Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 51
Found at i:394875 original size:20 final size:20
Alignment explanation
Indices: 394850--394893 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
394840 GCACTTTGCA
*
394850 AATTTGACTTCTGTGTTACG
1 AATTTGACTTATGTGTTACG
* *
394870 AATTTGTCTTATGTGTTGCG
1 AATTTGACTTATGTGTTACG
394890 AATT
1 AATT
394894 ATAAATTCGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.48
Consensus pattern (20 bp):
AATTTGACTTATGTGTTACG
Found at i:403202 original size:24 final size:24
Alignment explanation
Indices: 403169--403234 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
403159 GCCCTCTGTT
403169 CGAACATAAACAAACGAACATAAA
1 CGAACATAAACAAACGAACATAAA
* **
403193 TGAACATAAATGAACGAACATAAA
1 CGAACATAAACAAACGAACATAAA
403217 CGAACATATAATCAAACG
1 CGAACATA-AA-CAAACG
403235 TTCACGAACA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 28 0.82
25 2 0.06
26 4 0.12
ACGTcount: A:0.58, C:0.18, G:0.11, T:0.14
Consensus pattern (24 bp):
CGAACATAAACAAACGAACATAAA
Found at i:403211 original size:14 final size:14
Alignment explanation
Indices: 403169--403221 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
403159 GCCCTCTGTT
*
403169 CGAACATAAACAAA
1 CGAACATAAACGAA
403183 CGAACAT--A--AA
1 CGAACATAAACGAA
* *
403193 TGAACATAAATGAA
1 CGAACATAAACGAA
403207 CGAACATAAACGAA
1 CGAACATAAACGAA
403221 C
1 C
403222 ATATAATCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 8 0.25
12 2 0.06
14 22 0.69
ACGTcount: A:0.58, C:0.19, G:0.11, T:0.11
Consensus pattern (14 bp):
CGAACATAAACGAA
Found at i:405637 original size:3 final size:3
Alignment explanation
Indices: 405631--405662 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
405621 AAAAATAGTA
405631 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
405663 ATCTAAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:408394 original size:117 final size:117
Alignment explanation
Indices: 408180--408399 Score: 307
Period size: 117 Copynumber: 1.9 Consensus size: 117
408170 AATACTATTT
* * * * * * * * *
408180 CCATCCAATTACTTCGATTACTATAATTTGTATGTTCTTCAGAACCATACACTCACCTGCACACC
1 CCATCCAATCACTCCGATCACCAAAATGTGTAGGTTCCTCAGAACCATACACCCACCTGCACACC
* * *
408245 AGTAAGGACTTACCCTGAGCACAAAGCCAAGGAGCCTGCGGTAATAACTTCC
66 AATAAGAACTTACCCTGAGCACAAAGCAAAGGAGCCTGCGGTAATAACTTCC
408297 CCATCCAATCACTCCGATCACCAAAATGTGTAGGTTCCTCAGAACCATACACCCACCTGCACACC
1 CCATCCAATCACTCCGATCACCAAAATGTGTAGGTTCCTCAGAACCATACACCCACCTGCACACC
*
408362 AATGAGAACTTACCCTGAGCACACAA-CAAAGGAGCCTG
66 AATAAGAACTTACCCTGAGCACA-AAGCAAAGGAGCCTG
408400 AAATACTTCC
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
117 87 0.98
118 2 0.02
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.21
Consensus pattern (117 bp):
CCATCCAATCACTCCGATCACCAAAATGTGTAGGTTCCTCAGAACCATACACCCACCTGCACACC
AATAAGAACTTACCCTGAGCACAAAGCAAAGGAGCCTGCGGTAATAACTTCC
Found at i:409383 original size:27 final size:28
Alignment explanation
Indices: 409345--409454 Score: 93
Period size: 27 Copynumber: 4.0 Consensus size: 28
409335 AATATTTACT
*
409345 AAAATAT-CAAATATCACCCTTTTCAAA
1 AAAATATGAAAATATCACCCTTTTCAAA
** *
409372 AAAA-ATGAAAATATCACTTTTTTTTAAAA
1 AAAATATGAAAATATCAC--CCTTTTCAAA
*
409401 AAAATATGAAATTATCA-CCTTTT-AAA
1 AAAATATGAAAATATCACCCTTTTCAAA
* * *
409427 AAAATTACGAAAATAGCACCATTTTCAA
1 AAAA-TATGAAAATATCACCCTTTTCAA
409455 TATAATCACC
Statistics
Matches: 65, Mismatches: 11, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
26 9 0.14
27 27 0.42
28 5 0.08
29 13 0.20
30 11 0.17
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.32
Consensus pattern (28 bp):
AAAATATGAAAATATCACCCTTTTCAAA
Found at i:409410 original size:30 final size:29
Alignment explanation
Indices: 409364--409423 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
409354 AATATCACCC
* *
409364 TTTTCAAAAAAAATGAAAATATCACTTTT
1 TTTTAAAAAAAAATGAAAATATCACCTTT
*
409393 TTTTAAAAAAAATATGAAATTATCACCTTT
1 TTTTAAAAAAAA-ATGAAAATATCACCTTT
409423 T
1 T
409424 AAAAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (29 bp):
TTTTAAAAAAAAATGAAAATATCACCTTT
Found at i:409412 original size:29 final size:30
Alignment explanation
Indices: 409364--409423 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
409354 AATATCACCC
* *
409364 TTTTCAAAAAAAATGAAAA-TATCACTTTT
1 TTTTAAAAAAAAATGAAAATTATCACCTTT
409393 TTTTAAAAAAAATATG-AAATTATCACCTTT
1 TTTTAAAAAAAA-ATGAAAATTATCACCTTT
409423 T
1 T
409424 AAAAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (30 bp):
TTTTAAAAAAAAATGAAAATTATCACCTTT
Found at i:409468 original size:29 final size:29
Alignment explanation
Indices: 409436--409504 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
409426 AAAAATTACG
* * * *
409436 AAAATAGCACCATTTTCAATATAATCACC
1 AAAATACCACCAATTTCAAAATAATCACA
*
409465 AAAATACCACCAATTTCAAAATAATTACA
1 AAAATACCACCAATTTCAAAATAATCACA
409494 AAAATACCACC
1 AAAATACCACC
409505 CGGTCAACGG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.51, C:0.25, G:0.01, T:0.23
Consensus pattern (29 bp):
AAAATACCACCAATTTCAAAATAATCACA
Found at i:409552 original size:18 final size:18
Alignment explanation
Indices: 409512--409554 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
409502 ACCCGGTCAA
**
409512 CGGTCAACGGGTCGGGTC
1 CGGTCAACGGGTCGGAAC
*
409530 GGGTCAACGGGTCGGAAC
1 CGGTCAACGGGTCGGAAC
409548 CGGTCAA
1 CGGTCAA
409555 ACATGTTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.26, G:0.42, T:0.14
Consensus pattern (18 bp):
CGGTCAACGGGTCGGAAC
Found at i:419194 original size:22 final size:21
Alignment explanation
Indices: 419136--419195 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
419126 AGTAGTATTT
* * *
419136 AAAATATGTTTATATTCTAATC
1 AAAATAT-TTTATATACGAATA
*
419158 AAAATATTTCAATATACGAATA
1 AAAATATTT-TATATACGAATA
419180 AAAATATATTTATATA
1 AAAATAT-TTTATATA
419196 AATGTATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (21 bp):
AAAATATTTTATATACGAATA
Found at i:419196 original size:16 final size:16
Alignment explanation
Indices: 419177--419210 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
419167 CAATATACGA
419177 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
419193 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
419209 AT
1 AT
419211 TTAGAGTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:419971 original size:130 final size:130
Alignment explanation
Indices: 419738--419974 Score: 393
Period size: 130 Copynumber: 1.8 Consensus size: 130
419728 TTAATTTTCT
* * **
419738 TGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGATCCTGGTTAAAT
1 TGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGATCCTAATTAAAT
*
419803 GATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAATAATTAGGTGG
66 GATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAATAATTAGGTGG
* * * *
419868 TGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCATATCCTAATTAAAT
1 TGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGATCCTAATTAAAT
419933 GATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 GATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
419975 TATATAAATA
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 98 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (130 bp):
TGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGATCCTAATTAAAT
GATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAATAATTAGGTGG
Found at i:420418 original size:35 final size:35
Alignment explanation
Indices: 420368--420443 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
420358 AATTGAATTT
* *
420368 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
420403 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
420438 AATTGA
1 AATTGA
420444 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:421689 original size:2 final size:2
Alignment explanation
Indices: 421682--421710 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
421672 AAATAAACAA
421682 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
421711 ATAAAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:428964 original size:13 final size:13
Alignment explanation
Indices: 428946--428970 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
428936 TGATCAACCA
428946 GTATGAAAAATTC
1 GTATGAAAAATTC
428959 GTATGAAAAATT
1 GTATGAAAAATT
428971 GGATTCAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (13 bp):
GTATGAAAAATTC
Found at i:431734 original size:42 final size:42
Alignment explanation
Indices: 431673--431830 Score: 131
Period size: 42 Copynumber: 3.5 Consensus size: 42
431663 ATGATGCTGA
*
431673 TCCAACTCC-TATATGATGGATGAGCCAAGTATTGGTGTTGT
1 TCCAACTCCGTATGTGATGGATGAGCCAAGTATTGGTGTTGT
* *
431714 TCTAACTCCGTATGTGATGGAATCGAG-CAAGAATGACAATGTTGATGATGTTGA
1 TCCAACTCCGTATGTGATGG-AT-GAGCCAAG--T----A--TTG--G-TGTTGT
** *
431768 TCCAACTCCGTATGCAATGGATGAGCCAAGCATTGGTGTTGT
1 TCCAACTCCGTATGTGATGGATGAGCCAAGTATTGGTGTTGT
431810 TCCAACTCCGTATGTGATGGA
1 TCCAACTCCGTATGTGATGGA
431831 ATCGAGCAAG
Statistics
Matches: 92, Mismatches: 10, Indels: 29
0.70 0.08 0.22
Matches are distributed among these distances:
41 8 0.09
42 33 0.36
43 7 0.08
44 3 0.03
45 4 0.04
47 1 0.01
49 1 0.01
51 3 0.03
52 3 0.03
53 7 0.08
54 22 0.24
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (42 bp):
TCCAACTCCGTATGTGATGGATGAGCCAAGTATTGGTGTTGT
Found at i:431908 original size:97 final size:96
Alignment explanation
Indices: 431614--432082 Score: 673
Period size: 97 Copynumber: 4.9 Consensus size: 96
431604 AGTAAGGTGT
* * * * *
431614 TGCTGATT-CAACTCCATATGCGAT-GAATCGAGCGAGAATAACAATGTTGATGATGCTGATCCA
1 TGCTG-TTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATGATGTTGATCCA
**
431677 ACTCC-TATATGATGGATGAGCCAAGTATTGG
65 ACTCCGTATGCGATGGATGAGCCAAGTATTGG
* *
431708 TGTTGTTCTAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATGATGTTGATCCAA
1 TGCTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATGATGTTGATCCAA
* *
431773 CTCCGTATGCAATGGATGAGCCAAGCATTGG
66 CTCCGTATGCGATGGATGAGCCAAGTATTGG
* *
431804 TGTTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTTCATGATGTTGATCCA
1 TGCTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATG-TTGATGATGTTGATCCA
* *
