Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 131 of 150
Found at i:39421948 original size:25 final size:25
Alignment explanation
Indices: 39421917--39421985 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
39421907 GGAAACTCAT
39421917 GCGAGCCAATATCGGGAAGGTTCAA
1 GCGAGCCAATATCGGGAAGGTTCAA
* *
39421942 GCGAGCCAATATCAGGAAGGTTTAA
1 GCGAGCCAATATCGGGAAGGTTCAA
39421967 GCGAGCCAATATCGGGAAG
1 GCGAGCCAATATCGGGAAG
39421986 CTCATGAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.33, C:0.19, G:0.32, T:0.16
Consensus pattern (25 bp):
GCGAGCCAATATCGGGAAGGTTCAA
Found at i:39422032 original size:25 final size:27
Alignment explanation
Indices: 39421969--39422041 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 27
39421959 AGGTTTAAGC
*
39421969 GAGCCA-ATATCGGGAAGCTCATGAAA
1 GAGCCATATATCGGGAAGCTCACGAAA
*
39421995 GAGCC-TTTAATCGGGAAGCTC-CG-AA
1 GAGCCATAT-ATCGGGAAGCTCACGAAA
* *
39422020 GAGCCATATATCGAGACGCTCA
1 GAGCCATATATCGGGAAGCTCA
39422042 TAAGATTTGC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
25 17 0.45
26 9 0.24
27 12 0.32
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (27 bp):
GAGCCATATATCGGGAAGCTCACGAAA
Found at i:39422142 original size:25 final size:25
Alignment explanation
Indices: 39422108--39422167 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
39422098 AAAAAGTTGT
* *
39422108 TAACGGGAAGATCGCAAGAACCATA
1 TAACAGGAAGATCGCAAAAACCATA
39422133 TAACAGGAAGATCGCAAAAACCATA
1 TAACAGGAAGATCGCAAAAACCATA
39422158 TAACAGGAAG
1 TAACAGGAAG
39422168 CTCATGAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (25 bp):
TAACAGGAAGATCGCAAAAACCATA
Found at i:39442324 original size:9 final size:9
Alignment explanation
Indices: 39442310--39442373 Score: 69
Period size: 9 Copynumber: 7.2 Consensus size: 9
39442300 AAACTTAACC
39442310 AATTAACTA
1 AATTAACTA
39442319 AATTAACTA
1 AATTAACTA
39442328 AATTTAACTA
1 AA-TTAACTA
* **
39442338 ATTTAGGT-
1 AATTAACTA
39442346 AATTAACTA
1 AATTAACTA
*
39442355 AATTAAC-C
1 AATTAACTA
39442363 AATTAACTA
1 AATTAACTA
39442372 AA
1 AA
39442374 ATAAATAATG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
8 12 0.27
9 24 0.55
10 8 0.18
ACGTcount: A:0.52, C:0.11, G:0.03, T:0.34
Consensus pattern (9 bp):
AATTAACTA
Found at i:39442329 original size:27 final size:26
Alignment explanation
Indices: 39442299--39442373 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 26
39442289 TTTTCATATA
39442299 TAAACTTAACCAATTAACTAAATTAAC
1 TAAA-TTAACCAATTAACTAAATTAAC
* **
39442326 TAAATTTAACTAATTTAGGT-AATTAAC
1 TAAA-TTAACCAA-TTAACTAAATTAAC
39442353 TAAATTAACCAATTAACTAAA
1 TAAATTAACCAATTAACTAAA
39442374 ATAAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
25 4 0.10
26 9 0.23
27 22 0.56
28 4 0.10
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (26 bp):
TAAATTAACCAATTAACTAAATTAAC
Found at i:39442366 original size:17 final size:17
Alignment explanation
Indices: 39442299--39442373 Score: 78
Period size: 17 Copynumber: 4.2 Consensus size: 17
39442289 TTTTCATATA
39442299 TAAACTTAACCAATTAAC
1 TAAA-TTAACCAATTAAC
*
39442317 TAAATTAACTAAATTTAAC
1 TAAATTAAC-CAA-TTAAC
* ***
39442336 TAATTTAGGTAATTAAC
1 TAAATTAACCAATTAAC
39442353 TAAATTAACCAATTAAC
1 TAAATTAACCAATTAAC
39442370 TAAA
1 TAAA
39442374 ATAAATAATG
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
17 27 0.59
18 8 0.17
19 11 0.24
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAATTAACCAATTAAC
Found at i:39451210 original size:24 final size:24
Alignment explanation
Indices: 39451175--39451247 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
39451165 CGGACCCGCA
39451175 GCAAGAGTCAGAGCCAAAACCGGAG
1 GCAAGAGTCAGAG-CAAAACCGGAG
* *
39451200 GC-AGAGCCAGAGCAAGAACC-GAA
1 GCAAGAGTCAGAGCAA-AACCGGAG
*
39451223 GCAAGAGTTAGAGGCAAAACCGGAG
1 GCAAGAGTCAGA-GCAAAACCGGAG
39451248 CCGGATCCAG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
23 7 0.18
24 24 0.62
25 8 0.21
ACGTcount: A:0.41, C:0.22, G:0.33, T:0.04
Consensus pattern (24 bp):
GCAAGAGTCAGAGCAAAACCGGAG
Found at i:39451298 original size:66 final size:66
Alignment explanation
Indices: 39451183--39451330 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 66
39451173 CAGCAAGAGT
* * * **
39451183 CAGAGCCAAAACCGGAGGCAGAGCCAGAGCAAGAACCGAAGCAAGAGTTAGAGGCAAAACCGGAG
1 CAGATCCAGAACCGGAGGCAGAGCCAAAGCAAGAACCGAAGCAAGAGTTAGAGGCAAAACCAAAG
39451248 C
66 C
* ** * *
39451249 CGGATCCAGAACCGGAGGCAGAGCCAAAGCAAGAATGGGAGCCAA-AGTTAGAGGGAAAACCAAA
1 CAGATCCAGAACCGGAGGCAGAGCCAAAGCAAGAACCGAAG-CAAGAGTTAGAGGCAAAACCAAA
39451313 GC
65 GC
39451315 CAGATCCAGAACCGGA
1 CAGATCCAGAACCGGA
39451331 ACCAAAACCG
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
66 67 0.96
67 3 0.04
ACGTcount: A:0.41, C:0.24, G:0.31, T:0.05
Consensus pattern (66 bp):
CAGATCCAGAACCGGAGGCAGAGCCAAAGCAAGAACCGAAGCAAGAGTTAGAGGCAAAACCAAAG
C
Found at i:39451370 original size:30 final size:30
Alignment explanation
Indices: 39451336--39451396 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
39451326 CCGGAACCAA
* *
39451336 AACCGGAGACAGAGCCAGAGTTAGAGGCAG
1 AACCGAAGACAGAGCCAGAGTTAGAGCCAG
* * *
39451366 AACCGAAGTCGGATCCAGAGTTAGAGCCAG
1 AACCGAAGACAGAGCCAGAGTTAGAGCCAG
39451396 A
1 A
39451397 GTCAGAACCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.21, G:0.33, T:0.10
Consensus pattern (30 bp):
AACCGAAGACAGAGCCAGAGTTAGAGCCAG
Found at i:39451465 original size:24 final size:24
Alignment explanation
Indices: 39451438--39451486 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
39451428 CCAGAATCGA
* *
39451438 AGTCAGACCCGCAGCTAGAGTCAG
1 AGTCAGACCCGCAGCCAGAGACAG
**
39451462 AGTCAGAGTCGCAGCCAGAGACAG
1 AGTCAGACCCGCAGCCAGAGACAG
39451486 A
1 A
39451487 ACCAGTGTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.27, G:0.31, T:0.10
Consensus pattern (24 bp):
AGTCAGACCCGCAGCCAGAGACAG
Found at i:39454977 original size:20 final size:19
Alignment explanation
Indices: 39454939--39454977 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
39454929 AGCATATGCG
*
39454939 AATTTGTATTTTGATAATT
1 AATTTGTATTTTGAAAATT
*
39454958 AATTTTTATGTTTGAAAATT
1 AATTTGTAT-TTTGAAAATT
39454978 TTGATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (19 bp):
AATTTGTATTTTGAAAATT
Found at i:39455978 original size:42 final size:42
Alignment explanation
Indices: 39455916--39455998 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
39455906 ATAAGATGTA
* * *
39455916 TTAATATGATAAGTAAAAACCGGTATCTCTCATTGATCAGCG
1 TTAATATGATAAGTAAAAACCGGCATCTCACACTGATCAGCG
* *
39455958 TTAATATGATTAGTAGAAACCGGCATCTCACACTGATCAGC
1 TTAATATGATAAGTAAAAACCGGCATCTCACACTGATCAGC
39455999 CGCAACAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (42 bp):
TTAATATGATAAGTAAAAACCGGCATCTCACACTGATCAGCG
Found at i:39461045 original size:25 final size:25
Alignment explanation
Indices: 39461015--39461069 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
39461005 AGTGGAAGCA
* *
39461015 GTGGCAGTATATCTGCAAATCAGTG
1 GTGGCAATATATCTACAAATCAGTG
* *
39461040 GTGGCAATATATCTATAATTCAGTG
1 GTGGCAATATATCTACAAATCAGTG
39461065 GTGGC
1 GTGGC
39461070 TTTCCACAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (25 bp):
GTGGCAATATATCTACAAATCAGTG
Found at i:39464805 original size:3 final size:3
Alignment explanation
Indices: 39464797--39464823 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
39464787 CAAACGTCGG
39464797 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
39464824 TCAAGTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:39464822 original size:72 final size:72
Alignment explanation
Indices: 39464744--39464886 Score: 259
Period size: 72 Copynumber: 2.0 Consensus size: 72
39464734 ATCGTCGTTG
*
39464744 TCATCATCTCAAGTTCCTTCTTGGTTACAAATGCCTCCACCTCCAAACGTCGGATCATCATCATC
1 TCATCATCTCAAGTTCCTTCTTGGTTACAAACGCCTCCACCTCCAAACGTCGGATCATCATCATC
39464809 ATCATCA
66 ATCATCA
* *
39464816 TCATCATCTCAAGTTCCTTCTTGTTTACGAACGCCTCCACCTCCAAACGTCGGATCATCATCATC
1 TCATCATCTCAAGTTCCTTCTTGGTTACAAACGCCTCCACCTCCAAACGTCGGATCATCATCATC
39464881 ATCATC
66 ATCATC
39464887 TCCTCAAGTT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.25, C:0.34, G:0.10, T:0.31
Consensus pattern (72 bp):
TCATCATCTCAAGTTCCTTCTTGGTTACAAACGCCTCCACCTCCAAACGTCGGATCATCATCATC
ATCATCA
Found at i:39470736 original size:93 final size:93
Alignment explanation
Indices: 39470618--39470809 Score: 332
Period size: 98 Copynumber: 2.0 Consensus size: 93
39470608 GAGTGTTAGC
39470618 TTAATGCTACACTTACTTGGGACATGTTAGACTC-TATGAGTCATTAGTGTAATAGAGATCTATG
1 TTAATGCTACACTTACTTGGGACATGTTAGACTCATATGAGTCATTAGTGTAATAGAGATCTATG
39470682 TATCCGATGTGCTGTATTTTTATACATA
66 TATCCGATGTGCTGTATTTTTATACATA
39470710 TTAATGCTACACTTTACTTGGGACATGTTAGACTCTATGATATGAGTCATTAGTGTAATAGAGAT
1 TTAATGCTACAC-TTACTTGGGACATGTTAGACTC----ATATGAGTCATTAGTGTAATAGAGAT
39470775 CTATGTATCCGATGTGCTGTATTTTTATACATA
61 CTATGTATCCGATGTGCTGTATTTTTATACATA
39470808 TT
1 TT
39470810 TCATAATCAC
Statistics
Matches: 94, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
92 12 0.13
93 22 0.23
98 60 0.64
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (93 bp):
TTAATGCTACACTTACTTGGGACATGTTAGACTCATATGAGTCATTAGTGTAATAGAGATCTATG
TATCCGATGTGCTGTATTTTTATACATA
Found at i:39474849 original size:57 final size:57
Alignment explanation
Indices: 39474761--39474869 Score: 218
Period size: 57 Copynumber: 1.9 Consensus size: 57
39474751 GACAATCTCT
39474761 TGTTCTTCATGAAACCCACCAAAAGAAAGAATATTGGTATCCTCCTTACCATTTTCG
1 TGTTCTTCATGAAACCCACCAAAAGAAAGAATATTGGTATCCTCCTTACCATTTTCG
39474818 TGTTCTTCATGAAACCCACCAAAAGAAAGAATATTGGTATCCTCCTTACCAT
1 TGTTCTTCATGAAACCCACCAAAAGAAAGAATATTGGTATCCTCCTTACCAT
39474870 AACCGTTCCC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (57 bp):
TGTTCTTCATGAAACCCACCAAAAGAAAGAATATTGGTATCCTCCTTACCATTTTCG
Found at i:39478673 original size:21 final size:21
Alignment explanation
Indices: 39478647--39478702 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
39478637 AACAGCGGTG
*
39478647 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
39478668 GCGGTGAGATTAGATACTGTA
1 GCGGTGAGATTAGATACTGTA
39478689 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
39478703 AACAATGGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:39482031 original size:5 final size:5
Alignment explanation
Indices: 39482021--39482049 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
39482011 AAGAATACTT
39482021 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
39482050 TACAGTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:39484781 original size:120 final size:120
Alignment explanation
Indices: 39484616--39485437 Score: 1500
Period size: 120 Copynumber: 6.8 Consensus size: 120
39484606 GCCAATTGCT
**
39484616 TATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATA
1 TATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATA
39484681 TTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTA
66 TTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTA
39484736 TATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATA
1 TATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATA
39484801 TTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTA
66 TTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTA
**
39484856 TATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATA
1 TATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATA
39484921 TTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTA
