Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009056.1 Hibiscus syriacus cultivar Beakdansim tig00112471_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: 907955
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:2957 original size:16 final size:17
Alignment explanation
Indices: 2925--2958 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2915 ATTTATTTGA
*
2925 AAAAAAATTATACGCTT
1 AAAAAAATTATAAGCTT
2942 AAAAAAATTA-AAGCTT
1 AAAAAAATTATAAGCTT
2958 A
1 A
2959 TCTTTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAAAAATTATAAGCTT
Found at i:17491 original size:15 final size:15
Alignment explanation
Indices: 17471--17505 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
17461 AGTTTGCACA
17471 CATTCACAGTATGTC
1 CATTCACAGTATGTC
17486 CATTCACAGTATGTC
1 CATTCACAGTATGTC
17501 CATTC
1 CATTC
17506 TTTTCACACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (15 bp):
CATTCACAGTATGTC
Found at i:21631 original size:20 final size:21
Alignment explanation
Indices: 21603--21644 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
21593 CAACCAGCTG
21603 GCACATCAATTTCATCA-CCT
1 GCACATCAATTTCATCAGCCT
* *
21623 GCACCTCAATTTTATCAGCCT
1 GCACATCAATTTCATCAGCCT
21644 G
1 G
21645 TGCAGTCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.26, C:0.33, G:0.10, T:0.31
Consensus pattern (21 bp):
GCACATCAATTTCATCAGCCT
Found at i:23022 original size:128 final size:128
Alignment explanation
Indices: 22711--23086 Score: 604
Period size: 121 Copynumber: 3.0 Consensus size: 128
22701 GCTTTATGCT
* *
22711 GGCCTCAGAACTTGGGAATCAAATTATTCCTTTTCTAGATTATTTCGGTTGGCCAAAGCTTCATA
1 GGCCTCAGAACTTGGGAATCAAATTATTCCTTTTCTAGATTATTTAGGTTGGTCAAAGCTTCATA
* * *
22776 ATGAATATTGGGTTAGGAGCAGTATGGCTTGAGAAGAATATACAGTATG------ATTT-TCA
66 ATGAATATTGGGTTAGGAGCAGTATAGTTTGAGGAGAATATACAGTATGATTATCATTTATCA
22832 GGCCTCAGAACTTGGGAATCAAATTATTCCTTTTCTAGATTATTTAGGTTGGTCAAAGCTTCATA
1 GGCCTCAGAACTTGGGAATCAAATTATTCCTTTTCTAGATTATTTAGGTTGGTCAAAGCTTCATA
22897 ATGAATATTGGGTTAGGAGCAGTATAGTTTGAGGAGAATATACAGTATGATTATCATTTATCA
66 ATGAATATTGGGTTAGGAGCAGTATAGTTTGAGGAGAATATACAGTATGATTATCATTTATCA
* *
22960 GGCCTCAGAACTTGGCAATCAAATTATTCCTTTTCTAGATTATTTAGGTTGGTCAAAACTTCATA
1 GGCCTCAGAACTTGGGAATCAAATTATTCCTTTTCTAGATTATTTAGGTTGGTCAAAGCTTCATA
* *
23025 ATGAATATAATGGGATAGGAGCAGTACAGTTTGAGGAGAATATACAGTATGATTATCATTTA
66 ATGAATAT--TGGGTTAGGAGCAGTATAGTTTGAGGAGAATATACAGTATGATTATCATTTA
23087 CAAATTGTGT
Statistics
Matches: 237, Mismatches: 9, Indels: 9
0.93 0.04 0.04
Matches are distributed among these distances:
121 109 0.46
127 4 0.02
128 74 0.31
130 50 0.21
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.35
Consensus pattern (128 bp):
GGCCTCAGAACTTGGGAATCAAATTATTCCTTTTCTAGATTATTTAGGTTGGTCAAAGCTTCATA
ATGAATATTGGGTTAGGAGCAGTATAGTTTGAGGAGAATATACAGTATGATTATCATTTATCA
Found at i:27183 original size:14 final size:14
Alignment explanation
Indices: 27138--27184 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
27128 ATTAATTTAA
27138 AATAGAATGGTATT
1 AATAGAATGGTATT
* *
27152 ACTAGAATGGTCA-A
1 AATAGAATGGT-ATT
*
27166 AATAGAATGATATT
1 AATAGAATGGTATT
27180 AATAG
1 AATAG
27185 TTTGAGGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
13 1 0.04
14 24 0.92
15 1 0.04
ACGTcount: A:0.47, C:0.04, G:0.19, T:0.30
Consensus pattern (14 bp):
AATAGAATGGTATT
Found at i:33003 original size:20 final size:20
Alignment explanation
Indices: 32967--33004 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32957 ATCCTATTCC
**
32967 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
32987 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
33005 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:34309 original size:2 final size:2
Alignment explanation