431869 ACTCCATATGCGATGAATGAGCCAAGTATTGG
65 ACTCCGTATGCGATGGATGAGCCAAGTATTGG
* * *
431901 TGCTGTTCTAACTCCGTATGTGACGAAATCGAGCAAGAATGACAATGTTTGATGATGTTGATCCA
1 TGCTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATG-TTGATGATGTTGATCCA
431966 ACTCCGTATGCGATGGATGAGCCAAGTATTGG
65 ACTCCGTATGCGATGGATGAGCCAAGTATTGG
* * *
431998 TGCTGTTTCAACTCCATATGTGATGGAATCGAGCAAGAATGACAA---TG-TGATGCTGATCCAA
1 TGCTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATGATGTTGATCCAA
432059 CTCCGTATGCGATGGATGAGCCAA
66 CTCCGTATGCGATGGATGAGCCAA
432083 AAGAAACATT
Statistics
Matches: 341, Mismatches: 30, Indels: 10
0.90 0.08 0.03
Matches are distributed among these distances:
92 37 0.11
93 4 0.01
94 17 0.05
95 41 0.12
96 68 0.20
97 174 0.51
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (96 bp):
TGCTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATGATGTTGATCCAA
CTCCGTATGCGATGGATGAGCCAAGTATTGG
Found at i:432316 original size:91 final size:91
Alignment explanation
Indices: 432092--432989 Score: 912
Period size: 91 Copynumber: 9.7 Consensus size: 91
432082 AAAGAAACAT
* * **
432092 TTCTTCTCATTATGAACTTCTTCTCCTTCATTGGACGAGTTCTTCTCATTATGAACTCTTCGTTG
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCCACTG
* *
432157 GAAATGC-TGAGCTAAGGTTGAAACAAA
66 GAAAT-CTTGAGCCAAGGTTG-AACAAG
* * *
432184 TTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTCTCAACTG
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCCACTG
*
432249 GAAATCTTGAACCAAGGTTGAACAAG
66 GAAATCTTGAGCCAAGGTTGAACAAG
* ** * ***
432275 TTCTTCTCATTATGAACCTCTTCTCCCTCGCTGGACGAGTTCTTCTAATTATGAACTCTCTGTTG
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCCACTG
** * *
432340 GAAATGATGAGCTAAGGTTGAACACG
66 GAAATCTTGAGCCAAGGTTGAACAAG
* * *
432366 TTCTTCTCATTACGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCACTA
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCCACTG
* * *
432431 GAATTCTTGAACCAATGTTGAACAAG
66 GAAATCTTGAGCCAAGGTTGAACAAG
* * ***
432457 TTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGACGAGTTCTTCTCATTACGAACTCTCTGTTG
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCCACTG
* *
432522 GAAATGTTGAGCTAAGGTTGAACAAG
66 GAAATCTTGAGCCAAGGTTGAACAAG
* * **
432548 TTCTTCTCATTACGAACTTC-T-T-CC-CATT--ACGAACTTCTTCCCCCCCTCATTGGATGAGT
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACG-AGTTCTT------CTCATT--ATGAAC
* * * ** **
432607 TCTTCTCATTATGAACTCTCCACTGGAAATGTTGAGCTAAGGTTGAACAAG
57 TC-TC-CACT-GGAAATCTTGA--GCCAA----G-------GTTGAACAAG
* *
432658 TTCTTCTCATTATGAACTTCTTATCCCTCATTGGATGAGTTCTTCTCA-TATGAACTCTCCACTG
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCCACTG
*
432722 GAAATGTTGAGCCAAGGTTGAACAAG
66 GAAATCTTGAGCCAAGGTTGAACAAG
** **
432748 TTCTTCTCATTATGAACTTCTTCTCCCTCGCTGGACGAGTTCTTCTCATTATGAACTCTCCGTTG
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCCACTG
** * * *
432813 GAAATGATGAGCTAAGGTTGAATAGG
66 GAAATCTTGAGCCAAGGTTGAACAAG
** * *
432839 TTCTTCTCATTACAAACTTCTTCTCCCTCATTGGATGAGTTCTTCTTATTATGAACTCTCCACTG
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCCACTG
*
432904 GAAATCTTGAACCAAGGTTGAACAAG
66 GAAATCTTGAGCCAAGGTTGAACAAG
* * *
432930 TTCTTCTCAGTATGAATTTCTTCTCCCTCATTGGACGAGTTTTTCTCATTATGAACTCTC
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTC
432990 TATTGAAAAT
Statistics
Matches: 661, Mismatches: 112, Indels: 67
0.79 0.13 0.08
Matches are distributed among these distances:
85 3 0.00
86 6 0.01
87 3 0.00
88 2 0.00
89 1 0.00
90 55 0.08
91 421 0.64
92 80 0.12
94 5 0.01
95 2 0.00
96 2 0.00
97 7 0.01
99 3 0.00
101 3 0.00
103 7 0.01
104 3 0.00
105 2 0.00
106 6 0.01
108 1 0.00
109 4 0.01
110 29 0.04
111 1 0.00
112 1 0.00
113 2 0.00
114 4 0.01
115 6 0.01
116 2 0.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (91 bp):
TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCCACTG
GAAATCTTGAGCCAAGGTTGAACAAG
Found at i:432454 original size:182 final size:182
Alignment explanation
Indices: 432092--432989 Score: 1064
Period size: 182 Copynumber: 4.8 Consensus size: 182
432082 AAAGAAACAT
*
432092 TTCTTCTCATTATGAACTTCTTCTCCTTCATTGGACGAGTTCTTCTCATTATGAACTCT-TCGTT
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCT-GTT
* * *
432156 GGAAATGCTGAGCTAAGGTTGAAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATG
65 GGAAATGTTGAGCTAAGGTTG-AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATG
*
432221 AGTTCTTCTCATTATGAACTCTCAACTGGAAATCTTGAACCAAGGTTGAACAAG
129 AGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAG
* ** *
432275 TTCTTCTCATTATGAACCTCTTCTCCCTCGCTGGACGAGTTCTTCTAATTATGAACTCTCTGTTG
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCTGTTG
* * *
432340 GAAATGATGAGCTAAGGTTGAACACGTTCTTCTCATTACGAACTTCTTCTCCCTCATTGGATGAG
66 GAAATGTTGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAG
* * *
432405 TTCTTCTCATTATGAACTCTCCACTAGAATTCTTGAACCAATGTTGAACAAG
131 TTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAG
* *
432457 TTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGACGAGTTCTTCTCATTACGAACTCTCTGTTG
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCTGTTG
* *
432522 GAAATGTTGAGCTAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTC-CCATTACGAACTTCT
66 GAAATGTTGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC-CT-C--A----T
*** * * * *
432586 TCCCCCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAGCTAAGGTT
123 T----GGATGA--------GTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTT
432651 GAACAAG
176 GAACAAG
* * ***
432658 TTCTTCTCATTATGAACTTCTTATCCCTCATTGGATGAGTTCTTCTCA-TATGAACTCTCCACTG
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCTGTTG
* ** *
432722 GAAATGTTGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGCTGGACGAG
66 GAAATGTTGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAG
** ** * * * *
432787 TTCTTCTCATTATGAACTCTCCGTTGGAAATGATGAGCTAAGGTTGAATAGG
131 TTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAG
** * * ***
432839 TTCTTCTCATTACAAACTTCTTCTCCCTCATTGGATGAGTTCTTCTTATTATGAACTCTCCACTG
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCTGTTG
* * * * * *
432904 GAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCAGTATGAATTTCTTCTCCCTCATTGGACGAG
66 GAAATGTTGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAG
*
432969 TTTTTCTCATTATGAACTCTC
131 TTCTTCTCATTATGAACTCTC
432990 TATTGAAAAT
Statistics
Matches: 627, Mismatches: 65, Indels: 47
0.85 0.09 0.06
Matches are distributed among these distances:
181 94 0.15
182 292 0.47
183 78 0.12
184 1 0.00
185 1 0.00
189 3 0.00
193 3 0.00
199 1 0.00
200 60 0.10
201 94 0.15
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (182 bp):
TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCTGTTG
GAAATGTTGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAG
TTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAG
Found at i:432570 original size:17 final size:17
Alignment explanation
Indices: 432548--432589 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
432538 GTTGAACAAG
*
432548 TTCTTCTCATTACGAAC
1 TTCTTCCCATTACGAAC
432565 TTCTTCCCATTACGAAC
1 TTCTTCCCATTACGAAC
432582 TTCTTCCC
1 TTCTTCCC
432590 CCCCTCATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.19, C:0.36, G:0.05, T:0.40
Consensus pattern (17 bp):
TTCTTCCCATTACGAAC
Found at i:432613 original size:110 final size:108
Alignment explanation
Indices: 432457--432679 Score: 338
Period size: 110 Copynumber: 2.0 Consensus size: 108
432447 GTTGAACAAG
* * * * ***
432457 TTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGACGAGTTCTTCTCATTACGAACTCTCTGTTG
1 TTCTTCCCATTACGAACTTCTTCCCCCTCATTGGACGAGTTCTTCTCATTACGAACTCTCCACTG
432522 GAAATGTTGAGCTAAGGTTGAACAAGTTCTTCTCATTACGAAC
66 GAAATGTTGAGCTAAGGTTGAACAAGTTCTTCTCATTACGAAC
* *
432565 TTCTTCCCATTACGAACTTCTTCCCCCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCAC
1 TTCTTCCCATTACGAACTTCTT--CCCCCTCATTGGACGAGTTCTTCTCATTACGAACTCTCCAC
*
432630 TGGAAATGTTGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAAC
64 TGGAAATGTTGAGCTAAGGTTGAACAAGTTCTTCTCATTACGAAC
432675 TTCTT
1 TTCTT
432680 ATCCCTCATT
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
108 20 0.19
110 83 0.81
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (108 bp):
TTCTTCCCATTACGAACTTCTTCCCCCTCATTGGACGAGTTCTTCTCATTACGAACTCTCCACTG
GAAATGTTGAGCTAAGGTTGAACAAGTTCTTCTCATTACGAAC
Found at i:432614 original size:201 final size:198
Alignment explanation
Indices: 432366--432770 Score: 630
Period size: 201 Copynumber: 2.0 Consensus size: 198
432356 GTTGAACACG
* *
432366 TTCTTCTCATTACGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCACTA
1 TTCTTCCCATTACGAACTTCTTCCCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCACTA
* * * *
432431 GAATTCTTGAACCAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGACGAG
66 GAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATTGGACGAG
*** *
432496 TTCTTCTCATTACGAACTCTCTGTTGGAAATGTTGAGCTAAGGTTGAACAAGTTCTTCTCATTAC
131 TTCTTCTCA-TACGAACTCTCCACTGGAAATGTTGAGCCAAGGTTGAACAAGTTCTTCTCATTAC
432561 GAAC
195 GAAC
432565 TTCTTCCCATTACGAACTTCTTCCCCCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCAC
1 TTCTTCCCATTACGAACTTCTT--CCCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCAC
* * * * *
432630 TGGAAATGTTGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATTGGATG
64 TAGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATTGGACG
*
432695 AGTTCTTCTCATATGAACTCTCCACTGGAAATGTTGAGCCAAGGTTGAACAAGTTCTTCTCATTA
129 AGTTCTTCTCATACGAACTCTCCACTGGAAATGTTGAGCCAAGGTTGAACAAGTTCTTCTCATTA
*
432760 TGAAC
194 CGAAC
432765 TTCTTC
1 TTCTTC
432771 TCCCTCGCTG
Statistics
Matches: 187, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
199 21 0.11
200 59 0.32
201 107 0.57
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (198 bp):
TTCTTCCCATTACGAACTTCTTCCCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCACTA
GAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATTGGACGAG
TTCTTCTCATACGAACTCTCCACTGGAAATGTTGAGCCAAGGTTGAACAAGTTCTTCTCATTACG
AAC
Found at i:432807 original size:181 final size:182
Alignment explanation
Indices: 432565--432989 Score: 645
Period size: 181 Copynumber: 2.3 Consensus size: 182
432555 CATTACGAAC
* * * *