66 TTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTA
39484976 TATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATA
1 TATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATA
39485041 TTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTA
66 TTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTA
39485096 TATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATA
1 TATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATA
39485161 TTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTA
66 TTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTA
*
39485216 TATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATCATATA
1 TATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATA
* * * * *
39485281 TTTTAATTAAAATATATTTAATATTAATTATTTTAAATTATATTTTATAGTATCA
66 TTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTA
* * * *
39485336 TATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATA
1 TATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATA
* *
39485401 TTTTAATTAAAATATATTTAATAATAATTATGTTAAA
66 TTTTTATTAAATTATATTTAATAATAATTATGTTAAA
39485438 ATATGATTAA
Statistics
Matches: 683, Mismatches: 19, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 683 1.00
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (120 bp):
TATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATA
TTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTA
Found at i:39485411 original size:18 final size:17
Alignment explanation
Indices: 39485383--39485417 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39485373 ATTATTAAGA
*
39485383 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39485400 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39485418 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39485669 original size:16 final size:16
Alignment explanation
Indices: 39485648--39485694 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
39485638 TTGATTTGCT
39485648 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
39485664 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
39485680 ATTACACCTCTATTC
1 ATTACGCCTCTATTC
39485695 TAATACAGCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.21, C:0.36, G:0.04, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:39486614 original size:30 final size:29
Alignment explanation
Indices: 39486573--39486917 Score: 556
Period size: 29 Copynumber: 11.8 Consensus size: 29
39486563 GAATATAAAC
39486573 TATATTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTATTTTTAAAATACACTACA
39486602 TATATATTTTTATTTTTAAAATACACTACA
1 TATAT-TTTTTATTTTTAAAATACACTACA
39486632 TATATTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTATTTTTAAAATACACTACA
39486661 TATATTTTTTATTTTTAAAATACACTACATA
1 TATATTTTTTATTTTTAAAATACACTAC--A
39486692 TATATTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTATTTTTAAAATACACTACA
39486721 TATAATTTTTTATTTTTAAAATACACTACA
1 TAT-ATTTTTTATTTTTAAAATACACTACA
39486751 TATATTTTTTATTTTTAAAATACACTA-A
1 TATATTTTTTATTTTTAAAATACACTACA
* *
39486779 TATA-ATTTTAATTTTAAAATACACTAC-
1 TATATTTTTTATTTTTAAAATACACTACA
39486806 -ATATTTTTTA-TTTTAAAATACACTACA
1 TATATTTTTTATTTTTAAAATACACTACA
*
39486833 CATATTTTTTAATTTTTAAAATACACTACATA
1 TATATTTTTT-ATTTTTAAAATACACTAC--A
39486865 TATATTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTATTTTTAAAATACACTACA
39486894 TATATTTTTTAATTTTTAAAATAC
1 TATATTTTTT-ATTTTTAAAATAC
39486918 TCTAATACAG
Statistics
Matches: 299, Mismatches: 4, Indels: 25
0.91 0.01 0.08
Matches are distributed among these distances:
26 19 0.06
27 25 0.08
28 14 0.05
29 97 0.32
30 87 0.29
31 47 0.16
32 10 0.03
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (29 bp):
TATATTTTTTATTTTTAAAATACACTACA
Found at i:39486739 original size:61 final size:58
Alignment explanation
Indices: 39486573--39486917 Score: 556
Period size: 61 Copynumber: 5.9 Consensus size: 58
39486563 GAATATAAAC
39486573 TATATTTTTTATTTTTAAAATACACTACATATATATTTTTATTTTTAAAATACACTACA
1 TATATTTTTTATTTTTAAAATACACTACATATAT-TTTTTATTTTTAAAATACACTACA
39486632 TATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAAAATACACTACATA
1 TATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAAAATACACTAC--A
39486692 TATATTTTTTATTTTTAAAATACACTACATATAATTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTATTTTTAAAATACACTACATAT-ATTTTTTATTTTTAAAATACACTACA
* *
39486751 TATATTTTTTATTTTTAAAATACACTA-ATATA-ATTTTAATTTTAAAATACACTAC-
1 TATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAAAATACACTACA
*
39486806 -ATATTTTTTA-TTTTAAAATACACTACACATATTTTTTAATTTTTAAAATACACTACATA
1 TATATTTTTTATTTTTAAAATACACTACATATATTTTTT-ATTTTTAAAATACACTAC--A
39486865 TATATTTTTTATTTTTAAAATACACTACATATATTTTTTAATTTTTAAAATAC
1 TATATTTTTTATTTTTAAAATACACTACATATATTTTTT-ATTTTTAAAATAC
39486918 TCTAATACAG
Statistics
Matches: 269, Mismatches: 6, Indels: 20
0.91 0.02 0.07
Matches are distributed among these distances:
53 15 0.06
54 14 0.05
55 4 0.01
56 38 0.14
57 1 0.00
58 27 0.10
59 62 0.23
60 43 0.16
61 65 0.24
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (58 bp):
TATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAAAATACACTACA
Found at i:39489494 original size:21 final size:21
Alignment explanation
Indices: 39489470--39489542 Score: 101
Period size: 21 Copynumber: 3.4 Consensus size: 21
39489460 CAAAAAATAG
* *
39489470 GGGAGAAACCAGCAAAAACGA
1 GGGAGAAACCAGCAAGAACAA
* *
39489491 GGGACAAACCAACAAGAACAA
1 GGGAGAAACCAGCAAGAACAA
39489512 GGGAGAAACCAGCAAGAACAA
1 GGGAGAAACCAGCAAGAACAA
39489533 GGGGAGAAAC
1 -GGGAGAAAC
39489543 TGCTGTTTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
21 36 0.80
22 9 0.20
ACGTcount: A:0.52, C:0.19, G:0.29, T:0.00
Consensus pattern (21 bp):
GGGAGAAACCAGCAAGAACAA
Found at i:39492169 original size:14 final size:14
Alignment explanation
Indices: 39492136--39492162 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39492126 AATGCCTTTA
39492136 AAAATAATAGTAAC
1 AAAATAATAGTAAC
39492150 AAAATAATAGTAA
1 AAAATAATAGTAA
39492163 TATAATAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (14 bp):
AAAATAATAGTAAC
Found at i:39494917 original size:204 final size:203
Alignment explanation
Indices: 39494541--39495142 Score: 839
Period size: 204 Copynumber: 3.0 Consensus size: 203
39494531 AAGGTTTAAT
* *
39494541 GTGTAAAACCATA-TCTCGACTATGGA-AACCAATAGAGTCTGCTAGGATATTAAACATGGGGTT
1 GTGTAAGACCATAGT-TCGACTAT-GACAACCAATAGAGTCTGC-AGGACATTAAACATGGGGTT
* * * * ** *
39494604 ATAAGGTGTAAGACCATAGCTCAACTATGGCAACTAATGGAGTCTGCCAAGACATTAAACATGGG
63 ATAAGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCCACCAAAACATTAAACATGGG
*
39494669 GTTACAAGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACAT
128 GTTACAAGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACGTTAAACAT
39494734 GAAGTTACAAA
193 GAAGTTACAAA
* * *
39494745 GTGTAAGACCATAGTTCGGCTATGACAACCAATAGGGTCCGTCAGGACATTAAACATGGGGTTAT
1 GTGTAAGACCATAGTTCGACTATGACAACCAATAGAGTCTG-CAGGACATTAAACATGGGGTTAT
* *
39494810 AAGGTGTAAGACCATAGCTCGGCTATAACAACCAATAGAGTCCACCAAAACATTAAACATGGGGT
65 AAGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCCACCAAAACATTAAACATGGGGT
* * * *
39494875 TACAAGGTGTAAGACCATAGCTTGTCTATGACAACCAATAGAGTTTGCCAGGACGTTAAACATAA
130 TACAAGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACGTTAAACATGA
*
39494940 AGTTACAAG
195 AGTTACAAA
* * * * * * * *
39494949 GTGTAAGACTATAGCTCGTCTATGGCAACCAATAGAGTTTGCCAGGACGTTAAACATGGAGTTAC
1 GTGTAAGACCATAGTTCGACTATGACAACCAATAGAGTCTG-CAGGACATTAAACATGGGGTTAT
*
39495014 AAGGTGTAAGACCATAGCTTGACTATGACAACCAATAGAGTCCACCAAAACATTAAACATGGGGT
65 AAGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCCACCAAAACATTAAACATGGGGT
* * * * *
39495079 TATAAGGTGTAAGACCATAGCTCGGCTATGGCAACCAATAGAGTCTGCTAGGACGTTAAGCATG
130 TACAAGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACGTTAAACATG
39495143 GGCTTAGACT
Statistics
Matches: 353, Mismatches: 42, Indels: 6
0.88 0.10 0.01
Matches are distributed among these distances:
203 2 0.01
204 349 0.99
205 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (203 bp):
GTGTAAGACCATAGTTCGACTATGACAACCAATAGAGTCTGCAGGACATTAAACATGGGGTTATA
AGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCCACCAAAACATTAAACATGGGGTT
ACAAGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACGTTAAACATGAA
GTTACAAA
Found at i:39495169 original size:68 final size:68
Alignment explanation
Indices: 39494541--39495144 Score: 751
Period size: 68 Copynumber: 8.9 Consensus size: 68
39494531 AAGGTTTAAT
* * * *
39494541 GTGTAAAACCATATCTCGACTATGGA-AACCAATAGAGTCTGCTAGGATATTAAACATGGGGTTA
1 GTGTAAGACCATAGCTCGACTAT-GACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTA
*
39494605 TAAG
65 CAAG
* * * * *
39494609 GTGTAAGACCATAGCTCAACTATGGCAACTAATGGAGTCTGCCAAGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTAC
39494674 AAG
66 AAG
**
39494677 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGAAGTTAC
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTAC
*
39494742 AAA
66 AAG
* * * * * *
39494745 GTGTAAGACCATAGTTCGGCTATGACAACCAATAGGGTCCGTCAGGACATTAAACATGGGGTTAT
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTAC
39494810 AAG
66 AAG
* * ** **
39494813 GTGTAAGACCATAGCTCGGCTATAACAACCAATAGAGTCCACCAAAACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTAC
39494878 AAG
66 AAG
* * * * ***
39494881 GTGTAAGACCATAGCTTGTCTATGACAACCAATAGAGTTTGCCAGGACGTTAAACATAAAGTTAC
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTAC
39494946 AAG
66 AAG
* * * * * *
39494949 GTGTAAGACTATAGCTCGTCTATGGCAACCAATAGAGTTTGCCAGGACGTTAAACATGGAGTTAC
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTAC
39495014 AAG
66 AAG
* ** ** *
39495017 GTGTAAGACCATAGCTTGACTATGACAACCAATAGAGTCCACCAAAACATTAAACATGGGGTTAT
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTAC
39495082 AAG
66 AAG
* * * * *
39495085 GTGTAAGACCATAGCTCGGCTATGGCAACCAATAGAGTCTGCTAGGACGTTAAGCATGGG
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGG
39495145 CTTAGACTGT
Statistics
Matches: 461, Mismatches: 74, Indels: 2
0.86 0.14 0.00
Matches are distributed among these distances:
67 1 0.00
68 460 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (68 bp):
GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTAC
AAG
Found at i:39497459 original size:21 final size:21
Alignment explanation
Indices: 39497391--39497459 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
39497381 CACAAAAGCA
* *
39497391 CATAAGTGCCAAACAGAAACC
1 CATAAGAGCTAAACAGAAACC
* * * *
39497412 CATAAGGGTTGAAC-GAAAGCT
1 CATAAGAGCTAAACAGAAA-CC
*
39497433 CGTAAGAGCTAAACAGAAACC
1 CATAAGAGCTAAACAGAAACC
39497454 CATAAG
1 CATAAG
39497460 GGTTATACTG
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
20 4 0.11
21 27 0.77
22 4 0.11
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.13
Consensus pattern (21 bp):
CATAAGAGCTAAACAGAAACC
Found at i:39497474 original size:42 final size:41
Alignment explanation
Indices: 39497401--39497518 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 41
39497391 CATAAGTGCC
**
39497401 AAACAGAAACCCATAAGGGTTGAACGAAAGCTCGTAAGAGCT
1 AAACAGAAACCCATAAGGGTT-AACGAAAGCTCAAAAGAGCT
*
39497443 AAACAGAAACCCATAAGGGTTATACTG-AAGCTTAAAAGAGCT
1 AAACAGAAACCCATAAGGGTTA-AC-GAAAGCTCAAAAGAGCT
* * * * *
39497485 GAATAAAAACCCATTAGGGTTAAACGAAAACTCA
1 AAACAGAAACCCATAAGGGTT-AACGAAAGCTCA
39497519 TATGAGTTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
41 2 0.03
42 59 0.94