Indices: 34302--34336 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
34292 TACCAAATTG
34302 AT AT AT 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 AT AT AT A
34337 ACAATAATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35438 original size:19 final size:20
Alignment explanation
Indices: 35402--35439 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
35392 ATATAATCTA
*
35402 AAATAATCAGTTAATAAATC
1 AAATAATCAGTGAATAAATC
*
35422 AAAT-ATCAGTGATTAAAT
1 AAATAATCAGTGAATAAAT
35440 AAAAAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.32
Consensus pattern (20 bp):
AAATAATCAGTGAATAAATC
Found at i:36140 original size:38 final size:38
Alignment explanation
Indices: 36098--36175 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
36088 TAATTTTTTT
* * *
36098 TGGGCTCTTGCTATTTTGGGCCCCTGTTCGGTCGTACA
1 TGGGCCCTTGCTATTCTGGGCCCCTGTTCGGTCGCACA
36136 TGGGCCCTTGCTATTCTGGGCCCCTGTTCGGTCGCACA
1 TGGGCCCTTGCTATTCTGGGCCCCTGTTCGGTCGCACA
36174 TG
1 TG
36176 TTGTGCTGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.08, C:0.29, G:0.29, T:0.33
Consensus pattern (38 bp):
TGGGCCCTTGCTATTCTGGGCCCCTGTTCGGTCGCACA
Found at i:36344 original size:2 final size:2
Alignment explanation
Indices: 36337--36370 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
36327 CAACTAGAGG
36337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36371 ATCACCGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38284 original size:2 final size:2
Alignment explanation
Indices: 38279--38313 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
38269 TCTCTCTCTC
38279 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38314 CCAGCACTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45758 original size:24 final size:23
Alignment explanation
Indices: 45731--45776 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
45721 ATGAATTCGG
*
45731 ATAT-TACATTAATGTTAGATATAA
1 ATATGTAC-TTAATATTA-ATATAA
45755 ATATGTACTTAATATTAATATA
1 ATATGTACTTAATATTAATATA
45777 TTTAAATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 12 0.60
25 3 0.15
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (23 bp):
ATATGTACTTAATATTAATATAA
Found at i:55601 original size:35 final size:35
Alignment explanation
Indices: 55555--55630 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
55545 AAAACAGTCC
* * *
55555 TCAATTTCATTCTAAACCCCAATTTCTAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
55590 TCAATTTCATTCTCAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
55625 TCAATT
1 TCAATT
55631 AAATTCAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:56173 original size:130 final size:130
Alignment explanation
Indices: 56027--56274 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
56017 TATTTATATA
* ** *
56027 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* *
56092 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
56157 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * *
56222 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
56275 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:56247 original size:23 final size:21
Alignment explanation
Indices: 56201--56247 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
56191 AATTAATCAT
56201 TTAACCAGGATCTGACATATG
1 TTAACCAGGATCTGACATATG
* *
56222 TTAACACATGATCATGATATATG
1 TTAAC-CAGGATC-TGACATATG
56245 TTA
1 TTA
56248 TTGGTGACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (21 bp):
TTAACCAGGATCTGACATATG
Found at i:56629 original size:28 final size:27
Alignment explanation
Indices: 56598--56660 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
56588 AGTTGATACA
56598 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGATTT
** * *
56626 ATATATTTTTAAACTAAATTTAATATTT
1 ATAT-TTTAAAAAATAAATTTAAGATTT