432565 TTCTTCCCATTACGAACTTCTTCCCCCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCAC
1 TTCTTCTCATTATGAACTTCTT--CTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCCAC
* **
432630 TGGAAATGTTGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATTGGATG
64 TGGAAATGATGAGCTAAGGTTGAACAAGTTCTTCTCATTACAAACTTCTTATCCCTCATTGGATG
* *
432695 AGTTCTTCTCA-TATGAACTCTCCACTGGAAATGTTGAGCCAAGGTTGAACAAG
129 AGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAG
** **
432748 TTCTTCTCATTATGAACTTCTTCTCCCTCGCTGGACGAGTTCTTCTCATTATGAACTCTCCGTTG
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCCACTG
* * *
432813 GAAATGATGAGCTAAGGTTGAATAGGTTCTTCTCATTACAAACTTCTTCTCCCTCATTGGATGAG
66 GAAATGATGAGCTAAGGTTGAACAAGTTCTTCTCATTACAAACTTCTTATCCCTCATTGGATGAG
*
432878 TTCTTCTTATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAG
131 TTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAG
* * *
432930 TTCTTCTCAGTATGAATTTCTTCTCCCTCATTGGACGAGTTTTTCTCATTATGAACTCTC
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTC
432990 TATTGAAAAT
Statistics
Matches: 219, Mismatches: 22, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
181 104 0.47
182 95 0.43
183 20 0.09
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (182 bp):
TTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCCACTG
GAAATGATGAGCTAAGGTTGAACAAGTTCTTCTCATTACAAACTTCTTATCCCTCATTGGATGAG
TTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAG
Found at i:432990 original size:473 final size:473
Alignment explanation
Indices: 432092--433004 Score: 1497
Period size: 473 Copynumber: 1.9 Consensus size: 473
432082 AAAGAAACAT
* * * * * **
432092 TTCTTCTCATTATGAACTTCTTCTCCTTCATTGGACGAGTTCTTCTCATTATGAACTCTTCGTTG
1 TTCTTCCCATTACGAACTTCTTCCCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCCACTG
* *
432157 GAAATGCTGAGCTAAGGTTGAAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGA
66 GAAATGCTGAGCTAAGGTTGAAACAAATTCTTCTCATTATGAACTTCTTATCCCTCATTGGATGA
432222 GTTCTTCTCATTATGAACTCTCAACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCATTA
131 GTTCTTCTCATTATGAACTCTCAACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCATTA
*
432287 TGAACCTCTTCTCCCTCGCTGGACGAGTTCTTCTAATTATGAACTCTCTGTTGGAAATGATGAGC
196 TGAACCTCTTCTCCCTCGCTGGACGAGTTCTTCTAATTATGAACTCTCCGTTGGAAATGATGAGC
*
432352 TAAGGTTGAACACGTTCTTCTCATTACGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTA
261 TAAGGTTGAACACGTTCTTCTCATTACAAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTA
* * *
432417 TGAACTCTCCACTAGAATTCTTGAACCAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
326 TGAACTCTCCACTAGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCAGTATGAACTTCTTCTC
* * * *
432482 CCTCTTTGGACGAGTTCTTCTCATTACGAACTCTCTGTTGGAAATGTTGAGCTAAGGTTGAACAA
391 CCTCATTGGACGAGTTCTTCTCATTACGAACTCTCTATTGAAAATATTGAGCTAAGGTTGAACAA
432547 GTTCTTCTCATTACGAAC
456 GTTCTTCTCATTACGAAC
*
432565 TTCTTCCCATTACGAACTTCTTCCCCCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCAC
1 TTCTTCCCATTACGAACTTCTT--CCCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCCAC
* *
432630 TGGAAATGTTGAGCTAAGGTTG-AACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATTGGAT
64 TGGAAATGCTGAGCTAAGGTTGAAACAAATTCTTCTCATTATGAACTTCTTATCCCTCATTGGAT
* * *
432694 GAGTTCTTCTCA-TATGAACTCTCCACTGGAAATGTTGAGCCAAGGTTGAACAAGTTCTTCTCAT
129 GAGTTCTTCTCATTATGAACTCTCAACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCAT
* *
432758 TATGAACTTCTTCTCCCTCGCTGGACGAGTTCTTCTCATTATGAACTCTCCGTTGGAAATGATGA
194 TATGAACCTCTTCTCCCTCGCTGGACGAGTTCTTCTAATTATGAACTCTCCGTTGGAAATGATGA
* * *
432823 GCTAAGGTTGAATAGGTTCTTCTCATTACAAACTTCTTCTCCCTCATTGGATGAGTTCTTCTTAT
259 GCTAAGGTTGAACACGTTCTTCTCATTACAAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCAT
* *
432888 TATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCAGTATGAATTTCTTC
324 TATGAACTCTCCACTAGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCAGTATGAACTTCTTC
* *
432953 TCCCTCATTGGACGAGTTTTTCTCATTATGAACTCTCTATTGAAAATATTGA
389 TCCCTCATTGGACGAGTTCTTCTCATTACGAACTCTCTATTGAAAATATTGA
433005 TCAATTTATC
Statistics
Matches: 405, Mismatches: 33, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
473 298 0.74
474 51 0.13
475 56 0.14
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (473 bp):
TTCTTCCCATTACGAACTTCTTCCCCCTCATTGGACGAGTTCTTCTCATTATGAACTCTCCACTG
GAAATGCTGAGCTAAGGTTGAAACAAATTCTTCTCATTATGAACTTCTTATCCCTCATTGGATGA
GTTCTTCTCATTATGAACTCTCAACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCATTA
TGAACCTCTTCTCCCTCGCTGGACGAGTTCTTCTAATTATGAACTCTCCGTTGGAAATGATGAGC
TAAGGTTGAACACGTTCTTCTCATTACAAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTA
TGAACTCTCCACTAGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCAGTATGAACTTCTTCTC
CCTCATTGGACGAGTTCTTCTCATTACGAACTCTCTATTGAAAATATTGAGCTAAGGTTGAACAA
GTTCTTCTCATTACGAAC
Found at i:433571 original size:67 final size:67
Alignment explanation
Indices: 433394--433658 Score: 252
Period size: 67 Copynumber: 3.9 Consensus size: 67
433384 GAAAACACAA
* * * *
433394 TCAAAGGTTTTTTGTTTCAAGAGGAATTGTCT-ATAGGGAGACAAAATTCAG-TTCAAGGGAAAC
1 TCAAAGATTTTTTGTTTCAAGAGAAACTGTCTCA-AGGGAGACAAAATTC-GTTTCAAGAGAAAC
*
433457 GATC
64 GAAC
*** * *
433461 TCAAAGATCAGTT-TTTCAAG-GAAAACTGTCTCAAGAGAGACAAAACTCGTTTCAAGAGAAACG
1 TCAAAGATTTTTTGTTTCAAGAG-AAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGAGAAACG
*
433524 ACC
65 AAC
* * * *
433527 TCAAAGATTTTCTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAA-TA
1 TCAAAGATTTTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGAGAAACGA
*
433591 TAT
66 -AC
* ** * *
433594 TCAAAGATTTTTTTTGTTTCAAAAGAAACTGTCTCAATCGAGACAAAATTTGTTTCAAGTGAAAC
1 TCAAAGA--TTTTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGAGAAAC
433659 TGTCTTAAGA
Statistics
Matches: 162, Mismatches: 27, Indels: 15
0.79 0.13 0.07
Matches are distributed among these distances:
65 2 0.01
66 51 0.31
67 59 0.36
68 1 0.01
69 49 0.30
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (67 bp):
TCAAAGATTTTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGAGAAACGA
AC
Found at i:433586 original size:36 final size:36
Alignment explanation
Indices: 433539--433895 Score: 254
Period size: 36 Copynumber: 10.1 Consensus size: 36
433529 AAAGATTTTC
* *
433539 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *****
433575 TGTTTCAAGAGAAA-TATATTC-A-A-AGATTTTTTT
1 TGTTTCAAGAGAAACTGT-CTCAAGAGAGACAAAATT
* **
433608 TGTTTCAAAAGAAACTGTCTCAATCGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
433644 TGTTTCAAGTGAAACTGTCTTAAGAGTGACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * * *
433680 CGTTTAAAGGGAAACTGTCTTAAGAGAGACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
433716 CGTTTAAAGGGAAACTGTCTCAATG-GAGACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAA-GAGAGACAAAATT
* * *
433752 GGTTTCAAGGGAAACTGTCTTAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* **
433789 TGTTTCAAGGGAAACAATCTCAA-AG-G------TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * **
433817 GGCGTTTCAAGAGAAACTATCTCAAGAGATACAAAACA
1 --TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
433855 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
433891 TGTTT
1 TGTTT
433896 TGAAAAAAAA
Statistics
Matches: 255, Mismatches: 48, Indels: 36
0.75 0.14 0.11
Matches are distributed among these distances:
28 2 0.01
30 20 0.08
31 2 0.01
33 20 0.08
34 3 0.01
35 5 0.02
36 182 0.71
37 21 0.08
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:433639 original size:69 final size:67
Alignment explanation
Indices: 433483--433658 Score: 210
Period size: 69 Copynumber: 2.6 Consensus size: 67
433473 TTTTCAAGGA
* * * *
433483 AAACTGTCTCAAGAGAGACAAAACTCGTTTCAAGAGAAACGACCTCAAAGATTTTCTGTTTCAAG
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACGAACTCAAAGATTTTCTGTTTCAAA
433548 AG
66 AG
* * * * *
433550 AAATTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAA-TATATTCAAAGATTTTTTTTGTTTC
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACGA-ACTCAAAGA--TTTTCTGTTTC
433614 AAAAG
63 AAAAG
** *
433619 AAACTGTCTCAATCGAGACAAAATTTGTTTCAAGTGAAAC
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAC
433659 TGTCTTAAGA
Statistics
Matches: 92, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
66 1 0.01
67 42 0.46
69 49 0.53
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (67 bp):
AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACGAACTCAAAGATTTTCTGTTTCAAA
AG
Found at i:433686 original size:20 final size:19
Alignment explanation
Indices: 433663--433722 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
433653 TGAAACTGTC
433663 TTAAGAGTGACAAAACTCGT
1 TTAAGAG-GACAAAACTCGT
*
433683 TTAA-AGG--GAAACT-GT
1 TTAAGAGGACAAAACTCGT
433698 CTTAAGAGAGACAAAACTCGT
1 -TTAAGAG-GACAAAACTCGT
433719 TTAA
1 TTAA
433723 AGGGAAACTG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
15 2 0.06
16 9 0.28
17 2 0.06
18 2 0.06
19 2 0.06
20 13 0.41
21 2 0.06
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (19 bp):
TTAAGAGGACAAAACTCGT
Found at i:434337 original size:90 final size:90
Alignment explanation
Indices: 434102--434403 Score: 523
Period size: 90 Copynumber: 3.3 Consensus size: 90
434092 CCTAAAAATC
*
434102 AGGCTTAGTTTCTAAAAAACTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAA
1 AGGCTTAGTTTCT-AAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAA
*
434167 AGACTTACAAATCAAGAAAACCCCCGA
65 GGACTTACAAATCAAG-AAACCCCCGA
*
434194 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAG
1 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAG
*
434259 GACTTACAAATCAAGAAACCCACGA
66 GACTTACAAATCAAGAAACCCCCGA
*
434284 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTTTTATGGATGGCCCGAAG
1 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAG
434349 GACTTACAAATCAAGAAACCCCCGA
66 GACTTACAAATCAAGAAACCCCCGA
* *
434374 AGGCTTAGTTTCTAAAATCTAATTTAAAAA
1 AGGCTTAGTTTCTAAAATCTCATTTGAAAA
434404 TATCATGTTG
Statistics
Matches: 201, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
90 124 0.62
91 64 0.32
92 13 0.06
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (90 bp):
AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAG
GACTTACAAATCAAGAAACCCCCGA
Found at i:441794 original size:20 final size:20
Alignment explanation
Indices: 441766--441807 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
441756 TTAAAGCAGC
441766 AACAAGACTAAATTGAATAG
1 AACAAGACTAAATTGAATAG
*
441786 AACACGACTAAATTGAATAG
1 AACAAGACTAAATTGAATAG
441806 AA
1 AA
441808 TTAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.12, G:0.14, T:0.19
Consensus pattern (20 bp):
AACAAGACTAAATTGAATAG
Found at i:442670 original size:28 final size:28
Alignment explanation
Indices: 442630--442690 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
442620 TTTGATTCCC
442630 TGGGTGAGAGTTTAGTAGAGCAGGAGCA
1 TGGGTGAGAGTTTAGTAGAGCAGGAGCA
* * *
442658 TGGGTGAGGGTTTAGTGGAGCATGAGCA
1 TGGGTGAGAGTTTAGTAGAGCAGGAGCA
442686 TGGGT
1 TGGGT
442691 TTTGATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.23, C:0.07, G:0.46, T:0.25
Consensus pattern (28 bp):
TGGGTGAGAGTTTAGTAGAGCAGGAGCA
Found at i:444462 original size:24 final size:24
Alignment explanation
Indices: 444423--444492 Score: 122
Period size: 24 Copynumber: 2.9 Consensus size: 24
444413 CTTCCAGATT
444423 ATGTATAAAAACATCTATGTACACA
1 ATGTAT-AAAACATCTATGTACACA
*
444448 ATGTATAAAACATCTATGTACACG
1 ATGTATAAAACATCTATGTACACA
444472 ATGTATAAAACATCTATGTAC
1 ATGTATAAAACATCTATGTAC
444493 CATATCATGC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
24 38 0.86
25 6 0.14
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (24 bp):
ATGTATAAAACATCTATGTACACA
Found at i:445731 original size:30 final size:30
Alignment explanation
Indices: 445697--445755 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
445687 TTTAGTCTCT
* *
445697 AAACTTT-TCAAAGTTTATACTTTGATCACC
1 AAACTTTACCAAA-TTTATAATTTGATCACC
*
445727 AAACTTTACCAAATTTATAATTTGGTCAC
1 AAACTTTACCAAATTTATAATTTGATCAC
445756 TACATAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTACCAAATTTATAATTTGATCACC
Found at i:447557 original size:22 final size:22
Alignment explanation
Indices: 447530--447572 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
447520 TCCACGCAAT
*
447530 CTGCTGACTAGATCTTCTAGAG
1 CTGCTGACTAGACCTTCTAGAG
*
447552 CTGCTGACTAGGCCTTCTAGA
1 CTGCTGACTAGACCTTCTAGA
447573 AGATGTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (22 bp):
CTGCTGACTAGACCTTCTAGAG
Found at i:448009 original size:37 final size:37
Alignment explanation
Indices: 447989--448118 Score: 242
Period size: 37 Copynumber: 3.5 Consensus size: 37
447979 TGTTAGGTCC
*
447989 ACTTCTTTTACCCTTTTTTCTCTTTCTTCTTAGCTCA
1 ACTTCTTTTTCCCTTTTTTCTCTTTCTTCTTAGCTCA
448026 ACTTCTTTTTCCCTTTTTTCTCTTTCTTCTTAGCTCA
1 ACTTCTTTTTCCCTTTTTTCTCTTTCTTCTTAGCTCA
*
448063 ACTTCTTTTTCCCTTTTTTCTTTTTCTTCTTAGCTCA
1 ACTTCTTTTTCCCTTTTTTCTCTTTCTTCTTAGCTCA
448100 ACTTCTTTTTCCCTTTTTT
1 ACTTCTTTTTCCCTTTTTT
448119 TCCTTCATTC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 91 1.00
ACGTcount: A:0.08, C:0.28, G:0.02, T:0.61
Consensus pattern (37 bp):
ACTTCTTTTTCCCTTTTTTCTCTTTCTTCTTAGCTCA
Found at i:451310 original size:30 final size:31
Alignment explanation
Indices: 451276--451345 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
451266 TTGGGACAGG
451276 CTCATGATCATGAACTAGG-TTTAGGGCAC-A
1 CTCATGATCATGAA-TAGGATTTAGGGCACAA
* *
451306 CTCATGACCATGAATTGGATTTAGGGCACAA
1 CTCATGATCATGAATAGGATTTAGGGCACAA
451337 C-CATGATCA
1 CTCATGATCA
451346 AGAAGGGGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 3 0.09
30 30 0.86
31 2 0.06
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (31 bp):
CTCATGATCATGAATAGGATTTAGGGCACAA
Found at i:453359 original size:3 final size:3
Alignment explanation
Indices: 453351--453413 Score: 85
Period size: 3 Copynumber: 21.0 Consensus size: 3
453341 AATTATTTTT
453351 TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TATA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA
*
453396 TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
453414 ATAAATAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
2 4 0.07
3 44 0.81
4 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:453424 original size:15 final size:17
Alignment explanation
Indices: 453351--453425 Score: 72
Period size: 15 Copynumber: 4.6 Consensus size: 17
453341 AATTATTTTT
453351 TAATAATAATAAT-AATA
1 TAAT-ATAATAATAAATA
*
453368 T-ATATAATAATATATA
1 TAATATAATAATAAATA
*
453384 T-A-ATAATAATAATTA
1 TAATATAATAATAAATA
453399 TAATAATAATAATAAATA
1 TAAT-ATAATAATAAATA
453417 -AATA-AATAA
1 TAATATAATAA
453426 AATGGGTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
15 25 0.50
16 9 0.18
17 4 0.08
18 12 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAATATAATAATAAATA
Found at i:458638 original size:14 final size:14
Alignment explanation
Indices: 458604--458667 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
458594 GACCTGATCG
* *
458604 AGTCAATTCAGTCCG
1 AGTCAACTCA-TCCA
458619 AGTCAACTCATCCA
1 AGTCAACTCATCCA
* * *
458633 AGTCAACCCGTCTA
1 AGTCAACTCATCCA
*
458647 AGTCAACTCGTCCA
1 AGTCAACTCATCCA
458661 AGTCAAC
1 AGTCAAC
458668 CTGTTAACTT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
14 33 0.79
15 9 0.21
ACGTcount: A:0.31, C:0.33, G:0.14, T:0.22
Consensus pattern (14 bp):
AGTCAACTCATCCA
Found at i:458701 original size:13 final size:13
Alignment explanation
Indices: 458668--458710 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
458658 CCAAGTCAAC
*
458668 CTGTTAACTTTGA
1 CTGTTGACTTTGA
*
458681 CTTGTTGACTGTGA
1 C-TGTTGACTTTGA
458695 CTGTTGACTTTGA
1 CTGTTGACTTTGA
458708 CTG
1 CTG
458711 AAAAAGTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.44
Consensus pattern (13 bp):
CTGTTGACTTTGA
Found at i:458737 original size:20 final size:21
Alignment explanation
Indices: 458712--458750 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
458702 CTTTGACTGA
458712 AAAAGTC-AATTTTTTTTTCG
1 AAAAGTCTAATTTTTTTTTCG
*
458732 AAAAGTCTTATTTTTTTTT
1 AAAAGTCTAATTTTTTTTT
458751 TCGACGTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (21 bp):
AAAAGTCTAATTTTTTTTTCG
Found at i:459101 original size:18 final size:18
Alignment explanation
Indices: 459078--459113 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
459068 CATTGGACTC
459078 AAACGGAA-ATTGGAATAA
1 AAACGGAACATT-GAATAA
459096 AAACGGAACATTGAATAA
1 AAACGGAACATTGAATAA
459114 GACTCTAGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.56, C:0.08, G:0.19, T:0.17
Consensus pattern (18 bp):
AAACGGAACATTGAATAA
Found at i:462935 original size:6 final size:6
Alignment explanation
Indices: 462924--462948 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
462914 GTCTTTATTT
462924 GATGTA GATGTA GATGTA GATGTA G
1 GATGTA GATGTA GATGTA GATGTA G
462949 TCTTCTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (6 bp):
GATGTA
Found at i:463238 original size:26 final size:26
Alignment explanation
Indices: 463187--463243 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
463177 CCTCAGTTTG
*
463187 GTTTTAGAAAATATTTTCTATTTTTA
1 GTTTTAGAAAATATTTTCTAATTTTA
* *
463213 TTTTTAGAAATTAGTTTTC-AATTTTA
1 GTTTTAGAAAATA-TTTTCTAATTTTA
463239 GTTTT
1 GTTTT
463244 CTGAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.60
Consensus pattern (26 bp):
GTTTTAGAAAATATTTTCTAATTTTA
Found at i:463243 original size:27 final size:26
Alignment explanation
Indices: 463188--463251 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
463178 CTCAGTTTGG
*
463188 TTTTAGAAAATATTTTCTATTTTTAT
1 TTTTAGAAAATATTTTCTAATTTTAT
*
463214 TTTTAGAAATTAGTTTTC-AATTTTAGT
1 TTTTAGAAAATA-TTTTCTAATTTTA-T
463241 TTTCT-GAAAAT
1 TTT-TAGAAAAT
463252 TAGAAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
26 17 0.53
27 14 0.44
28 1 0.03
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (26 bp):
TTTTAGAAAATATTTTCTAATTTTAT
Found at i:463910 original size:51 final size:50
Alignment explanation
Indices: 463855--463952 Score: 169
Period size: 50 Copynumber: 1.9 Consensus size: 50
463845 AAAAAATTAT
463855 TAAGATATTCAATACATCAAATATAAAAATACTACAAAATTAAAGTATCAA
1 TAAGATATTCAATACATCAAATAT-AAAATACTACAAAATTAAAGTATCAA
* *
463906 TAAGATATTCAATATATTAAATATAAAATACTACAAAATTAAAGTAT
1 TAAGATATTCAATACATCAAATATAAAATACTACAAAATTAAAGTAT
463953 TAAAAAATCA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 23 0.51
51 22 0.49
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (50 bp):
TAAGATATTCAATACATCAAATATAAAATACTACAAAATTAAAGTATCAA
Found at i:464458 original size:16 final size:16
Alignment explanation
Indices: 464437--464470 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
464427 TTTATTATAT
464437 TGATGTATTAAGTTAG
1 TGATGTATTAAGTTAG
*
464453 TGATGTGTTAAGTTAG
1 TGATGTATTAAGTTAG
464469 TG
1 TG
464471 CTGACCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.44
Consensus pattern (16 bp):
TGATGTATTAAGTTAG
Found at i:468570 original size:21 final size:21
Alignment explanation
Indices: 468544--468584 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
468534 AACAACTTCC
*
468544 CTTAACTAACTAC-TAACAACA
1 CTTAACCAACT-CTTAACAACA
468565 CTTAACCAACTCTTAACAAC
1 CTTAACCAACTCTTAACAAC
468585 TTTTGTGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (21 bp):
CTTAACCAACTCTTAACAACA
Found at i:470506 original size:27 final size:27
Alignment explanation
Indices: 470462--470641 Score: 245
Period size: 27 Copynumber: 6.7 Consensus size: 27
470452 TCAACTTTTT
*
470462 AGCAATATTCCCAGGTGGTGATTCTTC
1 AGCAACATTCCCAGGTGGTGATTCTTC
* * *
470489 AGTAACATTCCCAGGTGGCGACTCTTC
1 AGCAACATTCCCAGGTGGTGATTCTTC
* *
470516 AACAATATTCCCAGGTGGTGATTCTTC
1 AGCAACATTCCCAGGTGGTGATTCTTC
*
470543 AACAACATTCCCAGGTGGTGATTCTTC
1 AGCAACATTCCCAGGTGGTGATTCTTC
* *
470570 AGTAACATTCCCAGGTGGTGACTCTTC
1 AGCAACATTCCCAGGTGGTGATTCTTC
470597 AGCAACATTCCCATGG-GGTGATTCTTC
1 AGCAACATTCCCA-GGTGGTGATTCTTC
* *
470624 AGCAATATTTCCAGGTGG
1 AGCAACATTCCCAGGTGG
470642 CGTAGAGTGT
Statistics
Matches: 134, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
26 2 0.01
27 130 0.97
28 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (27 bp):
AGCAACATTCCCAGGTGGTGATTCTTC
Found at i:470566 original size:81 final size:81
Alignment explanation
Indices: 470468--470641 Score: 278
Period size: 81 Copynumber: 2.1 Consensus size: 81
470458 TTTTAGCAAT