43 2 0.03
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.17
Consensus pattern (41 bp):
AAACAGAAACCCATAAGGGTTAACGAAAGCTCAAAAGAGCT
Found at i:39510054 original size:22 final size:22
Alignment explanation
Indices: 39510029--39510070 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39510019 TAACTAATTA
*
39510029 AATTAATGAAATAAATAATAAT
1 AATTAATGAAATAAAAAATAAT
*
39510051 AATTATTGAAATAAAAAATA
1 AATTAATGAAATAAAAAATA
39510071 TTGGGTTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (22 bp):
AATTAATGAAATAAAAAATAAT
Found at i:39510398 original size:20 final size:20
Alignment explanation
Indices: 39510369--39510417 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
39510359 AAGTAGTGAA
*
39510369 TTTATATTCTTA-GAATAAAT
1 TTTATTTTCTTAGGAAT-AAT
39510389 TTTATTTTC-TAGGAATAAT
1 TTTATTTTCTTAGGAATAAT
*
39510408 ATTATTTTCT
1 TTTATTTTCT
39510418 GGTTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (20 bp):
TTTATTTTCTTAGGAATAAT
Found at i:39514422 original size:2 final size:2
Alignment explanation
Indices: 39514415--39514446 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39514405 AAACAGAATT
39514415 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39514447 ATTTGCTTCA
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):
TA
Found at i:39518902 original size:7 final size:7
Alignment explanation
Indices: 39518865--39518892 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
39518855 AGACTCGAAT
39518865 TTAAAAA
1 TTAAAAA
39518872 TTAAAAA
1 TTAAAAA
39518879 TTAAAAA
1 TTAAAAA
39518886 TTAAAAA
1 TTAAAAA
39518893 AATTACAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Found at i:39523628 original size:20 final size:22
Alignment explanation
Indices: 39523591--39523630 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
39523581 TATTTTTAAA
*
39523591 AATATAAATTGTGTAACTACTT
1 AATAAAAATTGTGTAACTACTT
39523613 AATAAAAATT-TG-AACTAC
1 AATAAAAATTGTGTAACTAC
39523631 CAAATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.35
Consensus pattern (22 bp):
AATAAAAATTGTGTAACTACTT
Found at i:39523636 original size:20 final size:22
Alignment explanation
Indices: 39523590--39523636 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
39523580 ATATTTTTAA
* *
39523590 AAATATAAATTGTGTAACTACT
1 AAATAAAAATTGTGTAACTACC
*
39523612 TAATAAAAATT-TG-AACTACC
1 AAATAAAAATTGTGTAACTACC
39523632 AAATA
1 AAATA
39523637 TATATAGAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 10 0.48
21 2 0.10
22 9 0.43
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (22 bp):
AAATAAAAATTGTGTAACTACC
Found at i:39527150 original size:98 final size:98
Alignment explanation
Indices: 39527029--39527218 Score: 335
Period size: 98 Copynumber: 1.9 Consensus size: 98
39527019 ATATAAAAAT
*
39527029 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACGATCCC
1 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACAATCCC
39527094 TTTAGAATCCCAAACTCGGAATATTTCTTTTAA
66 TTTAGAATCCCAAACTCGGAATATTTCTTTTAA
* * *
39527127 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACAATCCC
*
39527192 TTTAGAATCTCAAACTCGGAATATTTC
66 TTTAGAATCCCAAACTCGGAATATTTC
39527219 CTTCATGATT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 87 1.00
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.27
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACAATCCC
TTTAGAATCCCAAACTCGGAATATTTCTTTTAA
Found at i:39527499 original size:12 final size:12
Alignment explanation
Indices: 39527482--39527506 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39527472 AACGAGCAAC
39527482 ATAATATAAATG
1 ATAATATAAATG
39527494 ATAATATAAATG
1 ATAATATAAATG
39527506 A
1 A
39527507 AAGCACAAAT
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATAATATAAATG
Found at i:39527702 original size:2 final size:2
Alignment explanation
Indices: 39527691--39527743 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
39527681 AAAAATACTA
*
39527691 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39527733 AT AT AT AT AT A
1 AT AT AT AT AT A
39527744 GATAGTAGGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39528417 original size:2 final size:2
Alignment explanation
Indices: 39528410--39528478 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
39528400 TACACAATTG
39528410 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39528452 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
39528479 CTAGAATAGG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39529720 original size:14 final size:14
Alignment explanation
Indices: 39529701--39529733 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
39529691 GCCATGTTTG
39529701 TTTGGGCCACTGAA
1 TTTGGGCCACTGAA
39529715 TTTGGGCCACTGAA
1 TTTGGGCCACTGAA
39529729 TTTGG
1 TTTGG
39529734 TTTTGGGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.33
Consensus pattern (14 bp):
TTTGGGCCACTGAA
Found at i:39530135 original size:44 final size:44
Alignment explanation
Indices: 39530087--39530535 Score: 192
Period size: 44 Copynumber: 10.2 Consensus size: 44
39530077 TATCTTGGAA
*
39530087 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
*** * *
39530131 AGATAAGA-TCTATAATCTTCAACCTCCTCCACTACTGCTTAGGG
1 AGATAAGATTC-ACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * *** * * *
39530175 AGACAAGGCTT-GGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCACCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* * *
39530219 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTTCTTAGGG
1 AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
*** * * *
39530263 AGATAAGA-TCTATAATCTTCAACCTTCTCCGCTACTGCTTAGGG
1 AGATAAGATTC-ACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * *** * * * *
39530307 AGACAAGGCTT-GGTGGCTTAAATCTACTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCACCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* * *
39530351 AGATAAGATTCGCCGTCTTCGATCTACTCCACTACTGCTTAGGG
1 AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
*** * * *
39530395 AGATAAGA-TCTATAATCTTCAACCTTCTCCGCTACTGCTTAGGG
1 AGATAAGATTC-ACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * *** * * *
39530439 AGACAAGGCTT-GGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCACCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
*
39530483 AGATAAGATTCACCGTCTTCGATCTG-TGCCACTACTGCTTAGGG
1 AGATAAGATTCACCGTCTTCAATCTGCT-CCACTACTGCTTAGGG
39530527 AGATAAGAT
1 AGATAAGAT
39530536 CTACAATCTT
Statistics
Matches: 291, Mismatches: 84, Indels: 60
0.67 0.19 0.14
Matches are distributed among these distances:
42 19 0.07
43 26 0.09
44 212 0.73
45 15 0.05
46 19 0.07
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (44 bp):
AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:39530204 original size:132 final size:132
Alignment explanation
Indices: 39530057--39530647 Score: 1031
Period size: 132 Copynumber: 4.5 Consensus size: 132
39530047 TAGGATTGTC
* *
39530057 GGCTTTAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCGATCTGCTCCACTAC
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
*
39530122 TGCTTAGGGAGATAAGATCTATAATCTTCAACCTCCTCCACTACTGCTTAGGGAGACAAGGCTTG
66 TGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCACTACTGCTTAGGGAGACAAGGCTTG
39530187 GT
131 GT
39530189 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
* *
39530254 TTCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTACTGCTTAGGGAGACAAGGCTTG
66 TGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCACTACTGCTTAGGGAGACAAGGCTTG
39530319 GT
131 GT
* *
39530321 GGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTACTCCACTAC
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
*
39530386 TGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTACTGCTTAGGGAGACAAGGCTTG
66 TGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCACTACTGCTTAGGGAGACAAGGCTTG
39530451 GT
131 GT
*
39530453 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCGATCTG-TGCCACTA
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCT-CCACTA
* * * *
39530517 CTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTGCTGCTCAGAGAGACAAGGCTT
65 CTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCACTACTGCTTAGGGAGACAAGGCTT
39530582 GGT
130 GGT
* *
39530585 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTTTTCGATCTGCTCCACT
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
39530648 GTCAATGCAG
Statistics
Matches: 438, Mismatches: 19, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
131 1 0.00
132 436 1.00
133 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (132 bp):
GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
TGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCACTACTGCTTAGGGAGACAAGGCTTG
GT
Found at i:39542433 original size:2 final size:2
Alignment explanation
Indices: 39542420--39542455 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
39542410 TAAATAACTA
39542420 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39542456 CGAGAATAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39543710 original size:14 final size:14
Alignment explanation
Indices: 39543691--39543723 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
39543681 GCCATGTTTG
39543691 TTTGGGCCACTGAA
1 TTTGGGCCACTGAA
39543705 TTTGGGCCACTGAA
1 TTTGGGCCACTGAA
39543719 TTTGG
1 TTTGG
39543724 TTTTGGGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.33
Consensus pattern (14 bp):
TTTGGGCCACTGAA
Found at i:39547018 original size:21 final size:22
Alignment explanation
Indices: 39546975--39547020 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
39546965 TTGCTTTAAG
39546975 TATTAGACTAACATGTAAATTAT
1 TATTAGACTAACATG-AAATTAT
39546998 TATT-GACTGAACATG-AATTAT
1 TATTAGACT-AACATGAAATTAT
39547019 TA
1 TA
39547021 AATTTCTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 8 0.36
22 4 0.18
23 10 0.45
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (22 bp):
TATTAGACTAACATGAAATTAT
Found at i:39549928 original size:36 final size:36
Alignment explanation
Indices: 39549879--39549951 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 36
39549869 CATTCACTTA
39549879 GCTTCTCTACATCTATGGCCTTTACTGAA-GTCAAGG
1 GCTTCTCTACATCTATGGCCTTTACT-AATGTCAAGG
*
39549915 GCTTCTCTTCATCTATGGCCTTTACTAATGTCAAGG
1 GCTTCTCTACATCTATGGCCTTTACTAATGTCAAGG
39549951 G
1 G
39549952 ACACTTCACG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 2 0.06
36 33 0.94
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (36 bp):
GCTTCTCTACATCTATGGCCTTTACTAATGTCAAGG
Found at i:39552232 original size:3 final size:3
Alignment explanation
Indices: 39552224--39552278 Score: 65
Period size: 3 Copynumber: 17.3 Consensus size: 3
39552214 TCATTGTCAC
* *
39552224 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CCAT CACT CTTT CTT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT -CAT CA-T C-AT CAT CAT
39552272 CAT CAT C
1 CAT CAT C
39552279 TACTACCACT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 40 0.85
4 7 0.15
ACGTcount: A:0.27, C:0.36, G:0.00, T:0.36
Consensus pattern (3 bp):
CAT
Found at i:39552304 original size:15 final size:15
Alignment explanation
Indices: 39552280--39552309 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39552270 ATCATCATCT
39552280 ACTACCACTACCACC
1 ACTACCACTACCACC
*
39552295 ACTACTACTACCACC
1 ACTACCACTACCACC
39552310 GTGGATTCCT
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:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (15 bp):