56654 ATATTTT
1 ATATTTT
56661 TCATATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 3 0.10
28 22 0.73
29 5 0.17
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGATTT
Found at i:56763 original size:17 final size:17
Alignment explanation
Indices: 56737--56769 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
56727 ATTTCTTATT
56737 AAAAATAAAT-ATTCAA
1 AAAAATAAATGATTCAA
56753 AAAATATAAATGATTCA
1 AAAA-ATAAATGATTCA
56770 TACATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAAATAAATGATTCAA
Found at i:57444 original size:29 final size:30
Alignment explanation
Indices: 57385--57449 Score: 123
Period size: 29 Copynumber: 2.2 Consensus size: 30
57375 TTTTAAAATT
57385 GATAATGTGTGATGATGGGGTAATTTTTTA
1 GATAATGTGTGATGATGGGGTAATTTTTTA
57415 GATAATGTGTGATGAT-GGGTAATTTTTTA
1 GATAATGTGTGATGATGGGGTAATTTTTTA
57444 GATAAT
1 GATAAT
57450 ATGTTGGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 19 0.54
30 16 0.46
ACGTcount: A:0.29, C:0.00, G:0.28, T:0.43
Consensus pattern (30 bp):
GATAATGTGTGATGATGGGGTAATTTTTTA
Found at i:80609 original size:21 final size:21
Alignment explanation
Indices: 80580--80722 Score: 123
Period size: 21 Copynumber: 7.0 Consensus size: 21
80570 TCCACTATCG
80580 CAAATTCGCGTTGCGATAGTT
1 CAAATTCGCGTTGCGATAGTT
* * *
80601 GAAAATCGCGTTGCGAT-TTT
1 CAAATTCGCGTTGCGATAGTT
* *
80621 CCATTTCGCGTTGCGATAG-T
1 CAAATTCGCGTTGCGATAGTT
* * *
80641 CTACAGTCGCGTTGCGAT-TTT
1 C-AAATTCGCGTTGCGATAGTT
* *
80662 CCATTTCGCGTTGCGATAGTT
1 CAAATTCGCGTTGCGATAGTT
* *
80683 GAAATTCGCGTTGCGAT-TTT
1 CAAATTCGCGTTGCGATAGTT
* *
80703 CCATTTCGCGTTGCGATAGT
1 CAAATTCGCGTTGCGATAGT
80723 CTACAGTTGT
Statistics
Matches: 91, Mismatches: 26, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
20 45 0.49
21 46 0.51
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.36
Consensus pattern (21 bp):
CAAATTCGCGTTGCGATAGTT
Found at i:80631 original size:20 final size:20
Alignment explanation
Indices: 80606--80719 Score: 131
Period size: 20 Copynumber: 5.6 Consensus size: 20
80596 TAGTTGAAAA
80606 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
80626 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
80647 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** *
80667 TCGCGTTGCGATAGTTGAAAT
1 TCGCGTTGCGAT-TTTCCATT
80688 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
80708 TCGCGTTGCGAT
1 TCGCGTTGCGAT
80720 AGTCTACAGT
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.05
20 40 0.53
21 28 0.37
22 4 0.05
ACGTcount: A:0.14, C:0.23, G:0.25, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:80651 original size:41 final size:41
Alignment explanation
Indices: 80584--80722 Score: 235
Period size: 41 Copynumber: 3.4 Consensus size: 41
80574 CTATCGCAAA
*
80584 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAGTCGCGTTGCGATTTTCCAT
*
80625 TTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGT-TGAAAGTCGCGTTGCGATTTTCCAT
*
80666 TTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAGTCGCGTTGCGATTTTCCAT
80707 TTCGCGTTGCGATAGT
1 TTCGCGTTGCGATAGT
80723 CTACAGTTGT
Statistics
Matches: 92, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
40 1 0.01
41 90 0.98
42 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAGTCGCGTTGCGATTTTCCAT
Found at i:80721 original size:82 final size:83
Alignment explanation
Indices: 80584--80741 Score: 291
Period size: 82 Copynumber: 1.9 Consensus size: 83
80574 CTATCGCAAA
80584 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTC
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTC
80649 G-CGTTGCGATTTTCCAT
66 GTCGTTGCGATTTTCCAT
* *
80666 TTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTC
80731 GTCGTTGCGAT
66 GTCGTTGCGAT
80742 AGTCTACAGT