*
470468 ATTCCCAGGTGGTGATTCTTCAGTAACATTCCCAGGTGGCGACTCTTCAACAATATTCCCA-GGT
1 ATTCCCAGGTGGTGATTCTTCAGTAACATTCCCAGGTGGCGACTCTTCAACAACATTCCCATGG-
470532 GGTGATTCTTCAACAAC
65 GGTGATTCTTCAACAAC
* *
470549 ATTCCCAGGTGGTGATTCTTCAGTAACATTCCCAGGTGGTGACTCTTCAGCAACATTCCCATGGG
1 ATTCCCAGGTGGTGATTCTTCAGTAACATTCCCAGGTGGCGACTCTTCAACAACATTCCCATGGG
* *
470614 GTGATTCTTCAGCAAT
66 GTGATTCTTCAACAAC
*
470630 ATTTCCAGGTGG
1 ATTCCCAGGTGG
470642 CGTAGAGTGT
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
81 84 0.98
82 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (81 bp):
ATTCCCAGGTGGTGATTCTTCAGTAACATTCCCAGGTGGCGACTCTTCAACAACATTCCCATGGG
GTGATTCTTCAACAAC
Found at i:474761 original size:23 final size:22
Alignment explanation
Indices: 474733--474787 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
474723 CGTCCTAATT
*
474733 AAATAATATATTTTAATGATATA
1 AAATAATATATTTTAA-AATATA
* *
474756 AAATAAAAT-TTTTAAAATATT
1 AAATAATATATTTTAAAATATA
474777 AAATATATATA
1 AAATA-ATATA
474788 ATATAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 9 0.35
22 9 0.35
23 8 0.31
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AAATAATATATTTTAAAATATA
Found at i:483931 original size:25 final size:25
Alignment explanation
Indices: 483903--483958 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
483893 GTTTATTAGG
483903 AGTTAGTTGATAGGTTGTTAGAAGT
1 AGTTAGTTGATAGGTTGTTAGAAGT
483928 AGTTAGTTGATAGGTTGTTAGAAGT
1 AGTTAGTTGATAGGTTGTTAGAAGT
483953 AGTTAG
1 AGTTAG
483959 AAGCAGATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (25 bp):
AGTTAGTTGATAGGTTGTTAGAAGT
Found at i:486719 original size:15 final size:16
Alignment explanation
Indices: 486699--486731 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
486689 ATTCCCGATT
*
486699 TTGATTTTTTAAT-CC
1 TTGATTCTTTAATACC
486714 TTGATTCTTTAATACC
1 TTGATTCTTTAATACC
486730 TT
1 TT
486732 TTAATACATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.21, C:0.15, G:0.06, T:0.58
Consensus pattern (16 bp):
TTGATTCTTTAATACC
Found at i:490178 original size:12 final size:12
Alignment explanation
Indices: 490161--490185 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
490151 TCTTTTAATA
490161 TTTTGATTCATT
1 TTTTGATTCATT
490173 TTTTGATTCATT
1 TTTTGATTCATT
490185 T
1 T
490186 GCGGATACAG
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:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTTGATTCATT
Found at i:492037 original size:20 final size:19
Alignment explanation
Indices: 492009--492069 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
491999 TTAATATAAA
492009 TATTAATTTTTAATATTTTT
1 TATTAA-TTTTAATATTTTT
*
492029 TATTTATTTTAATATTTATT
1 TATTAATTTTAATATTT-TT
*
492049 T-TTAA-TTTAAAATTTGTT
1 TATTAATTTTAATATTT-TT
492067 TAT
1 TAT
492070 ATATGTTGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 12 0.34
19 15 0.43
20 8 0.23
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTAATTTTAATATTTTT
Found at i:492038 original size:19 final size:19
Alignment explanation
Indices: 492016--492069 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
492006 AAATATTAAT
492016 TTTTAATATTTTTTATTTA
1 TTTTAATATTTTTTATTTA
*
492035 TTTTAATATTTATT-TTTA
1 TTTTAATATTTTTTATTTA
* *
492053 ATTTAAAATTTGTTTAT
1 TTTTAATATTT-TTTAT
492070 ATATGTTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 13 0.45
19 15 0.52
20 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTAATATTTTTTATTTA
Found at i:492057 original size:18 final size:19
Alignment explanation
Indices: 492017--492063 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
492007 AATATTAATT
* *
492017 TTTAATATTTTTTATTTAT
1 TTTAATATTTATTATTTAA
492036 TTTAATATTTATT-TTTAA
1 TTTAATATTTATTATTTAA
*
492054 TTTAAAATTT
1 TTTAATATTT
492064 GTTTATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTAATATTTATTATTTAA
Found at i:494436 original size:22 final size:22
Alignment explanation
Indices: 494411--494479 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 22
494401 TAATAATTAT
494411 ATTATATACAATGAATTGATAG
1 ATTATATACAATGAATTGATAG
**
494433 ATTATCA-A-AAT-ATACAAGAT-G
1 ATTAT-ATACAATGA-A-TTGATAG
494454 ATT-TATACAATGAATTGATAG
1 ATTATATACAATGAATTGATAG
494475 ATTAT
1 ATTAT
494480 CAAAATATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
19 1 0.03
20 6 0.17
21 16 0.46
22 11 0.31
23 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (22 bp):
ATTATATACAATGAATTGATAG
Found at i:498420 original size:3 final size:3
Alignment explanation
Indices: 498414--498450 Score: 56
Period size: 3 Copynumber: 11.7 Consensus size: 3
498404 TTTTTTTAGT
498414 TTA TTA TTTA TTA TTA TTTA TTA TTA TTA TTA TTA TT
1 TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT
498451 TTCCTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 26 0.81
4 6 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:498429 original size:10 final size:10
Alignment explanation
Indices: 498414--498451 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
498404 TTTTTTTAGT
498414 TTATTATTTA
1 TTATTATTTA
498424 TTATTATTTA
1 TTATTATTTA
498434 TTATTA-TTA
1 TTATTATTTA
498443 TTATTATTT
1 TTATTATTT
498452 TCCTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.33
10 18 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTATTATTTA
Found at i:499849 original size:15 final size:15
Alignment explanation
Indices: 499804--499849 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
499794 TTAGCTGGGT
*
499804 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
*
499819 AGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
499834 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
499849 G
1 G
499850 AGGTCTTCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.09, C:0.17, G:0.65, T:0.09
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:501325 original size:61 final size:61
Alignment explanation
Indices: 501245--501383 Score: 172
Period size: 61 Copynumber: 2.3 Consensus size: 61
501235 TCACACGTGT
* * * * *
501245 ACATGCCACGTCAGTATTTAGTCTACGT-GGATCTACCACGTCATCATCTATTCTGATATGA
1 ACATGCCACGTCAGCATTTAGTATAC-TAGGATATACCACGTCATCATATACTCTGATATGA
* * * * *
501306 ACATGCCACATCAGCATTTAGTATACTATGATATGCCACGTCATCATATACTGTGATATGG
1 ACATGCCACGTCAGCATTTAGTATACTAGGATATACCACGTCATCATATACTCTGATATGA
501367 ACATGCCACGTCAGCAT
1 ACATGCCACGTCAGCAT
501384 CTCCCTCCAC
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
60 1 0.02
61 65 0.98
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (61 bp):
ACATGCCACGTCAGCATTTAGTATACTAGGATATACCACGTCATCATATACTCTGATATGA
Found at i:501374 original size:31 final size:31
Alignment explanation
Indices: 501280--501379 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 31
501270 CGTGGATCTA
* * * *
501280 CCACGTCATCATCTATTCTGATATGAACATG
1 CCACGTCATCATATACTATGATATGGACATG
* * * * *
501311 CCACATCAGCATTTAGTAT-ACTAT-GATATG
1 CCACGTCATCATATACTATGA-TATGGACATG
*
501341 CCACGTCATCATATACTGTGATATGGACATG
1 CCACGTCATCATATACTATGATATGGACATG
501372 CCACGTCA
1 CCACGTCA
501380 GCATCTCCCT
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
30 22 0.42
31 31 0.58
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (31 bp):
CCACGTCATCATATACTATGATATGGACATG
Found at i:508395 original size:78 final size:77
Alignment explanation
Indices: 508295--508513 Score: 279
Period size: 73 Copynumber: 2.8 Consensus size: 77
508285 AAACGACTTT
* * * *
508295 TAGTGCTTATTAAAGAAAT-GGGGCCACATTTTATAATTAAATGGTAAGAAAATGGTACAATAAC
1 TAGTGCTTATTAAATAAATGGGGGCC-CATTTTATAATTGAATTGTAAGAAAATTGTACAAT-AC
508359 GTTCATGTCTGCCA
64 GTTCATGTCTGCCA
* *
508373 TAGTACTTATTAAATAAATGGGGGGCCTATTTTATAATTGAATTGTAAG-AAATTGTAC----CG
1 TAGTGCTTATTAAATAAAT-GGGGGCCCATTTTATAATTGAATTGTAAGAAAATTGTACAATACG
508433 TTCATGTCTGCCA
65 TTCATGTCTGCCA
*
508446 TAGTGCTTATTAAATAAATGGGGGCCCTATTTTATAATTGAATTATAAGAAAAATTGTACAATCA
1 TAGTGCTTATTAAATAAATGGGGGCCC-ATTTTATAATTGAATTGTAAG-AAAATTGTACAAT-A
508511 CGT
63 CGT
508514 GAATGCAATT
Statistics
Matches: 122, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
72 7 0.06
73 53 0.43
75 9 0.07
78 25 0.20
79 19 0.16
80 9 0.07
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (77 bp):
TAGTGCTTATTAAATAAATGGGGGCCCATTTTATAATTGAATTGTAAGAAAATTGTACAATACGT
TCATGTCTGCCA
Found at i:509246 original size:12 final size:12
Alignment explanation
Indices: 509229--509253 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
509219 ACTGTTCATG
509229 TGGTACCGATAC
1 TGGTACCGATAC
509241 TGGTACCGATAC
1 TGGTACCGATAC
509253 T
1 T
509254 CCTTTTGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (12 bp):
TGGTACCGATAC
Found at i:510195 original size:30 final size:32
Alignment explanation
Indices: 510159--510225 Score: 120
Period size: 30 Copynumber: 2.2 Consensus size: 32
510149 GAAATAAAGT
510159 CGGTTTTCAGCCGATTCACCCCGG-TTTTA-C
1 CGGTTTTCAGCCGATTCACCCCGGTTTTTAGC
510189 CGGTTTTCAGCCGATTCACCCCGGTTTTTAGC
1 CGGTTTTCAGCCGATTCACCCCGGTTTTTAGC
510221 CGGTT
1 CGGTT
510226 CTATCGGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 24 0.69
31 5 0.14
32 6 0.17
ACGTcount: A:0.12, C:0.31, G:0.22, T:0.34
Consensus pattern (32 bp):
CGGTTTTCAGCCGATTCACCCCGGTTTTTAGC
Found at i:510212 original size:21 final size:19
Alignment explanation
Indices: 510187--510247 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
510177 CCCCGGTTTT
*
510187 ACCGGTTTTCAGCCGATTC
1 ACCGGTTTTCAGCCGGTTC
*
510206 ACCCCGGTTTTTAGCCGGTTC
1 A--CCGGTTTTCAGCCGGTTC
*
510227 TATCGGTTTTCAGCCGGTTC
1 -ACCGGTTTTCAGCCGGTTC
510247 A
1 A
510248 TTACCAGACT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 2 0.06
20 16 0.46
21 16 0.46
22 1 0.03
ACGTcount: A:0.13, C:0.30, G:0.23, T:0.34
Consensus pattern (19 bp):
ACCGGTTTTCAGCCGGTTC
Found at i:510481 original size:41 final size:42
Alignment explanation
Indices: 510378--510546 Score: 184
Period size: 41 Copynumber: 4.1 Consensus size: 42
510368 ATTTAGCAGC
* * *
510378 GTTTTTCCAATAAACGCCGCAATAGAGTGGTAATTTACCGGC
1 GTTTTTTCAATAAACGCCGCAATAGAGTAGTAATTTACCGGT
** *
510420 GTTTATAGC-ACAAACG-CGCAATAGAGTA-TAATTTACCGGT
1 GTTT-TTTCAATAAACGCCGCAATAGAGTAGTAATTTACCGGT
* * * *
510460 GTTTTTTCAATAAACGCCGCAAAATAATAGTAATTTAGCGGT
1 GTTTTTTCAATAAACGCCGCAATAGAGTAGTAATTTACCGGT