ACTACCACTACCACC
Found at i:39563482 original size:13 final size:13
Alignment explanation
Indices: 39563466--39563491 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39563456 AAAAATATTT
39563466 TAAAAATAAAAAA
1 TAAAAATAAAAAA
39563479 TAAAAATAAAAAA
1 TAAAAATAAAAAA
39563492 ATATTTTAAA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:39563490 original size:32 final size:35
Alignment explanation
Indices: 39563445--39563522 Score: 108
Period size: 32 Copynumber: 2.3 Consensus size: 35
39563435 CCCGATTTTT
* *
39563445 AATAAACACAAAAAAATATTTTAAAA-A-TAA-AA
1 AATAAAAATAAAAAAATATTTTAAAAGATTAATAA
39563477 AATAAAAATAAAAAAATATTTTAAAAGTATTAATAA
1 AATAAAAATAAAAAAATATTTTAAAAG-ATTAATAA
39563513 AATAAAAATA
1 AATAAAAATA
39563523 TATATTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
32 24 0.60
34 1 0.03
35 3 0.08
36 12 0.30
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.26
Consensus pattern (35 bp):
AATAAAAATAAAAAAATATTTTAAAAGATTAATAA
Found at i:39563512 original size:31 final size:32
Alignment explanation
Indices: 39563443--39563530 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
39563433 GGCCCGATTT
* *
39563443 TTAATAAACACAAAAAAATATTTTAAAAATAA
1 TTAATAAAAATAAAAAAATATTTTAAAAATAA
** *
39563475 AAAATAAAAATAAAAAAATATTTTAAAAGT-A
1 TTAATAAAAATAAAAAAATATTTTAAAAATAA
*
39563506 TTAAT-AAAATAAAAATATATATTTA
1 TTAATAAAAATAAAAAAATAT-TTTA
39563531 TTATATTCGG
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 14 0.30
31 8 0.17
32 25 0.53
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (32 bp):
TTAATAAAAATAAAAAAATATTTTAAAAATAA
Found at i:39563873 original size:6 final size:6
Alignment explanation
Indices: 39563862--39563903 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
39563852 ATAACAATTA
39563862 TATATT TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT
39563904 AAATCGCTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:39564409 original size:2 final size:2
Alignment explanation
Indices: 39564402--39564435 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39564392 TTTGAGTTTA
39564402 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39564436 TAAATCTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39565553 original size:113 final size:114
Alignment explanation
Indices: 39565362--39566029 Score: 482
Period size: 113 Copynumber: 5.9 Consensus size: 114
39565352 TTACCACAAT
* * * * * * *
39565362 GCGCCGCTAAATCTCTTAACCAAAACGCTGTGTTTTCGTCTTGATGTATCTTAAAAGTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATCTTAGAATTAGTGGCG
* * * *
39565427 TT-TACGCAAAACGCCGTTAAAGGACAGTAATAGCGGCGCTTTTTGGAA
66 TTATAGGTAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTTTATGGAA
* * *
39565475 ACGCCGCAAAATAGCTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATCTTAGAATTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATCTTAGAATTAGTGGCG
* * *
39565539 TTTATAGG-AAAACGCCGTTAAAGTACAGTAATAGCGGCGCTTCACGGAA
66 -TTATAGGTAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTTTATGGAA
* * * * ** * * *
39565588 GCGCCGCAAACTATCTGAACCGAAACACATCGTTTTGGTCTTGATTTATAC-TACAACTAGTGGC
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTAT-CTTAGAATTAGTGGC
* * * * * * * **
39565652 G-CATACGGTCAAACGCCAG-TAAAGAATAGTATTAGCGGCGATTTGTGTCTA
65 GTTATA-GGTAAAACGCC-GTTAAAGCACAGTAATAGCGGCGCTTTATG-GAA
* * * * * * *
39565703 GCGCCGCAAAATATCTTAACAAAAACGCAGTGTTGTGATCTTAATGTAT-ATAAAATTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATCTTAGAATTAGTGGCG
* ** * * * *
39565767 CTTAT-GGTAAACCGCCGCGAACG-ATATTAATAGCGGCGCTTTGTGAGAA
66 -TTATAGGTAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTTTATG-GAA
* * * * * * **
39565816 GCGCCGCAAAATATATTAACCAAAACGCATAATTTCGGCCTCGATGTATAGTAGAATTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATCTTAGAATTAGTGGCG
* * * * * * **
39565881 CT-TA-GTGAAACGCCGTTAAAGCATAGT-ATTGCGGTGCTTGGATAAAA
66 TTATAGGTAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTT-TATGGAA
* * * ** *
39565928 GCGCCACCAAATATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTT-GATTTAGTGGC
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTAT-CTTAGAATTAGTGGC
* * *
39565992 GATT-TCGGTAAAACGCCGCTAAAGCACAGTATTAGCGG
65 G-TTATAGGTAAAACGCCGTTAAAGCACAGTAATAGCGG
39566030 TGATTTGTTG
Statistics
Matches: 428, Mismatches: 107, Indels: 38
0.75 0.19 0.07
Matches are distributed among these distances:
112 107 0.25
113 159 0.37
114 114 0.27
115 46 0.11
116 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (114 bp):
GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATCTTAGAATTAGTGGCG
TTATAGGTAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTTTATGGAA
Found at i:39565879 original size:228 final size:225
Alignment explanation
Indices: 39565476--39565914 Score: 472
Period size: 228 Copynumber: 1.9 Consensus size: 225
39565466 TTTTTGGAAA
* * * * * *
39565476 CGCCGCAAAATAGCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATCTTAGAATTAGTGGCGTT
1 CGCCGCAAAATAGCTTAACAAAAACGCAGAGTTTGATCTTAAGGTATCATAAAATTAGTGGCGCT
** * *
39565541 TATAGGAAAACGCCGTTAAAGTACAGTAATAGCGGCGCTTCACGGAAGCGCCGCAAACTATCTGA
66 TATAGGAAAACGCCGCGAAAGTACAGTAATAGCGGCGCTTCACGGAAGCGCCGCAAAATATATGA
* ** * * * *
39565606 ACCGAAACACATCGTTTTGGTCTTGATTTATACTACAACTAGTGGCGCATACGGTCAAACGCCAG
131 ACCAAAACACATAATTTCGGCCTCGATGTATACTACAACTAGTGGCGCATA--GTCAAACGCC-G
39565671 -TAAAGAATAGTATTAGCGGCGATTTGTGTCTAG
193 TTAAAGAATAGTATT-GCGGCGATTTGTGTCTAG
* * *
39565704 CGCCGCAAAATATCTTAACAAAAACGCAGTGTTGTGATCTTAATGTAT-ATAAAATTAGTGGCGC
1 CGCCGCAAAATAGCTTAACAAAAACGCAGAGTT-TGATCTTAAGGTATCATAAAATTAGTGGCGC
* * * * ***
39565768 TTAT-GGTAAACCGCCGCGAACG-ATATTAATAGCGGCGCTTTGTGAGAAGCGCCGCAAAATATA
65 TTATAGG-AAAACGCCGCGAAAGTACAGTAATAGCGGCGCTTCACG-GAAGCGCCGCAAAATATA
* * * * * * *
39565831 TTAACCAAAACGCATAATTTCGGCCTCGATGTATAGTAGAATTAGTGGCGCTTAGTGAAACGCCG
128 TGAACCAAAACACATAATTTCGGCCTCGATGTATACTACAACTAGTGGCGCATAGTCAAACGCCG
*
39565896 TTAAAGCATAGTATTGCGG
193 TTAAAGAATAGTATTGCGG
39565915 TGCTTGGATA
Statistics
Matches: 172, Mismatches: 35, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
225 5 0.03
226 22 0.13
227 19 0.11
228 115 0.67
229 11 0.06
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (225 bp):
CGCCGCAAAATAGCTTAACAAAAACGCAGAGTTTGATCTTAAGGTATCATAAAATTAGTGGCGCT
TATAGGAAAACGCCGCGAAAGTACAGTAATAGCGGCGCTTCACGGAAGCGCCGCAAAATATATGA
ACCAAAACACATAATTTCGGCCTCGATGTATACTACAACTAGTGGCGCATAGTCAAACGCCGTTA
AAGAATAGTATTGCGGCGATTTGTGTCTAG
Found at i:39565948 original size:340 final size:340
Alignment explanation
Indices: 39565454--39566110 Score: 783
Period size: 340 Copynumber: 1.9 Consensus size: 340
39565444 TAAAGGACAG
* * * * *
39565454 TAATAGCGGCGCTTTTTGGAAACGCCGCAAAATAGCTTAACCAAAACGCAGAGTTTGGTCTTGAG
1 TAATAGCGGCGCTTTGTGGAAACGCCGCAAAATAGATTAACCAAAACGCAGAATTTGGCCTCGAG
** * *
39565519 GTATCTTAGAATTAGTGGCGTTTATAGGAAAACGCCGTTAAAGTACAGTAATAGCGGCGCTTCAC
66 GTATAGTAGAATTAGTGGCGCTTATA-GAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTTCAC
** * * *
39565584 GGAAGCGCCGCAAACTATCTGAACCGAAACACATCGTTTTGGTCTTGATTTATACTACAACTAGT
130 AAAAGCGCCCCAAACTATCTGAACCAAAACACATCGTTTTGGTCTTGATGTATACTACAACTAGT
* *
39565649 GGCGCA-TACGGTCAAACGCCAG-TAAAGAATAGTATTAGCGGCGATTTG-TGTCTAGCGCCGCA
195 GGCG-ATTACGGTAAAACGCC-GCTAAAGAACAGTATTAGCGGCGATTTGTTG-CTAGCGCCGCA
* * **
39565711 AAATATC-TTAACAAAAACGCAGTGTTGTGATCTTAATGTATA-TAAAATTAGTGGCGCTTATGG
257 AAATACCATAAAC-AAAACGCAACGTTGTGATCTTAATGTATACTAAAATTAGTGGCGCTTATGG
39565774 TAAACCGCCGCGAACGATAT
321 TAAACCGCCGCGAACGATAT
* * *
39565794 TAATAGCGGCGCTTTGTGAGAAGCGCCGCAAAATATATTAACCAAAACGCATAATTTCGGCCTCG
1 TAATAGCGGCGCTTTGTG-GAAACGCCGCAAAATAGATTAACCAAAACGCAGAATTT-GGCCTCG
* * * *
39565859 ATGTATAGTAGAATTAGTGGCGCTTAGT-G-AAACGCCGTTAAAGCATAGT-ATTGCGGTGCTTG
64 AGGTATAGTAGAATTAGTGGCGCTTA-TAGAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTT-
* * * ** **
39565921 GATAAAAGCGCCACCAAA-TATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTTGATT
127 CACAAAAGCGCC-CCAAACTATCTGAACCAAAACACATCGTTTTGGTCTTGATGTATACTACAAC
* * *
39565985 TAGTGGCGATTTCGGTAAAACGCCGCTAAAGCACAGTATTAGCGGTGATTTGTTGCTAGCGCCGC
191 TAGTGGCGATTACGGTAAAACGCCGCTAAAGAACAGTATTAGCGGCGATTTGTTGCTAGCGCCGC
* * * * *
39566050 GACATACCATAAACAAAACGCAACGTTTTGGTCTTAATTTATACTAAAATTAGTGGCGCTT
256 AAAATACCATAAACAAAACGCAACGTTGTGATCTTAATGTATACTAAAATTAGTGGCGCTT
39566111 TGTTGAAAGC
Statistics
Matches: 265, Mismatches: 42, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
339 12 0.05
340 164 0.62
341 61 0.23
342 27 0.10
343 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (340 bp):
TAATAGCGGCGCTTTGTGGAAACGCCGCAAAATAGATTAACCAAAACGCAGAATTTGGCCTCGAG
GTATAGTAGAATTAGTGGCGCTTATAGAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTTCACA
AAAGCGCCCCAAACTATCTGAACCAAAACACATCGTTTTGGTCTTGATGTATACTACAACTAGTG
GCGATTACGGTAAAACGCCGCTAAAGAACAGTATTAGCGGCGATTTGTTGCTAGCGCCGCAAAAT
ACCATAAACAAAACGCAACGTTGTGATCTTAATGTATACTAAAATTAGTGGCGCTTATGGTAAAC
CGCCGCGAACGATAT
Found at i:39566312 original size:90 final size:90
Alignment explanation
Indices: 39566204--39566367 Score: 294
Period size: 90 Copynumber: 1.8 Consensus size: 90
39566194 AATCATATTT
*
39566204 GGTTTAGGTATAGGGTATTAGGGTTCATTATATAATGTTTAATATTTTTGGATTACAGTGTAAAG
1 GGTTTAGGTATAGAGTATTAGGGTTCATTATATAATGTTTAATATTTTTGGATTACAGTGTAAAG
39566269 TTTAAAGTTTAGGATTTACGATGTA
66 TTTAAAGTTTAGGATTTACGATGTA
*
39566294 GGTTTAGGGT-TAGAGTATTAGGGTTCATTATATAATGTTTAGTATTTTTGGATTACAGTGTAAA
1 GGTTTA-GGTATAGAGTATTAGGGTTCATTATATAATGTTTAATATTTTTGGATTACAGTGTAAA
39566358 GTTTAAAGTT
65 GTTTAAAGTT
39566368 NNNNNNNNNN
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
90 68 0.96
91 3 0.04
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.44
Consensus pattern (90 bp):
GGTTTAGGTATAGAGTATTAGGGTTCATTATATAATGTTTAATATTTTTGGATTACAGTGTAAAG
TTTAAAGTTTAGGATTTACGATGTA
Found at i:39569257 original size:9 final size:9
Alignment explanation
Indices: 39569234--39569386 Score: 58
Period size: 9 Copynumber: 17.9 Consensus size: 9
39569224 ATATATTCAT
39569234 TTACATAAC
1 TTACATAAC
39569243 --ACATAAC
1 TTACATAAC
39569250 TTACATAAC
1 TTACATAAC
* *
39569259 CTACTTAA-
1 TTACATAAC
*
39569267 -TATATAAC
1 TTACATAAC
*
39569275 TTGCATAAC
1 TTACATAAC
* *
39569284 TTAAATAAG
1 TTACATAAC
39569293 TTACATAA-
1 TTACATAAC
39569301 TAATACATAA-
1 T--TACATAAC
*
39569311 -TACACAAC
1 TTACATAAC
*
39569319 TTACAT--G
1 TTACATAAC
*
39569326 TGTAAATAA-
1 T-TACATAAC
* *
39569335 -TACAGAGC
1 TTACATAAC
39569343 TTACATAAC
1 TTACATAAC
*
39569352 TTACATATC
1 TTACATAAC
* *
39569361 CTACATAAA
1 TTACATAAC
* *
39569370 TTAAATAAG
1 TTACATAAC
39569379 TTACATAA
1 TTACATAA
39569387 TAATACATAC
Statistics
Matches: 104, Mismatches: 27, Indels: 26
0.66 0.17 0.17
Matches are distributed among these distances:
7 23 0.22
8 5 0.05
9 69 0.66
10 7 0.07
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.31
Consensus pattern (9 bp):
TTACATAAC
Found at i:39569401 original size:37 final size:37
Alignment explanation
Indices: 39569353--39569426 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
39569343 TTACATAACT
*
39569353 TACATATCCTACATAAATTAAATAAGTTACATAATAA
1 TACATACCCTACATAAATTAAATAAGTTACATAATAA
*
39569390 TACATACCCTACATAAATTAAATAAGTTACATTATAA
1 TACATACCCTACATAAATTAAATAAGTTACATAATAA
39569427 GGTTTCTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.32
Consensus pattern (37 bp):
TACATACCCTACATAAATTAAATAAGTTACATAATAA
Found at i:39569459 original size:15 final size:15