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
82 64 0.88
83 9 0.12
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.37
Consensus pattern (83 bp):
TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTC
GTCGTTGCGATTTTCCAT
Found at i:80739 original size:22 final size:22
Alignment explanation
Indices: 80711--80763 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
80701 TTCCATTTCG
80711 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
80733 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
80755 TGTTGCGAT
1 CGTTGCGAT
80764 TTTCCAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:80827 original size:6 final size:6
Alignment explanation
Indices: 80816--80847 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
80806 CTTAAGAATT
80816 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
80848 CGAGACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:81352 original size:5 final size:5
Alignment explanation
Indices: 81342--81385 Score: 79
Period size: 5 Copynumber: 8.6 Consensus size: 5
81332 GCCGTCCGTC
81342 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG
81386 TGGTAATACG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 33 0.87
6 5 0.13
ACGTcount: A:0.00, C:0.20, G:0.57, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:81553 original size:48 final size:48
Alignment explanation
Indices: 81498--81645 Score: 167
Period size: 48 Copynumber: 3.3 Consensus size: 48
81488 ACAACTGTAG
81498 ACTATCGCAACGCGAATTTGCGATGATGGAGATCGCGTTGCGATTTCA
1 ACTATCGCAACGCGAATTTGCGATGATGGAGATCGCGTTGCGATTTCA
* * * *
81546 ACTATCGCAACGCGAA-ATG-GA--A---A-AACGCGAT-C---TCCA
1 ACTATCGCAACGCGAATTTGCGATGATGGAGATCGCGTTGCGATTTCA
*
81582 ACTATCGCAACACGAATTTGCGATGATGGAGATCGCGTTGCGATTTCA
1 ACTATCGCAACGCGAATTTGCGATGATGGAGATCGCGTTGCGATTTCA
81630 ACTATCGCAACGCGAA
1 ACTATCGCAACGCGAA
81646 ATGGAAAATC
Statistics
Matches: 78, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
36 18 0.23
37 2 0.03
38 2 0.03
39 1 0.01
40 7 0.09
41 1 0.01
43 1 0.01
44 7 0.09
45 1 0.01
46 2 0.03
47 2 0.03
48 34 0.44
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (48 bp):
ACTATCGCAACGCGAATTTGCGATGATGGAGATCGCGTTGCGATTTCA
Found at i:81639 original size:84 final size:86
Alignment explanation
Indices: 81498--81680 Score: 316
Period size: 84 Copynumber: 2.1 Consensus size: 86
81488 ACAACTGTAG
*
81498 ACTATCGCAACGCGAATTTGCGATGATGGAGATCGCGTTGCGATTTCAACTATCGCAACGCGAAA
1 ACTATCGCAACACGAATTTGCGATGATGGAGATCGCGTTGCGATTTCAACTATCGCAACGCGAAA
81563 TGG-AAA-AACGCGATCTCCA
66 TGGAAAACAACGCGATCTCCA
81582 ACTATCGCAACACGAATTTGCGATGATGGAGATCGCGTTGCGATTTCAACTATCGCAACGCGAAA
1 ACTATCGCAACACGAATTTGCGATGATGGAGATCGCGTTGCGATTTCAACTATCGCAACGCGAAA
81647 TGGAAAATCGCAACGCGATCTCCA
66 TGGAAAA---CAACGCGATCTCCA
81671 ACTATCGCAA
1 ACTATCGCAA
81681 TGCGAAATGG
Statistics
Matches: 93, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
84 67 0.72
85 3 0.03
89 23 0.25
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (86 bp):
ACTATCGCAACACGAATTTGCGATGATGGAGATCGCGTTGCGATTTCAACTATCGCAACGCGAAA
TGGAAAACAACGCGATCTCCA
Found at i:81644 original size:20 final size:20
Alignment explanation
Indices: 81621--81726 Score: 54
Period size: 20 Copynumber: 5.2 Consensus size: 20
81611 AGATCGCGTT
*
81621 GCGATTTCAACTATCGCAAC
1 GCGATTGCAACTATCGCAAC
* * *
81641 GCGAAATGGAA-AATCGCAAC
1 GCG-ATTGCAACTATCGCAAC
* *
81661 GCGATCTCCAACTATCGCAAT
1 GCGAT-TGCAACTATCGCAAC
* * * *
81682 GCGAAATGGAA-AAACGCAAC
1 GCG-ATTGCAACTATCGCAAC
* *
81702 GCGATTTTCAACTATCGCAAT
1 GCGA-TTGCAACTATCGCAAC
81723 GCGA
1 GCGA
81727 AATGCAACGT
Statistics
Matches: 59, Mismatches: 21, Indels: 11
0.65 0.23 0.12
Matches are distributed among these distances:
19 2 0.03
20 29 0.49
21 27 0.46
22 1 0.02
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