* * *
510502 G-TTTTTCAAAAAACGCCGCAATATAGTAGTAATTTAGCGGT
1 GTTTTTTCAATAAACGCCGCAATAGAGTAGTAATTTACCGGT
510543 GTTT
1 GTTT
510547 GTATAAAAAC
Statistics
Matches: 107, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
39 2 0.02
40 21 0.20
41 58 0.54
42 24 0.22
43 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Consensus pattern (42 bp):
GTTTTTTCAATAAACGCCGCAATAGAGTAGTAATTTACCGGT
Found at i:511197 original size:22 final size:22
Alignment explanation
Indices: 511169--511211 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
511159 GTTTTTGTGC
*
511169 TTTCGAATTGAAAAATAATAAT
1 TTTCGAATAGAAAAATAATAAT
*
511191 TTTCGAATAGGAAAATAATAA
1 TTTCGAATAGAAAAATAATAA
511212 CTGTTGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.33
Consensus pattern (22 bp):
TTTCGAATAGAAAAATAATAAT
Found at i:512501 original size:41 final size:40
Alignment explanation
Indices: 512434--512544 Score: 98
Period size: 41 Copynumber: 2.7 Consensus size: 40
512424 GGACATTAGT
* * * *
512434 GGCGTTTATAACAAATGCCG-ATATATAATAGTACTTTTGC
1 GGCGTTTTTAACAAACGCCGCA-ATATAATAGAACTTTGGC
* *
512474 GGCGTTTTTATACAAACGCCGCAATATATTTGAACTTTGGC
1 GGCGTTTTTA-ACAAACGCCGCAATATAATAGAACTTTGGC
* *
512515 GGCATTTTTAGACACAAACGCCACAATATA
1 GGCGTTTTT--A-ACAAACGCCGCAATATA
512545 TATGGACAGT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
40 9 0.16
41 31 0.53
42 1 0.02
43 17 0.29
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (40 bp):
GGCGTTTTTAACAAACGCCGCAATATAATAGAACTTTGGC
Found at i:514518 original size:15 final size:15
Alignment explanation
Indices: 514498--514526 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
514488 ATTACCCAGG
514498 TTTGTTTCTTTGAAC
1 TTTGTTTCTTTGAAC
514513 TTTGTTTCTTTGAA
1 TTTGTTTCTTTGAA
514527 TGGTAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.10, G:0.14, T:0.62
Consensus pattern (15 bp):
TTTGTTTCTTTGAAC
Found at i:515166 original size:2 final size:2
Alignment explanation
Indices: 515159--515188 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
515149 TATTTTCTAA
515159 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
515189 TTCATATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:517152 original size:12 final size:12
Alignment explanation
Indices: 517135--517176 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
517125 AAGTAGAGAG
517135 AGCAGCAGTGGA
1 AGCAGCAGTGGA
* *
517147 AGCAGCCAG-AGC
1 AGCAG-CAGTGGA
517159 AGCAGCAGTGGA
1 AGCAGCAGTGGA
517171 AGCAGC
1 AGCAGC
517177 CAGAGCAGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 3 0.12
12 18 0.75
13 3 0.12
ACGTcount: A:0.33, C:0.24, G:0.38, T:0.05
Consensus pattern (12 bp):
AGCAGCAGTGGA
Found at i:517167 original size:24 final size:24
Alignment explanation
Indices: 517131--517187 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
517121 AGGGAAGTAG
517131 AGAG-AGCAGCAGTGGAAGCAGCC
1 AGAGCAGCAGCAGTGGAAGCAGCC
517154 AGAGCAGCAGCAGTGGAAGCAGCC
1 AGAGCAGCAGCAGTGGAAGCAGCC
517178 AGAGCAGCAG
1 AGAGCAGCAG
517188 TAGAAGTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.12
24 29 0.88
ACGTcount: A:0.35, C:0.23, G:0.39, T:0.04
Consensus pattern (24 bp):
AGAGCAGCAGCAGTGGAAGCAGCC
Found at i:517202 original size:21 final size:21
Alignment explanation
Indices: 517123--517208 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 21
517113 ATGAAACAAG
*
517123 GGAAGTAGAGAGAGCAGCAGT
1 GGAAGCAGAGAGAGCAGCAGT
517144 GGAAGCAGCCAGAGCAGCAGCAGT
1 GGAAGCAG--AGAG-AGCAGCAGT
**
517168 GGAAGCAGCCAGAGCAGCAGT
1 GGAAGCAGAGAGAGCAGCAGT
* * *
517189 AGAAGTAGAGAGAGAAGCAG
1 GGAAGCAGAGAGAGCAGCAG
517209 CGGCAACACA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
21 31 0.57
22 2 0.04
23 4 0.07
24 17 0.31
ACGTcount: A:0.38, C:0.16, G:0.40, T:0.06
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGT
Found at i:517221 original size:21 final size:21
Alignment explanation
Indices: 517197--517251 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
517187 GTAGAAGTAG
* *
517197 AGAGAGAAGCAGCGGCAACAC
1 AGAGAGAAACAGCGACAACAC
* *
517218 AGAGAGAATCAACGACAACAC
1 AGAGAGAAACAGCGACAACAC
517239 AGAGAGAAACAGC
1 AGAGAGAAACAGC
517252 ATATCAACAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.49, C:0.22, G:0.27, T:0.02
Consensus pattern (21 bp):
AGAGAGAAACAGCGACAACAC
Found at i:517649 original size:44 final size:45
Alignment explanation
Indices: 517569--517680 Score: 131
Period size: 44 Copynumber: 2.6 Consensus size: 45
517559 ATTCTGTGTT
* * * *
517569 ATTTAGCGGTGTTTGTA-ACAAAAAACGCCGCAATATACCATA-C
1 ATTTAGCGGCGTTTGTATCCTAAAAACGCCGCAATATACCAGATC
*
517612 ATTTAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGATC
1 ATTTAGCGGCGTTTGTATCCTAAAAACGCCGCAATATACCAGATC
* * *
517657 -TTTAGTGACATTTGTATCCTAAAA
1 ATTTAGCGGCGTTTGTATCCTAAAA
517681 GTGCCACGAA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
43 16 0.27
44 42 0.71
45 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (45 bp):
ATTTAGCGGCGTTTGTATCCTAAAAACGCCGCAATATACCAGATC
Found at i:517749 original size:43 final size:42
Alignment explanation
Indices: 517701--517887 Score: 160
Period size: 43 Copynumber: 4.4 Consensus size: 42
517691 ATCCCAACAC
*
517701 CTATTGCGGCGTTTGTGAGAAAAACGCCGCTAAATCTCAATA
1 CTATTGCGGCGTTTGTGAGAAAAACGCCGCTAAATCTCAAAA
* * * *
517743 CTTATTGCGACGTTTGTCACAAAAACGCTGCTAAATCTCAAAA
1 C-TATTGCGGCGTTTGTGAGAAAAACGCCGCTAAATCTCAAAA
* * * * * *
517786 CTATTACGGCGTTTATGGGGAAAATGCCGTTAAA-CATCAAAA
1 CTATTGCGGCGTTTGTGAGAAAAACGCCGCTAAATC-TCAAAA
* ** * * * * *
517828 CCTATTACATCATTTGTAAGACAAACGCCGCTAAATATCAACA
1 -CTATTGCGGCGTTTGTGAGAAAAACGCCGCTAAATCTCAAAA
517871 CATATTGCGGCGTTTGT
1 C-TATTGCGGCGTTTGT
517888 TCTATATATC
Statistics
Matches: 109, Mismatches: 31, Indels: 9
0.73 0.21 0.06
Matches are distributed among these distances:
41 1 0.01
42 31 0.28
43 77 0.71
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (42 bp):
CTATTGCGGCGTTTGTGAGAAAAACGCCGCTAAATCTCAAAA
Found at i:519328 original size:20 final size:20
Alignment explanation
Indices: 519299--519374 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 20
519289 CTACGCGAAC
*
519299 TCCAATTTCGCAACACAGTT
1 TCCAAATTCGCAACACAGTT
*
519319 TCCAAATTCGCAACTCAGTT
1 TCCAAATTCGCAACACAGTT
*
519339 TCTGC-AA-TCGCAACGC-GATT
1 TC--CAAATTCGCAACACAG-TT
519359 TCCAAATTCGCAACAC
1 TCCAAATTCGCAACAC
519375 GGAATTTCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
18 1 0.02
19 3 0.06
20 40 0.85
21 2 0.04
22 1 0.02
ACGTcount: A:0.30, C:0.32, G:0.12, T:0.26
Consensus pattern (20 bp):
TCCAAATTCGCAACACAGTT
Found at i:519408 original size:20 final size:20
Alignment explanation
Indices: 519385--519480 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 20
519375 GGAATTTCAA
* *
519385 TTCGCAACGCAAATTTCTTT
1 TTCGCAACACAAATTTCCTT
*
519405 TTCGCAACACAAGTTTCCTT
1 TTCGCAACACAAATTTCCTT
* * * *
519425 TTCACAACA-AGATTTTCTAA
1 TTCGCAACACAAATTTCCT-T
* **
519445 ATCGCAACACAAATTTTGTT
1 TTCGCAACACAAATTTCCTT
*
519465 TTCGCAACACGAATTT
1 TTCGCAACACAAATTT
519481 TAATTTCGTA
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
19 6 0.10
20 46 0.78
21 7 0.12
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.35
Consensus pattern (20 bp):
TTCGCAACACAAATTTCCTT
Found at i:519487 original size:20 final size:20
Alignment explanation
Indices: 519446--519516 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
519436 ATTTTCTAAA
**
519446 TCGCAACACAAATTTTGTTT
1 TCGCAACACAAATTTTAATT
*
519466 TCGCAACACGAATTTTAATT
1 TCGCAACACAAATTTTAATT
* * *
519486 TCG-TA-ACAACTTTTATTT
1 TCGCAACACAAATTTTAATT
*
519504 TCGTAACACAAAT
1 TCGCAACACAAAT
519517 GTTTTGGGTA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 13 0.32
19 2 0.05
20 25 0.62
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (20 bp):
TCGCAACACAAATTTTAATT
Found at i:519677 original size:16 final size:16
Alignment explanation
Indices: 519656--519686 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
519646 ACTCTAATTT
519656 TTTTTACATAATTTTA
1 TTTTTACATAATTTTA
*
519672 TTTTTATATAATTTT
1 TTTTTACATAATTTT
519687 TCAATGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTACATAATTTTA
Found at i:520490 original size:24 final size:24
Alignment explanation
Indices: 520444--520490 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
520434 GTATTCGAAA
*
520444 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATAACCGGAC
* *
520468 TTTGATTTTGGTCAATAATCGGA
1 TTTGATCTTGGTCAATAACCGGA
520491 TTTTAATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (24 bp):
TTTGATCTTGGTCAATAACCGGAC
Found at i:523144 original size:20 final size:20
Alignment explanation
Indices: 523093--523145 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
523083 TTTCGCAGCA
*
523093 ATCGCAACGTGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* ***
523113 TTCGCGTTGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
523133 ATCGCAACGCGAA
1 ATCGCAACGCGAA
523146 AATAGCAATG
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:524687 original size:21 final size:21
Alignment explanation
Indices: 524661--524778 Score: 155
Period size: 21 Copynumber: 5.6 Consensus size: 21
524651 GTGAATCGGG
* *
524661 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGGGAGGGGC
*
524682 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* *
524703 CTCTTGAACGGTGGGAGAGGC
1 CTCTTGAACGATGGGAGGGGC
* *
524724 CTCTTGAATGATGAGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* *
524745 CTCTTGAATGATAGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
524766 CTCTTGAACGATG
1 CTCTTGAACGATG
524779 ACAGGTGAAT
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 83 1.00
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:524727 original size:42 final size:41
Alignment explanation
Indices: 524661--524779 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 41
524651 GTGAATCGGG
524661 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTGGGAGGG-CCTCTTGAACGATGAGAGGGGC
*
524703 CTCTTGAACGGTGGGAGAGGCCTCTTGAATGATGAGAGGGGC
1 CTCTTGAACGGTGGGAG-GGCCTCTTGAACGATGAGAGGGGC
* * *
524745 CTCTTGAATGATAGGAGGGGCCTCTTGAACGATGA
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAACGATGA
524780 CAGGTGAATC