Alignment explanation
Indices: 39569435--39569467 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
39569425 AAGGTTTCTA
*
39569435 TATTAGTATTAAATT
1 TATTACTATTAAATT
39569450 TATTACTATTAAATT
1 TATTACTATTAAATT
39569465 TAT
1 TAT
39569468 AAATAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (15 bp):
TATTACTATTAAATT
Found at i:39569727 original size:25 final size:25
Alignment explanation
Indices: 39569699--39569818 Score: 80
Period size: 25 Copynumber: 4.6 Consensus size: 25
39569689 ACACATACCG
*
39569699 TACATAAATTAAATAAGTTACATGATA
1 TACATAAATTAAATAACTTACAT-A-A
* * ** *
39569726 CACCAAAAAAAAAAAAACTTACATAA
1 TA-CATAAATTAAATAACTTACATAA
* *
39569752 CTTA-GTAAATTAAATAAGTTACATAA
1 --TACATAAATTAAATAACTTACATAA
* *
39569778 TACACAAATTACATAACTTACATAA
1 TACATAAATTAAATAACTTACATAA
* *
39569803 TACATAATTTACATAA
1 TACATAAATTAAATAA
39569819 TACACAACTG
Statistics
Matches: 70, Mismatches: 19, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
24 2 0.03
25 32 0.46
26 17 0.24
27 2 0.03
28 17 0.24
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.28
Consensus pattern (25 bp):
TACATAAATTAAATAACTTACATAA
Found at i:39569822 original size:41 final size:41
Alignment explanation
Indices: 39569765--39570009 Score: 211
Period size: 41 Copynumber: 6.3 Consensus size: 41
39569755 AGTAAATTAA
* * *
39569765 ATAAGTTACATAATACACAAATTACATAACTTACATAATAC
1 ATAATTTACATAATACACAACTGACATAACTTACATAATAC
39569806 ATAATTTACATAATACACAACTGACATAACTTACATAATAC
1 ATAATTTACATAATACACAACTGACATAACTTACATAATAC
* * *
39569847 ATATTTTACATCACTTACATAA--GACATAACTTAC---AT--
1 ATAATTTACAT-A-ATACACAACTGACATAACTTACATAATAC
*
39569883 A-AGTTT-CATAATACACAACTGACATAACTTACATAATAC
1 ATAATTTACATAATACACAACTGACATAACTTACATAATAC
* * *
39569922 ATATTTTACATCATTTACATAA--GACATAACTTAC---AT--
1 ATAATTTACAT-A-ATACACAACTGACATAACTTACATAATAC
*
39569958 A-AGTTT-CATAATACACAACTGACATAACTTACATAATAC
1 ATAATTTACATAATACACAACTGACATAACTTACATAATAC
* *
39569997 ACAACTTACATAA
1 ATAATTTACATAA
39570010 GTTTCATAAG
Statistics
Matches: 165, Mismatches: 17, Indels: 44
0.73 0.08 0.19
Matches are distributed among these distances:
32 12 0.07
33 2 0.01
34 30 0.18
35 8 0.05
36 2 0.01
37 4 0.02
38 4 0.02
39 2 0.01
40 7 0.04
41 80 0.48
42 2 0.01
43 12 0.07
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (41 bp):
ATAATTTACATAATACACAACTGACATAACTTACATAATAC
Found at i:39569832 original size:25 final size:25
Alignment explanation
Indices: 39569803--39570072 Score: 297
Period size: 25 Copynumber: 10.7 Consensus size: 25
39569793 ACTTACATAA
*
39569803 TACATAATTTACATAATACACAACT
1 TACATAACTTACATAATACACAACT
* * **
39569828 GACATAACTTACATAATACATATTT
1 TACATAACTTACATAATACACAACT
* * *
39569853 TACATCACTTACATAAGACATAACT
1 TACATAACTTACATAATACACAACT
* *
39569878 TACATAAGTTTCATAATACACAACT
1 TACATAACTTACATAATACACAACT
* * **
39569903 GACATAACTTACATAATACATATTT
1 TACATAACTTACATAATACACAACT
* * * *
39569928 TACATCATTTACATAAGACATAACT
1 TACATAACTTACATAATACACAACT
* *
39569953 TACATAAGTTTCATAATACACAACT
1 TACATAACTTACATAATACACAACT
*
39569978 GACATAACTTACATAATACACAACT
1 TACATAACTTACATAATACACAACT
* * *
39570003 TACATAAGTTTCATAAGACACAACT
1 TACATAACTTACATAATACACAACT
*
39570028 TACATAGCTTACATAACTTACACAACT
1 TACATAACTTACATAA--TACACAACT
39570055 TACATAACTTACATAATA
1 TACATAACTTACATAATA
39570073 AATAAGTTAT
Statistics
Matches: 199, Mismatches: 44, Indels: 4
0.81 0.18 0.02
Matches are distributed among these distances:
25 176 0.88
27 23 0.12
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (25 bp):
TACATAACTTACATAATACACAACT
Found at i:39569882 original size:75 final size:75
Alignment explanation
Indices: 39569803--39570072 Score: 400
Period size: 75 Copynumber: 3.6 Consensus size: 75
39569793 ACTTACATAA
39569803 TACATAA-TTTACATAATACACAACTGACATAACTTACATAATACATATTTTACATCACTTACAT
1 TACATAAGTTT-CATAATACACAACTGACATAACTTACATAATACATATTTTACATCACTTACAT
39569867 AAGACATAACT
65 AAGACATAACT
*
39569878 TACATAAGTTTCATAATACACAACTGACATAACTTACATAATACATATTTTACATCATTTACATA
1 TACATAAGTTTCATAATACACAACTGACATAACTTACATAATACATATTTTACATCACTTACATA
39569943 AGACATAACT
66 AGACATAACT
* ** * * *
39569953 TACATAAGTTTCATAATACACAACTGACATAACTTACATAATACACAACTTACATAAGTTTCATA
1 TACATAAGTTTCATAATACACAACTGACATAACTTACATAATACATATTTTACATCACTTACATA
*
39570018 AGACACAACT
66 AGACATAACT
* *
39570028 TACAT-AGCTTACATAACTTACACAACTTACATAACTTACATAATA
1 TACATAAG-TTTCATAA--TACACAACTGACATAACTTACATAATA
39570073 AATAAGTTAT
Statistics
Matches: 181, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
74 2 0.01
75 150 0.83
76 3 0.02
77 26 0.14
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (75 bp):
TACATAAGTTTCATAATACACAACTGACATAACTTACATAATACATATTTTACATCACTTACATA
AGACATAACT
Found at i:39575605 original size:21 final size:21
Alignment explanation
Indices: 39575540--39575608 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
39575530 CAGCAACTTA
* *
39575540 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGAG
* ** * *
39575561 AAACAGCA-GCTACAACGAAAG
1 AAGCAG-AGGCCGCAGCGAGAG
39575582 AAGCAGAGGCCGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
39575603 AAGCAG
1 AAGCAG
39575609 CGAGAGAAGC
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.39, C:0.22, G:0.38, T:0.01
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:39575610 original size:12 final size:12
Alignment explanation
Indices: 39575593--39575665 Score: 89
Period size: 12 Copynumber: 6.3 Consensus size: 12
39575583 AGCAGAGGCC
39575593 GCAGCGAGAGAA
1 GCAGCGAGAGAA
39575605 GCAGCGAGAGAA
1 GCAGCGAGAGAA
**
39575617 GCA--GAG-GCC
1 GCAGCGAGAGAA
39575626 GCAGCGAGAGAA
1 GCAGCGAGAGAA
39575638 GCAGCGAGAGAA
1 GCAGCGAGAGAA
* *
39575650 GCAGCAATAGAA
1 GCAGCGAGAGAA
39575662 GCAG
1 GCAG
39575666 AGGTTCAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
9 4 0.08
10 3 0.06
11 3 0.06
12 42 0.81
ACGTcount: A:0.40, C:0.19, G:0.40, T:0.01
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:39575622 original size:33 final size:33
Alignment explanation
Indices: 39575580--39575653 Score: 148
Period size: 33 Copynumber: 2.2 Consensus size: 33
39575570 CTACAACGAA
39575580 AGAAGCAGAGGCCGCAGCGAGAGAAGCAGCGAG
1 AGAAGCAGAGGCCGCAGCGAGAGAAGCAGCGAG
39575613 AGAAGCAGAGGCCGCAGCGAGAGAAGCAGCGAG
1 AGAAGCAGAGGCCGCAGCGAGAGAAGCAGCGAG
39575646 AGAAGCAG
1 AGAAGCAG
39575654 CAATAGAAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.38, C:0.20, G:0.42, T:0.00
Consensus pattern (33 bp):
AGAAGCAGAGGCCGCAGCGAGAGAAGCAGCGAG
Found at i:39576131 original size:42 final size:42
Alignment explanation
Indices: 39576081--39576352 Score: 268
Period size: 42 Copynumber: 6.4 Consensus size: 42
39576071 GCGTTTGTGA
*
39576081 AATAAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCGGTTTTT
1 AATAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTTT
* * * *
39576123 AATAAGCGCCGCTATAGAACATTA-CTTTTAGAGGCGCTTTCTTC
1 AATAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCG-TTT-TTT
* * *
39576167 CA-AAGCGTCACTAAAGAACATGATCTTTAGCGGCGTTTTTT
1 AATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
* *
39576208 CCA-AAGCGCCGCTAAAGAACATGATCTTTAGGGGCGTTTCTTT
1 -AATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTT
* * *
39576251 -CTAAGCGCCGCTAAAGAGCATGATCTTTAGCGGCATTTTTT
1 AATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
**
39576292 TCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
1 AATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTT
* *
39576335 ATGTAAGCGCCGCAAAAG
1 A-ATAAGCGCCGCTAAAG
39576353 TTAGTGACGT
Statistics
Matches: 197, Mismatches: 23, Indels: 18
0.83 0.10 0.08
Matches are distributed among these distances:
41 6 0.03
42 136 0.69
43 37 0.19
44 18 0.09
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (42 bp):
AATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
Found at i:39576275 original size:84 final size:83
Alignment explanation
Indices: 39576083--39576330 Score: 295
Period size: 84 Copynumber: 2.9 Consensus size: 83
39576073 GTTTGTGAAA
* * * *
39576083 TAAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCGGTTTTTAATAAGCGCCGCTATAGAACATT
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTTTCA-AAGCGCCGCTAAAGAACATG
39576146 A-CTTTTAGAGGCGCTTTCTTCC
63 ATC-TTTAGAGGCG-TTTCTTCC
* * *
39576168 AAAGCGTCACTAAAGAACATGATCTTTAGCGGCGTTTTTTCCAAAGCGCCGCTAAAGAACATGAT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-CAAAGCGCCGCTAAAGAACATGAT
* *
39576233 CTTTAGGGGCGTTTCTTTC
65 CTTTAGAGGCGTTTCTTCC
* * *
39576252 TAAGCGCCGCTAAAGAGCATGATCTTTAGCGGCATTTTTTTCTAAGCGCCGCTAAAGAACATGAT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGC-GTTTTTTCAAAGCGCCGCTAAAGAACATGAT
*
39576317 CTTTAGCGGCGTTT
65 CTTTAGAGGCGTTT
39576331 TTTTATGTAA
Statistics
Matches: 142, Mismatches: 16, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
84 73 0.51
85 66 0.46
86 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (83 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCAAAGCGCCGCTAAAGAACATGATC
TTTAGAGGCGTTTCTTCC
Found at i:39577935 original size:17 final size:16
Alignment explanation
Indices: 39577910--39577952 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
39577900 TACTGAACAT
39577910 AATTATTCTCAAACAAC
1 AATTATTCT-AAACAAC
* *
39577927 AATTGTTCTGAACAAC
1 AATTATTCTAAACAAC
*
39577943 AACTATTCTA
1 AATTATTCTA
39577953 TATAAGAGTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.33
Consensus pattern (16 bp):
AATTATTCTAAACAAC
Found at i:39579247 original size:20 final size:21
Alignment explanation
Indices: 39579205--39579251 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
39579195 AATATATATT
39579205 ATTTTT-TATAATATTTTTCA
1 ATTTTTATATAATATTTTTCA
* *
39579225 ATTTTTATATATTA-TTTTGA
1 ATTTTTATATAATATTTTTCA
39579245 ATTTTTA
1 ATTTTTA
39579252 AAATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
ATTTTTATATAATATTTTTCA
Found at i:39580095 original size:14 final size:16
Alignment explanation
Indices: 39580055--39580095 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
39580045 ACATAAATTG
39580055 TGATTATATTTTAATC
1 TGATTATATTTTAATC
*
39580071 TGGTTAT-TTTTAAT-
1 TGATTATATTTTAATC
39580085 T-ATTATATTTT
1 TGATTATATTTT
39580096 TCGAGTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.18
14 5 0.23
15 7 0.32
16 6 0.27
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.63
Consensus pattern (16 bp):
TGATTATATTTTAATC
Found at i:39598937 original size:20 final size:20
Alignment explanation
Indices: 39598912--39598952 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39598902 TCATAAAAAT
39598912 AAAAATAATATAATATAAAC
1 AAAAATAATATAATATAAAC
* **
39598932 AAAAATATTATTTTATAAAC
1 AAAAATAATATAATATAAAC
39598952 A
1 A
39598953 GTAAAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATAATATAATATAAAC
Found at i:39599661 original size:11 final size:11
Alignment explanation
Indices: 39599625--39599705 Score: 94
Period size: 11 Copynumber: 7.4 Consensus size: 11
39599615 TAAATCCTTT
*
39599625 CTCTC-AATTT
1 CTCTCAAATTC
39599635 CTCTCCAATATT-
1 CTCT-CAA-ATTC
39599647 CTCTCAAATTC
1 CTCTCAAATTC
39599658 CTCTCAAATTC
1 CTCTCAAATTC
39599669 CTCTCAAATTC
1 CTCTCAAATTC
* *
39599680 CTTTCAATTTC
1 CTCTCAAATTC
*
39599691 CTCTCAATTTC
1 CTCTCAAATTC
39599702 CTCT
1 CTCT
39599706 TAAAAAAGCT
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
10 7 0.11
11 49 0.77
12 5 0.08
13 3 0.05
ACGTcount: A:0.22, C:0.35, G:0.00, T:0.43
