTAA
*
52679027 TTAACTAAATTATTAAATATTCCT
1 TTAACTAAATTATTAAATAAT--T
* * *
52679051 TTAAATTAATTATTAATTAATT
1 TTAACTAAATTATTAAATAATT
52679073 TTAACTAAAT
1 TTAACTAAAT
52679083 ATTTTAGTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 9 0.35
24 17 0.65
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAACTAAATTATTAAATAATT
Found at i:52680863 original size:21 final size:21
Alignment explanation
Indices: 52680839--52680878 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
52680829 ATATTAAAAT
52680839 TATTTATATTTATTT-TATAAA
1 TATTTATATTT-TTTATATAAA
*
52680860 TATTTTTATTTTTTATATA
1 TATTTATATTTTTTATATA
52680879 TCCTAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTATATTTTTTATATAAA
Found at i:52681473 original size:21 final size:21
Alignment explanation
Indices: 52681448--52681498 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
52681438 TAACATCAAA
*
52681448 ATAAAGATTTGATTGGTAAAT
1 ATAAAGATTTGATCGGTAAAT
52681469 ATAAATG-TTTGATCGGTAAAT
1 ATAAA-GATTTGATCGGTAAAT
*
52681490 -TTAAGATTT
1 ATAAAGATTT
52681499 TAATAACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.04
20 6 0.23
21 18 0.69
22 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.41
Consensus pattern (21 bp):
ATAAAGATTTGATCGGTAAAT
Found at i:52684199 original size:3 final size:3
Alignment explanation
Indices: 52684191--52684223 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
52684181 TCGTTCTCTT
52684191 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
52684224 ATATACTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:52694179 original size:138 final size:138
Alignment explanation
Indices: 52693842--52694593 Score: 1162
Period size: 138 Copynumber: 5.5 Consensus size: 138
52693832 AATGAAAATG
*
52693842 AATTATATTCTTTCCAAAAGAATATTAATTT-ACATGTCTTTTATATTTTGATCGAAATTAATTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCA-ATGTCTTTTATATTTTGACCGAAATTAATTA
* *
52693906 ATATAACTATTTATATTAAAAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATC--A-
65 ATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
52693968 --ATATATT
130 TCATATATT
* * * *
52693975 AATTATATTCTTTCTAAAAGAATTTTAATTTCTATGTCTTTTATATTTTGACAGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCAATGTCTTTTATATTTTGACCGAAATTAATTAA
52694040 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAAT-TATTTGTATGAATCAAAT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATAT-TTTGTATGAATCAAAT
*
52694104 CCATATATT
130 TCATATATT
52694113 AATTATATTCTTTCCAAAAGAATATTAATTTCAATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCAATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * *
52694178 TATAACTATTTAGATTAATAATTTCGGTAAAAAATATACAATTAAT-TATTTGTATGAATCAAAT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATAT-TTTGTATGAATCAAAT
52694242 TCATATATT
130 TCATATATT
* *
52694251 AATTAAATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCAATGTCTTTTATATTTTGACCGAAATTAATTAA
* *
52694316 TACAACTGTTTATATTAATAAATTCGGTAAAATATATACAATCAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
52694381 CATATATT
131 CATATATT
* ** * *
52694389 AATTATATTCTTTCTAAAAGAATATTAATTTCCTTGCCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCAATGTCTTTTATATTTTGACCGAAATTAATTAA
* *
52694454 TACAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
* *
52694519 AAAATATT
131 CATATATT
*
52694527 AATTATATTCTTTCCAAAAGAATATTAATTTTC-ATATCTTTTATATTTTGACCGAAATTAATAT
1 AATTATATTCTTTCCAAAAGAATATTAA-TTTCAATGTCTTTTATATTTTGACCGAAATTAAT-T
52694591 AAT
64 AAT
52694594 TGTTCATATT
Statistics
Matches: 571, Mismatches: 38, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
132 1 0.00
133 115 0.20
135 1 0.00
138 445 0.78
139 9 0.02
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCAATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:52695498 original size:11 final size:11
Alignment explanation
Indices: 52695482--52695540 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
52695472 ACTACTACAA
52695482 ACCATATCACC
1 ACCATATCACC
52695493 ACCATA-CAACC
1 ACCATATC-ACC
52695504 ACCATATCACC
1 ACCATATCACC
* * *
52695515 GCCATTTAACC
1 ACCATATCACC
* *
52695526 ACCTTAGCACC
1 ACCATATCACC
52695537 ACCA
1 ACCA
52695541 CACCGCCACC
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
10 1 0.03
11 35 0.95
12 1 0.03
ACGTcount: A:0.36, C:0.44, G:0.03, T:0.17
Consensus pattern (11 bp):
ACCATATCACC
Found at i:52695508 original size:22 final size:22
Alignment explanation
Indices: 52695482--52695540 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
52695472 ACTACTACAA
52695482 ACCATATCACCACCATACAACC
1 ACCATATCACCACCATACAACC
* **
52695504 ACCATATCACCGCCATTTAACC
1 ACCATATCACCACCATACAACC
* *
52695526 ACCTTAGCACCACCA
1 ACCATATCACCACCA
52695541 CACCGCCACC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.36, C:0.44, G:0.03, T:0.17
Consensus pattern (22 bp):
ACCATATCACCACCATACAACC
Found at i:52701725 original size:23 final size:22
Alignment explanation
Indices: 52701682--52701725 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
52701672 TTCTAAGTCG
52701682 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
52701705 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
52701726 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:52701838 original size:45 final size:45
Alignment explanation
Indices: 52701770--52701856 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
52701760 AACAGATACT
* *
52701770 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATATG
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATATG
*
52701815 CGGTGGAATCAGCACAT-GACAACCACTTTACTAATCAATGAT
1 CGGTGGAATCAGCACATAG-CAACCACCTTACTAATCAATGAT
52701857 GTTTGGTTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATATG
Found at i:52701930 original size:51 final size:51
Alignment explanation
Indices: 52701868--52702005 Score: 163
Period size: 51 Copynumber: 2.7 Consensus size: 51
52701858 TTTGGTTCAT
* *
52701868 ATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCGATACAC
1 ATAGTAGCCTGCACATAGTACTACACATGTGACCATAACCATCCGATACAC
* * * * * * *
52701919 GTTGTAGCCTGCACATAGTACTACACACGTGATCGA-AACTATCCGGTACGC
1 ATAGTAGCCTGCACATAGTACTACACATGTGA-CCATAACCATCCGATACAC
52701970 ATAGTAGCCTGCACATAGTACTACACACT-TGACCAT
1 ATAGTAGCCTGCACATAGTACTACACA-TGTGACCAT
52702006 GACTTTCACT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
50 2 0.03
51 67 0.94
52 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (51 bp):
ATAGTAGCCTGCACATAGTACTACACATGTGACCATAACCATCCGATACAC
Done.