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
42 67 0.96
43 3 0.04
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGCCTCTTGAACGATGAGAGGGGC
Found at i:524944 original size:4 final size:4
Alignment explanation
Indices: 524923--524960 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
524913 GGGCCACTAA
* *
524923 AAAT AAAT TAAT ACAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
524961 TGCCGAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:525147 original size:21 final size:20
Alignment explanation
Indices: 525070--525149 Score: 52
Period size: 21 Copynumber: 3.9 Consensus size: 20
525060 CGTAGAGCGG
* *
525070 CTACCTCATCACGTAAAATA
1 CTACCTCACCACGTAAAACA
* *
525090 GATACCTCACCACGTAAAGCA
1 -CTACCTCACCACGTAAAACA
* ** * *
525111 CCATTGTCATCGCGTAAAACA
1 CTA-CCTCACCACGTAAAACA
525132 TCTACCTCACCACGTAAA
1 -CTACCTCACCACGTAAA
525150 GACCGTACCT
Statistics
Matches: 41, Mismatches: 16, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
20 1 0.02
21 38 0.93
22 2 0.05
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.21
Consensus pattern (20 bp):
CTACCTCACCACGTAAAACA
Found at i:525163 original size:42 final size:43
Alignment explanation
Indices: 525071--525165 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 43
525061 GTAGAGCGGC
*
525071 TACCTCATCACGTAAAATAGATACCTCACCACGTAAAGCACCA
1 TACCTCATCACGTAAAACAGATACCTCACCACGTAAAGCACCA
** * ** *
525114 T-TGTCATCGCGTAAAACATCTACCTCACCACGTAAAG-ACCG
1 TACCTCATCACGTAAAACAGATACCTCACCACGTAAAGCACCA
525155 TACCTCATCAC
1 TACCTCATCAC
525166 ACCATGCACC
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
41 4 0.10
42 36 0.88
43 1 0.02
ACGTcount: A:0.35, C:0.34, G:0.11, T:0.21
Consensus pattern (43 bp):
TACCTCATCACGTAAAACAGATACCTCACCACGTAAAGCACCA
Found at i:527363 original size:22 final size:22
Alignment explanation
Indices: 527316--527363 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
527306 GAGGGGGGTC
* * * *
527316 GCCGGATATGGGGACGGATTTC
1 GCCGGAGATGGGGACAGATATA
527338 GCCGGAGATGGGGACAGATATA
1 GCCGGAGATGGGGACAGATATA
527360 GCCG
1 GCCG
527364 TAGAGAGTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.42, T:0.17
Consensus pattern (22 bp):
GCCGGAGATGGGGACAGATATA
Found at i:527553 original size:20 final size:20
Alignment explanation
Indices: 527530--527666 Score: 105
Period size: 20 Copynumber: 6.8 Consensus size: 20
527520 TGACTTATGT
527530 GTTGCGAATTACAAATTCGC
1 GTTGCGAATTACAAATTCGC
* * *
527550 GTTGCGATTTACAAATTATGT
1 GTTGCGAATTACAAATT-CGC
* *
527571 GTTACGAATTATAAATTCGC
1 GTTGCGAATTACAAATTCGC
* * *
527591 GTTGCGATTTACATATTCGT
1 GTTGCGAATTACAAATTCGC
** *
527611 GTTGCGAATTTGGAAAATCGC
1 GTTGCGAA-TTACAAATTCGC
* * *
527632 GTTGCGGAA-AAGAAATTCGA
1 GTTGC-GAATTACAAATTCGC
*
527652 GTTGCGAATTTCAAA
1 GTTGCGAATTACAAA
527667 ACTGAGTTGC
Statistics
Matches: 87, Mismatches: 26, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
19 3 0.03
20 54 0.62
21 27 0.31
22 3 0.03
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGC
Found at i:527572 original size:41 final size:41
Alignment explanation
Indices: 527524--527620 Score: 151
Period size: 41 Copynumber: 2.4 Consensus size: 41
527514 CGAATTTGAC
527524 TTATGTGTTGCGAATTACAAATTCGCGTTGCGATTTACAAA
1 TTATGTGTTGCGAATTACAAATTCGCGTTGCGATTTACAAA
* * *
527565 TTATGTGTTACGAATTATAAATTCGCGTTGCGATTTACATA
1 TTATGTGTTGCGAATTACAAATTCGCGTTGCGATTTACAAA
*
527606 TT-CGTGTTGCGAATT
1 TTATGTGTTGCGAATT
527621 TGGAAAATCG
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 11 0.22
41 40 0.78
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (41 bp):
TTATGTGTTGCGAATTACAAATTCGCGTTGCGATTTACAAA
Found at i:527632 original size:41 final size:40
Alignment explanation
Indices: 527528--527637 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 40
527518 TTTGACTTAT
* *
527528 GTGTTGCGAATTACAAATTCGCGTTGCGATTTACAAATTAT
1 GTGTTGCGAATT-TAAATTCGCGTTGCGATTTACAAATTAC
* *
527569 GTGTTACGAATTATAAATTCGCGTTGCGATTTACATATT-C
1 GTGTTGCGAATT-TAAATTCGCGTTGCGATTTACAAATTAC
*
527609 GTGTTGCGAATTTGGAAAATCGCGTTGCG
1 GTGTTGCGAATTT--AAATTCGCGTTGCG
527638 GAAAAGAAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
39 1 0.02
40 11 0.18
41 49 0.80
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (40 bp):
GTGTTGCGAATTTAAATTCGCGTTGCGATTTACAAATTAC
Found at i:529710 original size:14 final size:14
Alignment explanation
Indices: 529691--529731 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
529681 GCTGGGCATC
529691 CGAGGCCATCCGAA
1 CGAGGCCATCCGAA
529705 CGAGGCCATCCGAA
1 CGAGGCCATCCGAA
529719 CGAGGCCATCCGA
1 CGAGGCCATCCGA
529732 GGGCATCCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.27, C:0.37, G:0.29, T:0.07
Consensus pattern (14 bp):
CGAGGCCATCCGAA
Found at i:529738 original size:10 final size:10
Alignment explanation
Indices: 529719--529785 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
529709 GCCATCCGAA
*
529719 CGAGGCCATC
1 CGAGGGCATC
529729 CGAGGGCATC
1 CGAGGGCATC
*
529739 CGAGGGCAAC
1 CGAGGGCATC
*
529749 CGAGCGAGCTATG
1 CGAG-G-GC-ATC
*
529762 CGAGGGAATC
1 CGAGGGCATC
* *
529772 AGAGGGCAAC
1 CGAGGGCATC
529782 CGAG
1 CGAG
529786 CGAGGGTAGG
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
10 34 0.77
11 2 0.05
12 3 0.07
13 5 0.11
ACGTcount: A:0.27, C:0.27, G:0.39, T:0.07
Consensus pattern (10 bp):
CGAGGGCATC
Found at i:529878 original size:10 final size:10
Alignment explanation
Indices: 529855--529945 Score: 62
Period size: 10 Copynumber: 8.8 Consensus size: 10
529845 GCATAGCTCG
* *
529855 CTCGGTTGCC
1 CTCGGATGCT
529865 CTCGGATGCT
1 CTCGGATGCT
*
529875 CTCGCATAGCT
1 CTCGGAT-GCT
529886 CGTTCGGATGGC-
1 C--TCGGAT-GCT
529898 CTCGGATGCT
1 CTCGGATGCT
529908 CTCGGATGGC-
1 CTCGGAT-GCT
529918 CTCGGATGCT
1 CTCGGATGCT
* *
529928 TTCAGATGGC-
1 CTCGGAT-GCT
529938 CTCGGATG
1 CTCGGATG
529946 TCCAGCCTGT
Statistics
Matches: 65, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
9 5 0.08
10 44 0.68
11 8 0.12
12 1 0.02
13 7 0.11
ACGTcount: A:0.11, C:0.30, G:0.32, T:0.27
Consensus pattern (10 bp):
CTCGGATGCT
Found at i:529879 original size:33 final size:33
Alignment explanation
Indices: 529842--529911 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
529832 CTCCGATTCC
*
529842 CTCGCATAGCTCGCTCGGTTGCCCTCGGATGCT
1 CTCGCATAGCTCGCTCGGATGCCCTCGGATGCT
* *
529875 CTCGCATAGCTCGTTCGGATGGCCTCGGATGCT
1 CTCGCATAGCTCGCTCGGATGCCCTCGGATGCT
529908 CTCG
1 CTCG
529912 GATGGCCTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.10, C:0.34, G:0.29, T:0.27
Consensus pattern (33 bp):
CTCGCATAGCTCGCTCGGATGCCCTCGGATGCT
Found at i:529914 original size:20 final size:20
Alignment explanation
Indices: 529889--529945 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
529879 CATAGCTCGT
529889 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
*
529909 TCGGATGGCCTCGGATGCTT
1 TCGGATGGCCTCGGATGCTC
*
529929 TCAGATGGCCTCGGATG
1 TCGGATGGCCTCGGATG
529946 TCCAGCCTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.12, C:0.26, G:0.35, T:0.26
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:530158 original size:20 final size:19
Alignment explanation
Indices: 530133--530266 Score: 61
Period size: 20 Copynumber: 7.3 Consensus size: 19
530123 CAAATGAAAT
530133 AAATAAGATAAGATAAAGAA
1 AAATAAGATAA-ATAAAGAA
* * *
530153 AAATAAAATAAAATGAAGAC
1 AAATAAGAT-AAATAAAGAA
* *
530173 AAATAGGAT-AA-AAATAA
1 AAATAAGATAAATAAAGAA
*
530190 TAATAAGA-AATATAAAG-A
1 AAATAAGATAA-ATAAAGAA
*
530208 AAA-AAG--AAATAAGGAAA
1 AAATAAGATAAATAAAG-AA
* * *
530225 AAATAA-AAAAATATAGAT
1 AAATAAGATAAATAAAGAA
* *
530243 AAATAGGATAAATATA-AA
1 AAATAAGATAAATAAAGAA
530261 AAATAA
1 AAATAA
530267 TAATAAAAAA
Statistics
Matches: 84, Mismatches: 20, Indels: 22
0.67 0.16 0.17
Matches are distributed among these distances:
15 5 0.06
16 2 0.02
17 17 0.20
18 20 0.24
19 17 0.20
20 21 0.25
21 2 0.02
ACGTcount: A:0.71, C:0.01, G:0.11, T:0.17
Consensus pattern (19 bp):
AAATAAGATAAATAAAGAA
Found at i:530236 original size:70 final size:74
Alignment explanation
Indices: 530151--530312 Score: 181
Period size: 78 Copynumber: 2.1 Consensus size: 74
530141 TAAGATAAAG
*
530151 AAAAATAAAATAAA-ATGAAGACAAATAGG-AT-AAAAATAATAAT-AAGAAATATAAAGAAAAA
1 AAAAATAAAA-AAATAT--AGACAAATAGGAATAAAAAATAATAATAAAAAAATATAAAGAAAAA
530212 AGAAATAA-GGA
63 AGAAATAAGGGA
*
530223 AAAAATAAAAAAATATAGATAAATAGGATAAATATAAAAAATAATAATAAAAAAATATAAAGAAA
1 AAAAATAAAAAAATATAGACAAATAGG----A-ATAAAAAATAATAATAAAAAAATATAAAGAAA
*
530288 GAAGAAATAAGGGA
61 AAAGAAATAAGGGA
530302 ACAAAATAAAA
1 A-AAAATAAAA
530313 TACACAATAA
Statistics
Matches: 76, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
70 10 0.13
71 3 0.04
72 12 0.16
76 2 0.03
77 12 0.16
78 24 0.32
79 4 0.05
80 9 0.12
ACGTcount: A:0.72, C:0.01, G:0.11, T:0.16
Consensus pattern (74 bp):
AAAAATAAAAAAATATAGACAAATAGGAATAAAAAATAATAATAAAAAAATATAAAGAAAAAAGA
AATAAGGGA
Found at i:530282 original size:13 final size:13
Alignment explanation
Indices: 530226--530282 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
530216 ATAAGGAAAA
530226 AATAAAAAAATAT
1 AATAAAAAAATAT
**
530239 AGATAAATAGGATA-
1 A-ATAAA-AAAATAT
530253 AATATAAAAAATAAT
1 AATA-AAAAAAT-AT
530268 AATAAAAAAATAT
1 AATAAAAAAATAT
530281 AA
1 AA
530283 AGAAAGAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
13 11 0.31
14 16 0.46
15 8 0.23
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (13 bp):
AATAAAAAAATAT
Found at i:530323 original size:78 final size:77
Alignment explanation
Indices: 530182--530325 Score: 202
Period size: 78 Copynumber: 1.9 Consensus size: 77
530172 CAAATAGGAT
* * *
530182 AAAAATAATAATAAGAAATATAAAGAAAAAAGAAATAAGGAAAAAATAAAAAAATATAGATAAAT
1 AAAAATAATAATAAAAAATATAAAGAAAAAAGAAATAAGGAAAAAATAAAAAAACACAGATAAAT
530247 AGGATAAATATA
66 AGGATAAATATA
* *
530259 AAAAATAATAATAAAAAAATATAAAGAAAGAAGAAATAAGGGAACAAAAT-AAAATACACA-ATA
1 AAAAATAATAAT-AAAAAATATAAAGAAAAAAGAAATAA-GGAA-AAAATAAAAAAACACAGATA
530322 AATA
63 AATA
530326 AAAACTAGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
77 12 0.20
78 31 0.53
79 11 0.19
80 5 0.08
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.17
Consensus pattern (77 bp):
AAAAATAATAATAAAAAATATAAAGAAAAAAGAAATAAGGAAAAAATAAAAAAACACAGATAAAT