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:39601839 original size:21 final size:21
Alignment explanation
Indices: 39601815--39601854 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39601805 CAACTAGAGG
* * *
39601815 AACCAGAATCCTCGCCGGAGC
1 AACCACAACCCTCACCGGAGC
39601836 AACCACAACCCTCACCGGA
1 AACCACAACCCTCACCGGA
39601855 AGCTGGACAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.42, G:0.17, T:0.07
Consensus pattern (21 bp):
AACCACAACCCTCACCGGAGC
Found at i:39605595 original size:127 final size:127
Alignment explanation
Indices: 39605189--39605604 Score: 701
Period size: 126 Copynumber: 3.3 Consensus size: 127
39605179 GGCCAAACAG
* *
39605189 GAGCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTTTACTGACAAAGCATC
1 GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
** *
39605254 CTGCTTAAAGCG-TTTTTGACACTATTTGCTCAGAAATATCTACTCGATATTATTTTTTCAA
66 CTGCTTAAAGCGTTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAA
*
39605315 GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGTTTCTTTCAGTACTTTTGCTGACAAAGCATC
1 GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
*
39605380 CTGCTTAAAGCGTTTTTT-ACACTATTTACTCAGAAACGTCTACTCGAAATTATTTTTTCAA
66 CTGCTTAAAGCGTTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAA
*
39605441 GAGCTACTGTAGCAAAAGCACGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
1 GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
* **
39605506 CTGCTTAAAGCGTTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTCTG
66 CTGCTTAAAGCGTTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAA
* *
39605568 GAGTTACTGTAGCAAAAGCGCGTCCACGTGAGAGCTT
1 GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTT
39605605 TTTTAAATTA
Statistics
Matches: 272, Mismatches: 16, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
126 194 0.71
127 78 0.29
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (127 bp):
GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
CTGCTTAAAGCGTTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAA
Found at i:39608361 original size:30 final size:31
Alignment explanation
Indices: 39608306--39608373 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
39608296 ACCCTTAAAA
** * **
39608306 TATTTACACTATTGGTCCTTCAAATTTTTTG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
39608337 TATTTACACT-TTAATCCCTCAAATTTTGAG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
39608367 TATTTAC
1 TATTTAC
39608374 TCTTGGGCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (31 bp):
TATTTACACTATTAATCCCTCAAATTTTGAG
Found at i:39609495 original size:2 final size:2
Alignment explanation
Indices: 39609482--39609538 Score: 91
Period size: 2 Copynumber: 29.0 Consensus size: 2
39609472 ATTTTTTTTA
39609482 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39609522 AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT -AT AT
39609539 CTTTCCAAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.04
2 48 0.92
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39621512 original size:9 final size:9
Alignment explanation
Indices: 39621498--39621531 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
39621488 GAGATTTAGG
39621498 TAATGAAAA
1 TAATGAAAA
39621507 TAATGAAAA
1 TAATGAAAA
39621516 TAATGAAAA
1 TAATGAAAA
39621525 TAA-GAAA
1 TAATGAAA
39621532 TCTCGATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.16
9 21 0.84
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.21
Consensus pattern (9 bp):
TAATGAAAA
Found at i:39625750 original size:17 final size:18
Alignment explanation
Indices: 39625728--39625775 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
39625718 AAAATTGTAA
39625728 AAATATATAAAAGAAT-T
1 AAATATATAAAAGAATAT
* * *
39625745 AAATATTTATAATGTATAT
1 AAATATATA-AAAGAATAT
39625764 AAATATATAAAA
1 AAATATATAAAA
39625776 CAACTAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 8 0.33
18 7 0.29
19 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
AAATATATAAAAGAATAT
Found at i:39625774 original size:36 final size:36
Alignment explanation
Indices: 39625688--39625775 Score: 96
Period size: 35 Copynumber: 2.5 Consensus size: 36
39625678 TGATATATAA
39625688 TATATAAATCA-ATAAAAAATTTTAAAATTTAAAATTG
1 TATATAAAT-ATATAAAAAA-TTTAAAATTTAAAATTG
*
39625725 TA-A-AAATATATAAAAGAA-TTAAATATTTATAA-TG
1 TATATAAATATATAAAA-AATTTAAA-ATTTAAAATTG
39625759 TATATAAATATATAAAA
1 TATATAAATATATAAAA
39625776 CAACTAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
34 10 0.22
35 18 0.40
36 15 0.33
37 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (36 bp):
TATATAAATATATAAAAAATTTAAAATTTAAAATTG
Found at i:39626542 original size:18 final size:20
Alignment explanation
Indices: 39626500--39626542 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
39626490 GAGACAAATA
39626500 TAAAACTAAACACACCATAC
1 TAAAACTAAACACACCATAC
* *
39626520 TAAAAGTAAATAC-CCAT-C
1 TAAAACTAAACACACCATAC
39626538 TAAAA
1 TAAAA
39626543 ATCCTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 4 0.19
20 11 0.52
ACGTcount: A:0.56, C:0.23, G:0.02, T:0.19
Consensus pattern (20 bp):
TAAAACTAAACACACCATAC
Found at i:39627467 original size:31 final size:31
Alignment explanation
Indices: 39627409--39627469 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
39627399 TTTTTTAGTT
* * *
39627409 AAATTTGACTCTTAACCTTTTTAAAAGAGTC
1 AAATTTGACTATCAACCATTTTAAAAGAGTC
39627440 AAATTTGACTATCAA-CATTTTAGAAAGAGT
1 AAATTTGACTATCAACCATTTTA-AAAGAGT
39627470 TGAATTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.36
Consensus pattern (31 bp):
AAATTTGACTATCAACCATTTTAAAAGAGTC
Found at i:39631051 original size:12 final size:12
Alignment explanation
Indices: 39631034--39631076 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
39631024 GAACAAGCTT
39631034 GTTTATTGGCTC
1 GTTTATTGGCTC
**
39631046 GTTTATAAGCTC
1 GTTTATTGGCTC
* *
39631058 GCTTATTGACTC
1 GTTTATTGGCTC
39631070 GTTTATT
1 GTTTATT
39631077 TATTAATAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49
Consensus pattern (12 bp):
GTTTATTGGCTC
Found at i:39631220 original size:23 final size:23
Alignment explanation
Indices: 39631193--39631252 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
39631183 TCATATGTTT
*
39631193 ATGAATATGTTCGTTTAATGTT-C
1 ATGAATATGTTCGTTTAA-GTTAA
* * *
39631216 GTGAACATGTTCGATTAAGTTAA
1 ATGAATATGTTCGTTTAAGTTAA
39631239 ATGAATATGTTCGT
1 ATGAATATGTTCGT
39631253 GAACATAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
22 3 0.10
23 26 0.90
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (23 bp):
ATGAATATGTTCGTTTAAGTTAA
Found at i:39635152 original size:15 final size:15
Alignment explanation
Indices: 39635132--39635163 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39635122 GGGTTTCAGA
*
39635132 TCTTCATCTTTATCT
1 TCTTCATCTTCATCT
39635147 TCTTCATCTTCATCT
1 TCTTCATCTTCATCT
39635162 TC
1 TC
39635164 AGCTCGAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.31, G:0.00, T:0.56
Consensus pattern (15 bp):
TCTTCATCTTCATCT
Found at i:39640184 original size:23 final size:24
Alignment explanation
Indices: 39640142--39640186 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
39640132 AAGACTGGAC
**
39640142 TTTCCATGTTTGTTTCCAATGAGA
1 TTTCCATGTTTGTTAACAATGAGA
39640166 TTTCC-TGTTTGTTAACAATGA
1 TTTCCATGTTTGTTAACAATGA
39640187 TTTCCTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (24 bp):
TTTCCATGTTTGTTAACAATGAGA
Found at i:39643215 original size:15 final size:15
Alignment explanation
Indices: 39643195--39643224 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39643185 AACTAATAGC
*
39643195 ATCATCTTGATCATG
1 ATCATCTTCATCATG
39643210 ATCATCTTCATCATG
1 ATCATCTTCATCATG
39643225 GAACATAGCA
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:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (15 bp):
ATCATCTTCATCATG
Found at i:39656489 original size:17 final size:17
Alignment explanation
Indices: 39656454--39656492 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
39656444 TTGGACTTGG
*
39656454 ATTTAATACAAAATCTA
1 ATTTAATACAAAATATA
39656471 ATTTAATA-AAAATAATA
1 ATTTAATACAAAAT-ATA
39656488 ATTTA
1 ATTTA
39656493 TTAAGATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTTAATACAAAATATA
Found at i:39660698 original size:22 final size:22
Alignment explanation
Indices: 39660654--39660698 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39660644 ATAGTAAAAA
* *
39660654 TTATATATTTGTAATTCATATT
1 TTATATATTTATAATTCAAATT
39660676 TTATATATTTTATAATT-AAATT
1 TTATATA-TTTATAATTCAAATT
39660698 T
1 T
39660699 AAATTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATATATTTATAATTCAAATT
Found at i:39662207 original size:3 final size:3
Alignment explanation
Indices: 39662199--39662224 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39662189 TTCGGAATTT
39662199 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
39662225 TGAGTCGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:39667401 original size:28 final size:28
Alignment explanation
Indices: 39667337--39667401 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
39667327 ATTAACCTAT
39667337 AATATATATAACTAAGTCCAAAAAGGAA
1 AATATATATAACTAAGTCCAAAAAGGAA
* *
39667365 AATCA-ATATAGAC-AAGTTCAAAAAGTAA
1 AAT-ATATATA-ACTAAGTCCAAAAAGGAA
39667393 AATATATAT
1 AATATATAT
39667402 TAGTTTTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 1 0.03
28 28 0.88
29 3 0.09
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.25
Consensus pattern (28 bp):
AATATATATAACTAAGTCCAAAAAGGAA
Found at i:39684498 original size:2 final size:2
Alignment explanation
Indices: 39684491--39684530 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
39684481 ATTGTAACTT
39684491 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
39684531 GTTCTCTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39686016 original size:125 final size:125
Alignment explanation
Indices: 39685800--39686083 Score: 410
Period size: 125 Copynumber: 2.3 Consensus size: 125
39685790 ATTTTTGCAG
* * * **
39685800 TCGCGCCCACGTGTACGTGCTTTTGCTACAGTAGGTCCTGGAAAAATAATTTTGAGTTGGCGTTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAAATAATTTCGAGTTGAAGTTT
* *
39685865 CTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAA
66 CTGAGCAAATAGTATAAAAAACGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
** *
39685925 TCGCGTCCTTC-TGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGAAGT
1 TCGCG-CCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAA-AAATAATTTCGAGTTGAAGT
* * * *
39685989 TTCTGAGCAAATAGTATAAAATA-GCTTCTACCATGATGCTTTATGAGAAGAATTTGTGAAA
64 TTCTGAGCAAATAGTATAAAAAACGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
39686050 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
39686084 TATGTTTGGG
Statistics
Matches: 139, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
124 3 0.02
125 94 0.68
126 42 0.30
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (125 bp):
TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAAATAATTTCGAGTTGAAGTTT
CTGAGCAAATAGTATAAAAAACGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
Found at i:39689288 original size:22 final size:21
Alignment explanation
Indices: 39689263--39690516 Score: 393
Period size: 22 Copynumber: 59.4 Consensus size: 21
39689253 AAGTTAAGGA
39689263 TTTAGGGTTTAGTGTTTTTAAG
1 TTTAGGGTTTAG-GTTTTTAAG
* *
39689285 TTTATGGTTTATGATTTTT-AG
1 TTTAGGGTTTA-GGTTTTTAAG
* *
39689306 GTTAGGGTTTGTGGTTTTTAAG