GCGATTGCAACTATCGCAAC
Found at i:81678 original size:41 final size:41
Alignment explanation
Indices: 81628--81730 Score: 170
Period size: 41 Copynumber: 2.5 Consensus size: 41
81618 GTTGCGATTT
* *
81628 CAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTC
1 CAACTATCGCAATGCGAAATGGAAAAACGCAACGCGATCTC
* *
81669 CAACTATCGCAATGCGAAATGGAAAAACGCAACGCGATTTT
1 CAACTATCGCAATGCGAAATGGAAAAACGCAACGCGATCTC
81710 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAATGCGAAATG
81731 CAACGTGAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.17
Consensus pattern (41 bp):
CAACTATCGCAATGCGAAATGGAAAAACGCAACGCGATCTC
Found at i:81734 original size:21 final size:21
Alignment explanation
Indices: 81628--81734 Score: 83
Period size: 21 Copynumber: 5.2 Consensus size: 21
81618 GTTGCGATTT
81628 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
81649 GAA-AATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATG
*
81669 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
81690 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
81710 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
81731 CAAC
1 CAAC
81735 GTGAATTTGC
Statistics
Matches: 59, Mismatches: 25, Indels: 4
0.67 0.28 0.05
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:81779 original size:72 final size:72
Alignment explanation
Indices: 81694--81839 Score: 283
Period size: 72 Copynumber: 2.0 Consensus size: 72
81684 GAAATGGAAA
81694 AACGCAACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTGAATTTGCGATAATGGAGATCG
1 AACGCAACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTGAATTTGCGATAATGGAGATCG
81759 CAATGCG
66 CAATGCG
*
81766 AACGCAACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTGAATTTGCGATAGTGGAGATCG
1 AACGCAACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTGAATTTGCGATAATGGAGATCG
81831 CAATGCG
66 CAATGCG
81838 AA
1 AA
81840 TTAGAGATCA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.22
Consensus pattern (72 bp):
AACGCAACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTGAATTTGCGATAATGGAGATCG
CAATGCG
Found at i:82852 original size:23 final size:24
Alignment explanation
Indices: 82807--82853 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
82797 AAATTGGACG
*
82807 ACCGAATTTTTTACCGGATAAAAA
1 ACCGAATTTTTTACCGGAAAAAAA
82831 ACCG-ATTTTTTATCC-GAAAAAAA
1 ACCGAATTTTTTA-CCGGAAAAAAA
82854 TTCGGTTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.30
Consensus pattern (24 bp):
ACCGAATTTTTTACCGGAAAAAAA
Found at i:82853 original size:24 final size:24
Alignment explanation
Indices: 82807--82853 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
82797 AAATTGGACG
* *
82807 ACCGAATTTTTTACCGGATAAAAA
1 ACCGAATTTTTTACCGAAAAAAAA
82831 ACCG-ATTTTTTATCCGAAAAAAA
1 ACCGAATTTTTTA-CCGAAAAAAA
82854 TTCGGTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.30
Consensus pattern (24 bp):
ACCGAATTTTTTACCGAAAAAAAA
Found at i:85023 original size:22 final size:22
Alignment explanation
Indices: 84995--85036 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
84985 TCAACTGTTA
84995 TAACCCCTGGAATTAAATCATG
1 TAACCCCTGGAATTAAATCATG
*
85017 TAACCCCTGGATTTAAATCA
1 TAACCCCTGGAATTAAATCA
85037 AATAACTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.29
Consensus pattern (22 bp):
TAACCCCTGGAATTAAATCATG
Found at i:85042 original size:22 final size:22
Alignment explanation
Indices: 84994--85042 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
84984 TTCAACTGTT
*
84994 ATAACCCCTGGAATTAAATCAT
1 ATAACCCCTGGAATTAAATCAA
* *
85016 GTAACCCCTGGATTTAAATCAA
1 ATAACCCCTGGAATTAAATCAA
85038 ATAAC
1 ATAAC
85043 TCATGTAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (22 bp):
ATAACCCCTGGAATTAAATCAA