AGGATAAATATA
Found at i:530377 original size:13 final size:12
Alignment explanation
Indices: 530355--530386 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
530345 CAGTAAAGAT
530355 TAAAAAAATAAA
1 TAAAAAAATAAA
530367 TAAATAAAATAAA
1 TAAA-AAAATAAA
530380 TAAAAAA
1 TAAAAAA
530387 GTATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
TAAAAAAATAAA
Found at i:530552 original size:17 final size:17
Alignment explanation
Indices: 530530--530638 Score: 57
Period size: 18 Copynumber: 6.2 Consensus size: 17
530520 AACAAATGAA
530530 AAATAATAAAAATAATT
1 AAATAATAAAAATAATT
* *
530547 AAATAATTAAAATAAAAT
1 AAATAATAAAAAT-AATT
530565 AACGAT-A-AAAAATAATAT
1 AA--ATAATAAAAATAAT-T
* *
530583 CATATAA-AAAAATAA-A
1 -AAATAATAAAAATAATT
* *
530599 AAATAAAATAGAAATAAAAT
1 AAAT--AATAAAAAT-AATT
530619 AAATAATAAAAA-AATT
1 AAATAATAAAAATAATT
530635 AAAT
1 AAAT
530639 TAAAAGGGAA
Statistics
Matches: 70, Mismatches: 11, Indels: 23
0.67 0.11 0.22
Matches are distributed among these distances:
15 3 0.04
16 7 0.10
17 18 0.26
18 32 0.46
19 4 0.06
20 6 0.09
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (17 bp):
AAATAATAAAAATAATT
Found at i:530615 original size:11 final size:11
Alignment explanation
Indices: 530555--530629 Score: 55
Period size: 11 Copynumber: 6.8 Consensus size: 11
530545 TTAAATAATT
530555 AAAATAAAATA
1 AAAATAAAATA
**
530566 ACGATAAAA-A
1 AAAATAAAATA
* **
530576 ATAATATCATA
1 AAAATAAAATA
*
530587 TAAA-AAAATAA
1 AAAATAAAAT-A
530598 AAAATAAAATA
1 AAAATAAAATA
*
530609 GAAATAAAATA
1 AAAATAAAATA
530620 AATAATAAAA
1 AA-AATAAAA
530630 AAATTAAATT
Statistics
Matches: 47, Mismatches: 13, Indels: 7
0.70 0.19 0.10
Matches are distributed among these distances:
10 9 0.19
11 26 0.55
12 12 0.26
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:530627 original size:23 final size:22
Alignment explanation
Indices: 530523--530643 Score: 79
Period size: 23 Copynumber: 5.4 Consensus size: 22
530513 TACAATAAAC
* *
530523 AAATGAAAAATAATA-AAAAT-
1 AAATAAAAAATAAAATAAAATA
* *
530543 AATTAAATAATTAAAATAAAATA
1 AAATAAA-AAATAAAATAAAATA
*
530566 ACGATAAAAAATAATATCATATAAA-A
1 A-AATAAAAAATAA-A--ATA-AAATA
530592 AAATAAAAAATAAAATAGAAATA
1 AAATAAAAAATAAAATA-AAATA
* *
530615 AAATAAATAATAAAA-AAATTA
1 AAATAAAAAATAAAATAAAATA
*
530636 AATTAAAA
1 AAATAAAA
530644 GGGAAACAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
20 5 0.06
21 16 0.20
22 12 0.15
23 21 0.27
24 6 0.08
25 11 0.14
26 5 0.06
27 3 0.04
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (22 bp):
AAATAAAAAATAAAATAAAATA
Found at i:531685 original size:4 final size:4
Alignment explanation
Indices: 531672--531723 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
531662 AACAAACAAT
* * *
531672 AATA ATTA AATA AAT- AATA AATGA AATAA AATA AAGA AATA GATA AATA
1 AATA AATA AATA AATA AATA AAT-A AAT-A AATA AATA AATA AATA AATA
531721 AAT
1 AAT
531724 TAAAAACATT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
3 3 0.08
4 28 0.72
5 8 0.21
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:531790 original size:38 final size:39
Alignment explanation
Indices: 531733--532061 Score: 344
Period size: 38 Copynumber: 8.7 Consensus size: 39
531723 TTAAAAACAT
* * *
531733 TTTTTAAAACTATACAATATATGT-TTTTTAAAAAATAA
1 TTTTCAAAACTATATAATATATATATTTTTAAAAAATAA
* *
531771 TTTTCAAGA-TCATATAATATATAT-TTTTAAAAAAATAA
1 TTTTCAAAACT-ATATAATATATATATTTTTAAAAAATAA
*
531809 TTTTCAAAACTATATAATATATATATTTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATATATTTTTAAAAAATAA
*
531848 TTTTCAAAACTATATAATATATATATATATTTTAAAAACTAA
1 TTTTCAAAACTATAT-A-ATATATATAT-TTTTAAAAAATAA
*
531890 TTTTCAAAACTATATAATATATATA-TTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATATATTTTTAAAAAATAA
* * *
531928 TTTTCAAAACTATATAATATATATGTTTTTCAAAAATAT
1 TTTTCAAAACTATATAATATATATATTTTTAAAAAATAA
* *
531967 TTTTAAAAACTATAT-AT-TATATA-TTTT-CAAAAT-A
1 TTTTCAAAACTATATAATATATATATTTTTAAAAAATAA
** * * * *
532001 TTTAAAAAACCCATAT-AT-TATATAATTTT-CAAAATGA
1 TTTTCAAAA-CTATATAATATATATATTTTTAAAAAATAA
532038 -TTTC-AAACTATATAATATATATAT
1 TTTTCAAAACTATATAATATATATAT
532062 ATATATATAT
Statistics
Matches: 257, Mismatches: 22, Indels: 26
0.84 0.07 0.09
Matches are distributed among these distances:
34 13 0.05
35 23 0.09
36 22 0.09
37 7 0.03
38 91 0.35
39 52 0.20
40 10 0.04
41 11 0.04
42 28 0.11
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.43
Consensus pattern (39 bp):
TTTTCAAAACTATATAATATATATATTTTTAAAAAATAA
Found at i:531856 original size:13 final size:13
Alignment explanation
Indices: 531835--531939 Score: 56
Period size: 13 Copynumber: 7.9 Consensus size: 13
531825 ATATATATAT
531835 TTTTAAAAACTAA
1 TTTTAAAAACTAA
*
531848 TTTTCAAAACTATA
1 TTTTAAAAACTA-A
* * *
531862 TAATATATATA-TATA
1 T--TTTAAAAACTA-A
531877 TTTTAAAAACTAA
1 TTTTAAAAACTAA
*
531890 TTTTCAAAACT-A
1 TTTTAAAAACTAA
* *
531902 -TATAATATA-TATA
1 TTTTAA-AAACTA-A
531915 TTTTAAAAACTAA
1 TTTTAAAAACTAA
*
531928 TTTTCAAAACTA
1 TTTTAAAAACTA
531940 TATAATATAT
Statistics
Matches: 68, Mismatches: 15, Indels: 18
0.67 0.15 0.18
Matches are distributed among these distances:
11 4 0.06
12 3 0.04
13 42 0.62
14 10 0.15
15 5 0.07
16 4 0.06
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.42
Consensus pattern (13 bp):
TTTTAAAAACTAA
Found at i:531891 original size:119 final size:119
Alignment explanation
Indices: 531749--531990 Score: 355
Period size: 119 Copynumber: 2.0 Consensus size: 119
531739 AAACTATACA
* * *
531749 ATATATGTTTTTTAAAAAATAATTTTCAAGA-TCATATAATATATAT-TTTTAAAAAAATAATTT
1 ATATATATATTTTAAAAAATAATTTTCAAAACT-ATATAATATATATATTTT-AAAAAATAATTT
*
531812 TCAAAACTATATAATATATATATTTTT-AAAAACTAATTTTCAAAACTATATAATAT
64 TCAAAACTATATAATATATATATTTTTCAAAAA-TAATTTTAAAAACTATATAATAT
* *
531868 ATATATATATTTTAAAAACTAATTTTCAAAACTATATAATATATATATTTTAAAAACTAATTTTC
1 ATATATATATTTTAAAAAATAATTTTCAAAACTATATAATATATATATTTTAAAAAATAATTTTC
* * *
531933 AAAACTATATAATATATATGTTTTTCAAAAATATTTTTAAAAACTATATATTAT
66 AAAACTATATAATATATATATTTTTCAAAAATAATTTTAAAAACTATATAATAT
531987 ATAT
1 ATAT
531991 TTTCAAAATA
Statistics
Matches: 111, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
119 101 0.91
120 10 0.09
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.44
Consensus pattern (119 bp):
ATATATATATTTTAAAAAATAATTTTCAAAACTATATAATATATATATTTTAAAAAATAATTTTC
AAAACTATATAATATATATATTTTTCAAAAATAATTTTAAAAACTATATAATAT
Found at i:532057 original size:2 final size:2
Alignment explanation
Indices: 532046--532082 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
532036 GATTTCAAAC
532046 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
532083 AATAAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:533978 original size:16 final size:16
Alignment explanation
Indices: 533957--533991 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
533947 TTGGAGAATG
533957 ACAATGGATCTACACT
1 ACAATGGATCTACACT
*
533973 ACAATGGATCTACATT
1 ACAATGGATCTACACT
533989 ACA
1 ACA
533992 TATGTTACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (16 bp):
ACAATGGATCTACACT
Found at i:539220 original size:21 final size:21
Alignment explanation
Indices: 539196--539237 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
539186 AGTTTATTTT
*
539196 TAAACTTTATTTTAATTATCG
1 TAAACTTTATTTCAATTATCG
*
539217 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
539238 AACTTGAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:539302 original size:33 final size:32
Alignment explanation
Indices: 539226--539333 Score: 150
Period size: 33 Copynumber: 3.4 Consensus size: 32
539216 GTAAACTTTG
539226 TTTCAA-TTATCGAACTTGAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTGAAGTTTTTAAGTA
*
539257 -TTGAATTTATCGAACTTGAAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTG-AAGTTTTTAAGTA
* *
539289 TTTTAATTTATCGAACTTGGAAGTATTTAAGTA
1 TTTCAATTTATCGAACTT-GAAGTTTTTAAGTA
539322 TTTCAA-TTATCG
1 TTTCAATTTATCG
539334 TAAACTTTGT
Statistics
Matches: 69, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
30 4 0.06
31 12 0.17
32 19 0.28
33 33 0.48
34 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.45
Consensus pattern (32 bp):
TTTCAATTTATCGAACTTGAAGTTTTTAAGTA
Found at i:540724 original size:2 final size:2
Alignment explanation
Indices: 540717--540746 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
540707 TTTACCCTTA
540717 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
540747 TGATAAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:542061 original size:6 final size:6
Alignment explanation
Indices: 542026--542057 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
542016 TATTGTAGGT
*
542026 GTGGAA GTGGAA GTGGAA GTGGAA GTAGAA GT
1 GTGGAA GTGGAA GTGGAA GTGGAA GTGGAA GT
542058 AGAACGGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.34, C:0.00, G:0.47, T:0.19
Consensus pattern (6 bp):
GTGGAA
Found at i:544575 original size:23 final size:23
Alignment explanation
Indices: 544547--544594 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
544537 AATTATCTTT
*
544547 TAAATTTTATAAAAAATTATATA
1 TAAATTTTATAAAAAAGTATATA
*
544570 TAAATTTTATTAAAAAGTATATA
1 TAAATTTTATAAAAAAGTATATA
544593 TA
1 TA
544595 TTAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TAAATTTTATAAAAAAGTATATA
Found at i:548141 original size:19 final size:19
Alignment explanation
Indices: 548117--548159 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
548107 GCGATCAAAT
548117 AAAATAAATTTAATTATT-C
1 AAAATAAA-TTAATTATTGC
* *
548136 AAAATACATTAATTTTTGC
1 AAAATAAATTAATTATTGC
548155 AAAAT
1 AAAAT
548160 TTCAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATAAATTAATTATTGC
Found at i:550947 original size:31 final size:33
Alignment explanation
Indices: 550890--550950 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 33
550880 TTAGTCACAG
**
550890 TAGACTATTCAATAAATGTTTTTATTTTCATCA
1 TAGACTATTCAATAAATACTTTTATTTTCATCA
550923 TAGACTATT-AA-AAATACTTTTATTTTCA
1 TAGACTATTCAATAAATACTTTTATTTTCA
550951 AATAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 15 0.58
32 2 0.08
33 9 0.35
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (33 bp):
TAGACTATTCAATAAATACTTTTATTTTCATCA
Done.