1 TTTAGGGTTT-AGGTTTTTAAG
* *
39689328 TTTAGGGTATAAGG-TTTTAGG
1 TTTAGGGT-TTAGGTTTTTAAG
39689349 TTTAGGGTTT-GGTATTTTAAG
1 TTTAGGGTTTAGGT-TTTTAAG
* * *
39689370 TTAAAGG-TTAGGGTTTTTAGG
1 TTTAGGGTTTA-GGTTTTTAAG
* *
39689391 TTTAGGGTTTAGG-GTTTAGGG
1 TTTAGGGTTTAGGTTTTTA-AG
* *
39689412 TTTTTA-AGTTTAAGG-TTTAAAG
1 --TTTAGGGTTT-AGGTTTTTAAG
39689434 TTTTTA-GGTTTAGAGTTTTTAAG
1 --TTTAGGGTTTAG-GTTTTTAAG
*
39689457 TTTAGGGTTTAGGGTTTTTAGG
1 TTTAGGGTTTA-GGTTTTTAAG
*
39689479 TTTAAGGTTTAGGGTTTTTAAG
1 TTTAGGGTTTA-GGTTTTTAAG
* * * *
39689501 TTAAGAG-TTAGG--ATTAGG
1 TTTAGGGTTTAGGTTTTTAAG
* * *
39689519 GTTAGGATTTTAAAG---TTAAGG
1 TTTAGG-GTTT-AGGTTTTTAA-G
*
39689540 TTTTAGAGTTTAGGGTTTTTAAG
1 -TTTAGGGTTTA-GGTTTTTAAG
*
39689563 TTTAAGGTTTATGGTTTTTAAG
1 TTTAGGGTTTA-GGTTTTTAAG
* *
39689585 -TTAGAGTTTAGG-GTTTAAGG
1 TTTAGGGTTTAGGTTTTTAA-G
* ** *
39689605 TTTA------AAG-TTAAATG
1 TTTAGGGTTTAGGTTTTTAAG
* * *
39689619 TTTAAGGTTTATGTTTTTTAAC
1 TTTAGGGTTTA-GGTTTTTAAG
* *
39689641 TTTAGGGTTTATGATTTTAAG
1 TTTAGGGTTTAGGTTTTTAAG
* *
39689662 TTTAGGGTTTAGGGTTTTCAGG
1 TTTAGGGTTTA-GGTTTTTAAG
* *
39689684 TTTAAGGTTTGAGGGTTTTAAG
1 TTTAGGGTTT-AGGTTTTTAAG
* * * *
39689706 TTAAGAGTTAAGGTTTTTAGG
1 TTTAGGGTTTAGGTTTTTAAG
* *
39689727 TTTAGGGTTTTAAGATTTTAAG
1 TTTAGGG-TTTAGGTTTTTAAG
* * *
39689749 TTTAGGGTTCAAGGTTCTTAGG
1 TTTAGGGTT-TAGGTTTTTAAG
*
39689771 TTTAGTGTTTAGGGTTTTTAAG
1 TTTAGGGTTTA-GGTTTTTAAG
* *
39689793 TTTAGGGTTTATAGTTTAT-AG
1 TTTAGGGTTTA-GGTTTTTAAG
*
39689814 TTTTAAGGTTTAGGGTTTTTAAG
1 -TTTAGGGTTTA-GGTTTTTAAG
* *
39689837 TTAAGGG-TTAGTATTTTTAA-
1 TTTAGGGTTTAG-GTTTTTAAG
*
39689857 TTTAAGGG-CTAGGGTTTTTAAG
1 TTT-AGGGTTTA-GGTTTTTAAG
* *
39689879 TTAAGGG-TTAGG--GTTAGAG
1 TTTAGGGTTTAGGTTTTTA-AG
** *
39689898 TTGTAAAGTTAAGG-TTTTAGAG
1 TT-TAGGGTTTAGGTTTTTA-AG
*
39689920 TTTAGGGTTTTAAG---TTAAGGG
1 TTTAGGG-TTTAGGTTTTTAA--G
* *
39689941 TTTAGGGTTTAGGGTTTAAAG
1 TTTAGGGTTTAGGTTTTTAAG
* * *
39689962 TTTTATGATTTAAGGTTTTTAGG
1 -TTTAGGGTTT-AGGTTTTTAAG
* *
39689985 TTTAGTGTTTGTGGTTTTTAAG
1 TTTAGGGTTT-AGGTTTTTAAG
* * *
39690007 TTTAAGGTTTGGGGTTTTTAGG
1 TTTAGGGTTT-AGGTTTTTAAG
*
39690029 TTTAAGGTTTAGAGTTTTTAAG
1 TTTAGGGTTTAG-GTTTTTAAG
* *
39690051 TTAAGGG-TTAGGGTTTTTAGG
1 TTTAGGGTTTA-GGTTTTTAAG
* *
39690072 TTTGGGGTTTGGGGTTTTTAAG
1 TTTAGGGTTT-AGGTTTTTAAG
39690094 TTTAGGGTTTAAGGTTTTT-AG
1 TTTAGGGTTT-AGGTTTTTAAG
* * * *
39690115 ATTTAGAGATTGGGGTTTTAAG
1 -TTTAGGGTTTAGGTTTTTAAG
* * *
39690137 TTTAGTGTTTGGGGTTTTTAGG
1 TTTAGGGTTT-AGGTTTTTAAG
*
39690159 TTTAAGGTTTAGGGTTTTTAAG
1 TTTAGGGTTTA-GGTTTTTAAG
* ** *
39690181 TCTAAGTTTTTAGG--TTTAGGG
1 T-TTAGGGTTTAGGTTTTTA-AG
39690202 TTT-GGG---A--TTTTTAAG
1 TTTAGGGTTTAGGTTTTTAAG
* * * *
39690217 TTAAGGG-TTAAG--ATTAGG
1 TTTAGGGTTTAGGTTTTTAAG
* * *
39690235 GTTAGGATTTAAAG---TTAAGG
1 TTTAGGGTTT-AGGTTTTTAA-G
*
39690255 TTTTAGGGTTTATGATTTTTAAG
1 -TTTAGGGTTTA-GGTTTTTAAG
*
39690278 TTTAGGGCTTATA-GTTTTTAGG
1 TTTAGGG-TT-TAGGTTTTTAAG
39690300 TTTAGGGTTTTAAGG--TTT-AG
1 TTTAGGG-TTT-AGGTTTTTAAG
*
39690320 TGTT----TAT-GGTTTTTAAG
1 T-TTAGGGTTTAGGTTTTTAAG
*
39690337 TTTAGGGTTTAGGGTTTTTAGG
1 TTTAGGGTTTA-GGTTTTTAAG
** * *
39690359 TTTATAGTTTGGGGTTTTAAG
1 TTTAGGGTTTAGGTTTTTAAG
* ** *
39690380 TTAATAG-TTAGGGTTTTTAGG
1 TTTAGGGTTTA-GGTTTTTAAG
*
39690401 TTTGGGGTTT-GGTGTTTTAAG
1 TTTAGGGTTTAGGT-TTTTAAG
* * *
39690422 TTTAGAGTCTAAGGTTTTTAGG
1 TTTAGGGT-TTAGGTTTTTAAG
*
39690444 TTTAGGGTTTGAGGTTTTAAAG
1 TTTAGGGTTT-AGGTTTTTAAG
** *
39690466 TTTAACG-TTAGTGTTTTTAGG
1 TTTAGGGTTTAG-GTTTTTAAG
*
39690487 TTTAGGG-TTAGTGTTTTTAAA
1 TTTAGGGTTTAG-GTTTTTAAG
*
39690508 TTAAGGGTT
1 TTTAGGGTT
39690517 AGGATTAGGG
Statistics
Matches: 908, Mismatches: 218, Indels: 212
0.68 0.16 0.16
Matches are distributed among these distances:
14 7 0.01
15 7 0.01
16 15 0.02
17 3 0.00
18 19 0.02
19 18 0.02
20 55 0.06
21 283 0.31
22 444 0.49
23 47 0.05
24 10 0.01
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.48
Consensus pattern (21 bp):
TTTAGGGTTTAGGTTTTTAAG
Found at i:39689314 original size:21 final size:21
Alignment explanation
Indices: 39689264--39689358 Score: 77
Period size: 21 Copynumber: 4.4 Consensus size: 21
39689254 AGTTAAGGAT
*
39689264 TTAGGGTTTAGTGTTTTTAAGT
1 TTAGGGTTTA-TGTTTTTAAGG
*
39689286 TTATGGTTTATGATTTTT-AGG
1 TTAGGGTTTATG-TTTTTAAGG
* *
39689307 TTAGGGTTTGTGGTTTTTAAGT
1 TTAGGGTTTAT-GTTTTTAAGG
* * *
39689329 TTAGGGTATAAGGTTTT-AGG
1 TTAGGGTTTATGTTTTTAAGG
39689349 TTTAGGGTTT
1 -TTAGGGTTT
39689359 GGTATTTTAA
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.03
21 31 0.53
22 25 0.43
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (21 bp):
TTAGGGTTTATGTTTTTAAGG
Found at i:39689429 original size:7 final size:7
Alignment explanation
Indices: 39689388--39689831 Score: 77
Period size: 7 Copynumber: 61.9 Consensus size: 7
39689378 TAGGGTTTTT
39689388 AGGTTTA
1 AGGTTTA
*
39689395 GGGTTTA
1 AGGTTTA
*
39689402 GGGTTTA
1 AGGTTTA
*
39689409 GGGTTTTTA
1 AGG--TTTA
39689418 A-GTTTA
1 AGGTTTA
39689424 AGGTTTAA
1 AGGTTT-A
* *
39689432 AGTTTTT
1 AGGTTTA
39689439 AGGTTTA
1 AGGTTTA
*
39689446 GAGTTTTTA
1 -AG-GTTTA
39689455 A-GTTTA
1 AGGTTTA
*
39689461 GGGTTTA
1 AGGTTTA
* *
39689468 GGGTTTTT
1 AGG-TTTA
39689476 AGGTTTA
1 AGGTTTA
39689483 AGGTTTA
1 AGGTTTA
*
39689490 GGGTTTTTA
1 AGG--TTTA
39689499 A-G-TTA
1 AGGTTTA
39689504 AGAG-TT-
1 AG-GTTTA
*
39689510 AGGATT-
1 AGGTTTA
*
39689516 AGGGTT-
1 AGGTTTA
39689522 AGGATTTTA
1 AGG--TTTA
*
39689531 AAG-TTA
1 AGGTTTA
*
39689537 AGGTTTT
1 AGGTTTA
39689544 AGAGTTTA
1 AG-GTTTA
*
39689552 GGGTTTTTA
1 AGG--TTTA
39689561 A-GTTTA
1 AGGTTTA
39689567 AGGTTTA
1 AGGTTTA
*
39689574 TGGTTTTTA
1 AGG--TTTA
39689583 A-G-TT-
1 AGGTTTA
39689587 AGAGTTTA
1 AG-GTTTA
*
39689595 GGGTTTA
1 AGGTTTA
39689602 AGGTTTA
1 AGGTTTA
* *
39689609 AAGTTAA
1 AGGTTTA
*
39689616 ATGTTTA
1 AGGTTTA
39689623 AGGTTTA
1 AGGTTTA
* *
39689630 TGTTTTTTA
1 AG--GTTTA
*
39689639 A-CTTTA
1 AGGTTTA
*
39689645 GGGTTTA
1 AGGTTTA
* *
39689652 TGATTTTA
1 AG-GTTTA
39689660 A-GTTTA
1 AGGTTTA
*
39689666 GGGTTTA
1 AGGTTTA
* *
39689673 GGGTTTTC
1 AGG-TTTA
39689681 AGGTTTA
1 AGGTTTA
39689688 AGGTTTGA
1 AGGTTT-A
*
39689696 GGGTTTTA
1 AGG-TTTA
39689704 A-G-TTA
1 AGGTTTA
39689709 AGAG-TTA
1 AG-GTTTA
*
39689716 AGGTTTTT
1 AGG-TTTA
39689724 AGGTTTA
1 AGGTTTA
*
39689731 GGGTTTTA
1 AGG-TTTA
*
39689739 AGATTTTA
1 AG-GTTTA
39689747 A-GTTTA
1 AGGTTTA
* *
39689753 GGGTTCA
1 AGGTTTA
*
39689760 AGGTTCTT
1 AGGTT-TA
39689768 AGGTTT-
1 AGGTTTA
39689774 AGTGTTTA
1 AG-GTTTA
*
39689782 GGGTTTTTA
1 AGG--TTTA
39689791 A-GTTTA
1 AGGTTTA
*
39689797 GGGTTTA
1 AGGTTTA
39689804 TA-GTTTA
1 -AGGTTTA
*
39689811 TAGTTTTA
1 -AGGTTTA
39689819 AGGTTTA
1 AGGTTTA
*
39689826 GGGTTT
1 AGGTTT
39689832 TTAAGTTAAG
Statistics
Matches: 322, Mismatches: 65, Indels: 100
0.66 0.13 0.21
Matches are distributed among these distances:
4 1 0.00
5 11 0.03
6 51 0.16
7 161 0.50
8 65 0.20
9 33 0.10
ACGTcount: A:0.23, C:0.01, G:0.28, T:0.48
Consensus pattern (7 bp):
AGGTTTA
Found at i:39689446 original size:37 final size:37
Alignment explanation
Indices: 39689398--39689488 Score: 128
Period size: 37 Copynumber: 2.4 Consensus size: 37
39689388 AGGTTTAGGG
39689398 TTTAGGGTTTAGGGTTTTTAAGTTTAAGGTTTAAAGTT
1 TTTA-GGTTTAGGGTTTTTAAGTTTAAGGTTTAAAGTT
* * **
39689436 TTTAGGTTTAGAGTTTTTAAGTTTAGGGTTTAGGGTT
1 TTTAGGTTTAGGGTTTTTAAGTTTAAGGTTTAAAGTT
*
39689473 TTTAGGTTTAAGGTTT
1 TTTAGGTTTAGGGTTT
39689489 AGGGTTTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 43 0.91
38 4 0.09
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (37 bp):
TTTAGGTTTAGGGTTTTTAAGTTTAAGGTTTAAAGTT
Found at i:39689482 original size:15 final size:15
Alignment explanation
Indices: 39689377--39689466 Score: 67
Period size: 15 Copynumber: 5.6 Consensus size: 15
39689367 AAGTTAAAGG
39689377 TTAGGGTTTTTAGGT
1 TTAGGGTTTTTAGGT
39689392 TTAGGG--TTTAGGGT
1 TTAGGGTTTTTA-GGT
*
39689406 TTAGGGTTTTTAAGT
1 TTAGGGTTTTTAGGT
39689421 TTAAGGTTTAAAGTTTTTAGGT
1 TT-AGG------GTTTTTAGGT
* *
39689443 TTAGAGTTTTTAAGT
1 TTAGGGTTTTTAGGT
39689458 TTAGGGTTT
1 TTAGGGTTT
39689467 AGGGTTTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
13 4 0.07
14 9 0.15
15 27 0.45
16 7 0.12
21 2 0.03
22 11 0.18
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (15 bp):
TTAGGGTTTTTAGGT
Found at i:39689487 original size:15 final size:15
Alignment explanation
Indices: 39689381--39689488 Score: 55
Period size: 15 Copynumber: 7.3 Consensus size: 15
39689371 TAAAGGTTAG
39689381 GGTTTTTAGGTTT-A
1 GGTTTTTAGGTTTAA
* *
39689395 GG-GTTTAGGGTTTAG
1 GGTTTTTA-GGTTTAA
*
39689410 GGTTTTTAAGTTTAA
1 GGTTTTTAGGTTTAA
** * *
39689425 GGTTTAAAGTTTTTA
1 GGTTTTTAGGTTTAA
** *
39689440 GGTTTAGAGTTTTTAA
1 GGTTTTTAG-GTTTAA
*
39689456 -G--TTTAGGGTTTAG
1 GGTTTTTA-GGTTTAA
39689469 GGTTTTTAGGTTTAA
1 GGTTTTTAGGTTTAA
39689484 GGTTT
1 GGTTT
39689489 AGGGTTTTTA
Statistics
Matches: 69, Mismatches: 17, Indels: 15
0.68 0.17 0.15
Matches are distributed among these distances:
13 10 0.14
14 9 0.13
15 37 0.54
16 13 0.19
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (15 bp):
GGTTTTTAGGTTTAA
Found at i:39689543 original size:14 final size:15
Alignment explanation
Indices: 39689526--39689572 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
39689516 AGGGTTAGGA
39689526 TTTTAAAG-TTAAGG
1 TTTTAAAGTTTAAGG
* *
39689540 TTTTAGAGTTTAGGG
1 TTTTAAAGTTTAAGG
*
39689555 TTTTTAAGTTTAAGG
1 TTTTAAAGTTTAAGG
39689570 TTT
1 TTT
39689573 ATGGTTTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 7 0.26
15 20 0.74
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
TTTTAAAGTTTAAGG
Found at i:39689599 original size:28 final size:26
Alignment explanation
Indices: 39689561--39689678 Score: 91
Period size: 28 Copynumber: 4.5 Consensus size: 26
39689551 AGGGTTTTTA
*
39689561 AGTTTAAGGTTTATGGTTTTTAAGTTAG
1 AGTTTAGGGTTTAT-G-TTTTAAGTTAG
* * *
39689589 AGTTTAGGGTTTAAGGTTTAAAGTTAA
1 AGTTTAGGGTTT-ATGTTTTAAGTTAG
*
39689616 ATGTTTAAGGTTTATGTTTT---TTA-
1 A-GTTTAGGGTTTATGTTTTAAGTTAG
*
39689639 ACTTTAGGGTTTATGATTTTAAGTTTAG
1 AGTTTAGGGTTTATG-TTTTAAG-TTAG
*
39689667 GGTTTAGGGTTT
1 AGTTTAGGGTTT
39689679 TCAGGTTTAA
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
22 12 0.17
23 5 0.07
24 3 0.04
27 18 0.25
28 32 0.45
29 1 0.01
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.50
Consensus pattern (26 bp):
AGTTTAGGGTTTATGTTTTAAGTTAG
Found at i:39689616 original size:84 final size:85
Alignment explanation
Indices: 39689457--39689628 Score: 217
Period size: 84 Copynumber: 2.0 Consensus size: 85
39689447 AGTTTTTAAG
* *
39689457 TTTAGGGTTTAGGGTTTTTAGGTTTAAGGTTTAGGGTTTTTAAGTTAAGAGTTAGGATTAGGGTT
1 TTTAGAGTTTAGGGTTTTTAAGTTTAAGGTTTAGGGTTTTTAAGTTAAGAGTTAGGATTAGGGTT
**
39689522 AGGATTTTAAA-G-TTAAGGT
66 A-GAAGTTAAATGTTTAAGGT
* *
39689541 TTTAGAGTTTAGGGTTTTTAAGTTTAAGGTTTATGGTTTTTAAGTT-AGAGTTTAGGGTTTAAGG
1 TTTAGAGTTTAGGGTTTTTAAGTTTAAGGTTTAGGGTTTTTAAGTTAAGAG-TTA-GGATT-AGG
*
39689605 TTTA-AAGTTAAATGTTTAAGGT
63 GTTAGAAGTTAAATGTTTAAGGT
39689627 TT
1 TT
39689629 ATGTTTTTTA
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
83 4 0.05
84 52 0.68
85 5 0.07
86 15 0.20
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.47
Consensus pattern (85 bp):
TTTAGAGTTTAGGGTTTTTAAGTTTAAGGTTTAGGGTTTTTAAGTTAAGAGTTAGGATTAGGGTT
AGAAGTTAAATGTTTAAGGT
Found at i:39689629 original size:78 final size:79
Alignment explanation
Indices: 39689527--39689688 Score: 204
Period size: 78 Copynumber: 2.1 Consensus size: 79
39689517 GGGTTAGGAT
* * *
39689527 TTTAAAGTTAAGGTTTTAGAGTTTAGGGTTTTTAAGTTTAAGGTTTATGGTTTTTAAG-TTAGAG
1 TTTAAAGTTAAGGTTTAAGAGTTTAGGGTTTTTAACTTTAAGGTTTAT-GATTTTAAGTTTAGAG
39689591 TTTAGGG-TTTAAGG
65 TTTAGGGTTTTAAGG
* * * * *
39689605 TTTAAAGTTAAATGTTTAAG-GTTTATGTTTTTTAACTTTAGGGTTTATGATTTTAAGTTTAGGG
1 TTTAAAGTT-AAGGTTTAAGAGTTTAGGGTTTTTAACTTTAAGGTTTATGATTTTAAGTTTAGAG
*
39689669 TTTAGGGTTTTCAGG
65 TTTAGGGTTTTAAGG
39689684 TTTAA
1 TTTAA
39689689 GGTTTGAGGG
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
77 8 0.11
78 45 0.62
79 19 0.26
ACGTcount: A:0.25, C:0.01, G:0.24, T:0.49
Consensus pattern (79 bp):
TTTAAAGTTAAGGTTTAAGAGTTTAGGGTTTTTAACTTTAAGGTTTATGATTTTAAGTTTAGAGT
TTAGGGTTTTAAGG
Found at i:39689700 original size:15 final size:14
Alignment explanation
Indices: 39689656--39689831 Score: 66
Period size: 15 Copynumber: 12.2 Consensus size: 14
39689646 GGTTTATGAT
39689656 TTTAA-GTTTAGGG
1 TTTAAGGTTTAGGG
*
39689669 TTTAGGGTTTTCA-GG
1 TTTAAGG-TTT-AGGG
39689684 TTTAAGGTTTGAGGG
1 TTTAAGGTTT-AGGG
* *
39689699 TTTTAA-GTTAAGAG
1 -TTTAAGGTTTAGGG
39689713 -TTAAGGTTTTTA-GG
1 TTTAAGG--TTTAGGG
* **
39689727 TTTAGGGTTTTAAGAT
1 TTTAAGG-TTT-AGGG
39689743 TTTAA-GTTTAGGG
1 TTTAAGGTTTAGGG
*
39689756 TTCAAGGTTCTTA-GG
1 TTTAAGG-T-TTAGGG
39689771 TTT-AGTGTTTAGGG
1 TTTAAG-GTTTAGGG
39689785 TTTTTAA-GTTTAGGG
1 --TTTAAGGTTTAGGG
* *
39689800 TTTATA-GTTTATAGT
1 TTTA-AGGTTTA-GGG
39689815 TTTAAGGTTTAGGG
1 TTTAAGGTTTAGGG
39689829 TTT
1 TTT
39689832 TTAAGTTAAG
Statistics
Matches: 122, Mismatches: 19, Indels: 43
0.66 0.10 0.23
Matches are distributed among these distances:
12 4 0.03
13 18 0.15
14 33 0.27
15 50 0.41
16 16 0.13
17 1 0.01
ACGTcount: A:0.22, C:0.02, G:0.28, T:0.48
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:39689810 original size:14 final size:15
Alignment explanation
Indices: 39689777--39689845 Score: 70
Period size: 15 Copynumber: 4.7 Consensus size: 15
39689767 TAGGTTTAGT
*
39689777 GTTTAGGGTTTTTAA
1 GTTTAGGGTTTATAA
39689792 GTTTAGGGTTTAT-A
1 GTTTAGGGTTTATAA
**
39689806 GTTTATAGTTT-TAA
1 GTTTAGGGTTTATAA
*
39689820 GGTTTAGGGTTTTTAA
1 -GTTTAGGGTTTATAA
*
39689836 GTTAAGGGTT
1 GTTTAGGGTT
39689846 AGTATTTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
13 1 0.02
14 11 0.24
15 30 0.67
16 3 0.07
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.51
Consensus pattern (15 bp):
GTTTAGGGTTTATAA
Found at i:39689921 original size:14 final size:14
Alignment explanation
Indices: 39689904--39689945 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
39689894 AGAGTTGTAA
39689904 AGTTAAGGTTTTAG
1 AGTTAAGGTTTTAG
*
39689918 AGTTTAGGGTTTTA-
1 AG-TTAAGGTTTTAG
*
39689932 AGTTAAGGGTTTAG
1 AGTTAAGGTTTTAG
39689946 GGTTTAGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 9 0.39
14 4 0.17
15 10 0.43
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (14 bp):
AGTTAAGGTTTTAG
Found at i:39689935 original size:28 final size:26
Alignment explanation
Indices: 39689866--39689963 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 26
39689856 ATTTAAGGGC
* * *
39689866 TAGGGTTTTTAAGTTAAGGGTTAGGGT
1 TAGGG-TTTAAAGTTAAGGTTTAGGTT
*
39689893 TAGAGTTGTAAAGTTAAGGTTTTAGAGTT
1 TAGGGTT-TAAAGTTAAGG-TTTAG-GTT
*
39689922 TAGGGTTTTAAGTTAAGGGTTTAGGGTT
1 TAGGGTTTAAAGTTAA-GGTTTA-GGTT
39689950 TAGGGTTTAAAGTT
1 TAGGGTTTAAAGTT
39689964 TTATGATTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
26 2 0.03
27 14 0.24
28 32 0.54
29 11 0.19
ACGTcount: A:0.26, C:0.00, G:0.33, T:0.42
Consensus pattern (26 bp):
TAGGGTTTAAAGTTAAGGTTTAGGTT
Found at i:39689954 original size:14 final size:14
Alignment explanation
Indices: 39689913--39689964 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
39689903 AAGTTAAGGT
39689913 TTTAGAGTTTAGGG
1 TTTAGAGTTTAGGG
*
39689927 TTTTA-AGTTAAGGG
1 -TTTAGAGTTTAGGG
*
39689941 TTTAGGGTTTAGGG
1 TTTAGAGTTTAGGG
*
39689955 TTTAAAGTTT
1 TTTAGAGTTT
39689965 TATGATTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 4 0.13
14 23 0.74
15 4 0.13
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (14 bp):
TTTAGAGTTTAGGG
Found at i:39690190 original size:36 final size:35
Alignment explanation
Indices: 39690150--39690221 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 35
39690140 AGTGTTTGGG
39690150 GTTTTTAGGTTTAAGGTTTAGGG-TTTTTAAGTCTAA
1 GTTTTTAGGTTTAAGGTTT-GGGATTTTTAAGT-TAA
*
39690186 GTTTTTAGGTTTAGGGTTTGGGATTTTTAAGTTAA
1 GTTTTTAGGTTTAAGGTTTGGGATTTTTAAGTTAA
39690221 G
1 G
39690222 GGTTAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 7 0.21
36 27 0.79
ACGTcount: A:0.21, C:0.01, G:0.28, T:0.50
Consensus pattern (35 bp):
GTTTTTAGGTTTAAGGTTTGGGATTTTTAAGTTAA
Found at i:39690196 original size:87 final size:85
Alignment explanation
Indices: 39689655--39690197 Score: 274
Period size: 87 Copynumber: 6.3 Consensus size: 85
39689645 GGGTTTATGA
* * * * * * *
39689655 TTTTAAGTTTAGGGTTTAGGGTTTTCAGGTTTAAGG-TTTGAGGGTTTTAAGTTAAGAGTTAAGG
1 TTTTAAGTTTAAGGTTTAAGGTTTTTAGATTTAAGGATTAGA-GGTTTTAAGTTAAGGGTTAGGG
** *
39689719 TTTTTAGGTTTAGGGTTTTAAGA
65 TTTTTAGGTTTA-GG-TTTGGGT
* * * * * * *
39689742 TTTTAAGTTTAGGGTTCAAGGTTCTTAGGTTT-AGTGTTTAG-GGTTTTTAAGTTTAGGGTTTAT
1 TTTTAAGTTTAAGGTTTAAGGTTTTTAGATTTAAG-GATTAGAGG-TTTTAAGTTAAGGG-TTAG
* * *
39689805 AGTTTATAGTTTTAAGGTTTAGGGT
63 GGTTTTTAGGTTT-AGGTTT-GGGT
* * **
39689830 TTTTAAG-TTAAGGGTT-AGTATTTTTA-ATTTAAGGGCTAG-GGTTTTTAAGTTAAGGGTTAGG
1 TTTTAAGTTTAAGGTTTAAG-GTTTTTAGATTTAAGGATTAGAGG-TTTTAAGTTAAGGGTTAGG
* **
39689891 G---TTAGAGTTGTAAAGTTAAGG-
64 GTTTTTAG-GTT-T-AGGTTTGGGT
* * * * * * * **
39689912 TTTTAGAGTTTAGGGTTTTAA-G--TTAAGGGTTTAGGGTTTAG-GGTTTAAAGTTTTATGATTT
1 TTTTA-AGTTTAAGG-TTTAAGGTTTTTA-GATTTAAGGATTAGAGGTTTTAAG--TTAAGGGTT
*
39689973 AAGGTTTTTAGGTTTAGTGTTTGTGGT
61 AGGGTTTTTAGGTTTAG-GTTTG-GGT
** * * *
39690000 TTTTAAGTTTAAGGTTTGGGGTTTTTAGGTTTAAGGTTTAGAGTTTTTAAGTTAAGGGTTAGGGT
1 TTTTAAGTTTAAGGTTTAAGGTTTTTAGATTTAAGGATTAGAGGTTTTAAGTTAAGGGTTAGGGT
*
39690065 TTTTAGGTTTGGGGTTTGGGGT
66 TTTTAGGTTT-AGGTTT-GGGT
* * * * *
39690087 TTTTAAGTTTAGGGTTTAAGGTTTTTAGATTT-AGAGATT-GGGGTTTTAAGTTTAGTGTTTGGG
1 TTTTAAGTTTAAGGTTTAAGGTTTTTAGATTTAAG-GATTAGAGGTTTTAAGTTAAG-GGTTAGG
39690150 GTTTTTAGGTTTAAGGTTTAGGGT
64 GTTTTTAGGTTT-AGGTTT-GGGT
* * *
39690174 TTTTAAGTCTAAGTTTTTAGGTTT
1 TTTTAAGTTTAAGGTTTAAGGTTT
39690198 AGGGTTTGGG
Statistics
Matches: 349, Mismatches: 75, Indels: 64
0.72 0.15 0.13
Matches are distributed among these distances:
82 11 0.03
83 12 0.03
84 22 0.06
85 16 0.05
86 52 0.15
87 175 0.50
88 50 0.14
89 11 0.03
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.48
Consensus pattern (85 bp):
TTTTAAGTTTAAGGTTTAAGGTTTTTAGATTTAAGGATTAGAGGTTTTAAGTTAAGGGTTAGGGT
TTTTAGGTTTAGGTTTGGGT
Found at i:39690302 original size:37 final size:37
Alignment explanation
Indices: 39690255--39690346 Score: 96
Period size: 37 Copynumber: 2.5 Consensus size: 37
39690245 AAAGTTAAGG
*
39690255 TTTTAGGGTTTATGATTTTTAA-GTTTAGGGCTTATAGT
1 TTTTA-GGTTTA-GAGTTTTAAGGTTTAGGGCTTATAGT
* * * *
39690293 TTTTAGGTTTAGGGTTTTAAGGTTTAGTGTTTATGGT
1 TTTTAGGTTTAGAGTTTTAAGGTTTAGGGCTTATAGT
* *
39690330 TTTTAAGTTTAGGGTTT
1 TTTTAGGTTTAGAGTTT
39690347 AGGGTTTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
36 7 0.15
37 35 0.74
38 5 0.11
ACGTcount: A:0.18, C:0.01, G:0.26, T:0.54
Consensus pattern (37 bp):
TTTTAGGTTTAGAGTTTTAAGGTTTAGGGCTTATAGT
Found at i:39690315 original size:15 final size:15
Alignment explanation
Indices: 39690291--39690362 Score: 51
Period size: 15 Copynumber: 4.9 Consensus size: 15
39690281 AGGGCTTATA
*
39690291 GTTTTTAGGTTTAGG
1 GTTTTAAGGTTTAGG
*
39690306 GTTTTAAGGTTTAGT
1 GTTTTAAGGTTTAGG
* *
39690321 G-TTTATGGTTTTTA-A
1 GTTTTAAGG--TTTAGG
*
39690336 G-TTTAGGGTTTAGG
1 GTTTTAAGGTTTAGG
*
39690350 GTTTTTAGGTTTA
1 GTTTTAAGGTTTA
39690363 TAGTTTGGGG
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
13 4 0.09
14 7 0.16
15 30 0.67
16 4 0.09
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.54
Consensus pattern (15 bp):
GTTTTAAGGTTTAGG
Found at i:39690377 original size:43 final size:43
Alignment explanation
Indices: 39690294--39690495 Score: 214
Period size: 43 Copynumber: 4.7 Consensus size: 43
39690284 GCTTATAGTT
* * * *
39690294 TTTAG-GTTTAGGGTTTTAAGGTTTAGTGTTTATGGTTTTTAAG
1 TTTAGAGTTTAGGGTTTTTAGGTTTAGGGTTT-GGGGTTTTAAG
* **
39690337 TTTAGGGTTTAGGGTTTTTAGGTTTATAGTTTGGGGTTTTAAG
1 TTTAGAGTTTAGGGTTTTTAGGTTTAGGGTTTGGGGTTTTAAG
* * * *
39690380 TTAATAG-TTAGGGTTTTTAGGTTTGGGGTTTGGTGTTTTAAG
1 TTTAGAGTTTAGGGTTTTTAGGTTTAGGGTTTGGGGTTTTAAG
* * *
39690422 TTTAGAGTCTAAGGTTTTTAGGTTTAGGGTTTGAGGTTTTAAAG
1 TTTAGAGTTTAGGGTTTTTAGGTTTAGGGTTTGGGGTTTT-AAG
*
39690466 TTTA-ACG-TTAGTGTTTTTAGGTTTAGGGTT
1 TTTAGA-GTTTAGGGTTTTTAGGTTTAGGGTT
39690496 AGTGTTTTTA
Statistics
Matches: 133, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
42 36 0.27
43 66 0.50
44 31 0.23
ACGTcount: A:0.18, C:0.01, G:0.30, T:0.50
Consensus pattern (43 bp):
TTTAGAGTTTAGGGTTTTTAGGTTTAGGGTTTGGGGTTTTAAG
Found at i:39690514 original size:21 final size:21
Alignment explanation
Indices: 39690472--39690518 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
39690462 AAAGTTTAAC
** *
39690472 GTTAGTGTTTTTAGGTTTAGG
1 GTTAGTGTTTTTAAATTAAGG
39690493 GTTAGTGTTTTTAAATTAAGG
1 GTTAGTGTTTTTAAATTAAGG
39690514 GTTAG
1 GTTAG
39690519 GATTAGGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (21 bp):
GTTAGTGTTTTTAAATTAAGG
Found at i:39690525 original size:33 final size:33
Alignment explanation
Indices: 39690482--39690544 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
39690472 GTTAGTGTTT
* *
39690482 TTAGGTTTAGGGTTAGTGTTTTTAAA-TTAAGGG
1 TTAGGATTAGGGTTAATG-TTTTAAAGTTAAGGG
39690515 TTAGGATTAGGGTTAATGTTTTAAAGTTAA
1 TTAGGATTAGGGTTAATGTTTTAAAGTTAA
39690545 TGTTTTAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 7 0.26
33 20 0.74
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (33 bp):
TTAGGATTAGGGTTAATGTTTTAAAGTTAAGGG
Found at i:39690573 original size:22 final size:22
Alignment explanation
Indices: 39690548--39690615 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 22
39690538 AAGTTAATGT
*
39690548 TTTAGGGTTTATGGTTTTTAAG
1 TTTAAGGTTTATGGTTTTTAAG
* *
39690570 TTTAAGGTTTATAGTTTTTATG
1 TTTAAGGTTTATGGTTTTTAAG
* **
39690592 TTTAAGATTTGGGGTTTTTAAG
1 TTTAAGGTTTATGGTTTTTAAG
39690614 TT
1 TT
39690616 AATAGTTAGG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.56
Consensus pattern (22 bp):
TTTAAGGTTTATGGTTTTTAAG
Found at i:39690580 original size:29 final size:28
Alignment explanation
Indices: 39690521--39690580 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
39690511 AGGGTTAGGA
*
39690521 TTAGGGTTAATGTTTTAAAGTTAATGTT
1 TTAGGGTTAATGTTTTAAAGTTAATGGT
* *
39690549 TTAGGGTTTATGGTTTTTAAGTTTAA-GGT
1 TTAGGGTTAAT-GTTTTAAAG-TTAATGGT
39690578 TTA
1 TTA
39690581 TAGTTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 10 0.37
29 13 0.48
30 4 0.15
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (28 bp):
TTAGGGTTAATGTTTTAAAGTTAATGGT
Found at i:39690831 original size:21 final size:21
Alignment explanation
Indices: 39690807--39690853 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
39690797 TTGTCCAGGT
* *
39690807 TCCGGCGGCGGTTGTGGTTCC
1 TCCGGCGGAGATTGTGGTTCC
* *
39690828 TCCGGCGGAGATTTTGGTTCT
1 TCCGGCGGAGATTGTGGTTCC
39690849 TCCGG
1 TCCGG
39690854 TAGGACATCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.26, G:0.38, T:0.32
Consensus pattern (21 bp):
TCCGGCGGAGATTGTGGTTCC
Done.