Found at i:88650 original size:25 final size:26
Alignment explanation
Indices: 88607--88655 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
88597 CCAATCCAAA
* *
88607 ACTTCAAATTTTATGTAAAAACTTGC
1 ACTTCAAATCTTATATAAAAACTTGC
88633 ACTTCAAA-CTTATATAAAAACTT
1 ACTTCAAATCTTATATAAAAACTT
88656 AACTCGTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.37
Consensus pattern (26 bp):
ACTTCAAATCTTATATAAAAACTTGC
Found at i:88738 original size:71 final size:71
Alignment explanation
Indices: 88621--88765 Score: 227
Period size: 71 Copynumber: 2.0 Consensus size: 71
88611 CAAATTTTAT
* *
88621 GTAAAAACTTGCACTTCAAACTTATATAAAAACTTAACTCGTCCTGATTTATTTAGAATAATTCC
1 GTAAAAACTTACACTTCAAACTTATATAAAAACTTAACTCGACCTGATTTATTTAGAATAATTCC
88686 AATATA
66 AATATA
* * * * *
88692 GTAAAAACTTACACTTCAGATTTATATAAAAACTTATCTCGACCTGATTTATTTAGAATGATTCT
1 GTAAAAACTTACACTTCAAACTTATATAAAAACTTAACTCGACCTGATTTATTTAGAATAATTCC
88757 AATATA
66 AATATA
88763 GTA
1 GTA
88766 CATAATTATA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (71 bp):
GTAAAAACTTACACTTCAAACTTATATAAAAACTTAACTCGACCTGATTTATTTAGAATAATTCC
AATATA
Found at i:105362 original size:17 final size:16
Alignment explanation
Indices: 105336--105379 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
105326 AAATGACTAT
*
105336 ATAATAAAAATATTTAA
1 ATAATAAAAA-ATTAAA
105353 ATATATAAAAAATTAAA
1 ATA-ATAAAAAATTAAA
105370 ATAATAAAAA
1 ATAATAAAAA
105380 TACAATTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 7 0.28
17 11 0.44
18 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAATAAAAAATTAAA
Found at i:106283 original size:20 final size:20
Alignment explanation
Indices: 106252--106315 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
106242 TTTTGGTTGA
106252 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
106272 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
106292 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
106313 AAT
1 AAT
106316 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:106304 original size:21 final size:21
Alignment explanation
Indices: 106250--106314 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
106240 TCTTTTGGTT
106250 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
106271 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
106291 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
106312 GAA
1 GAA
106315 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:106375 original size:14 final size:14
Alignment explanation
Indices: 106356--106409 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
106346 TTTGGTTTCG
106356 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
106370 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
106389 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
106403 CGTTGCG
1 CGTTGCG
106410 GTTTTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.07, C:0.26, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:106388 original size:33 final size:33
Alignment explanation
Indices: 106340--106428 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
106330 AAAATCGCAA
**
106340 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
106373 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
* *
106406 TGCGGTTTTCATTTTCTCGTTGC
1 TGCGATTTTCA-TTTCGCGTTGC
106429 AGATAGTCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 41 0.80
34 10 0.20
ACGTcount: A:0.07, C:0.22, G:0.24, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:106425 original size:20 final size:20
Alignment explanation
Indices: 106367--106472 Score: 100
Period size: 21 Copynumber: 5.5 Consensus size: 20
106357 GTTGCGATTC
106367 TCTCGTTGCGATTTTCA-TT
1 TCTCGTTGCGATTTTCATTT
*
106386 TCGCGTTGCGA--TTC----
1 TCTCGTTGCGATTTTCATTT
*
106400 TCTCGTTGCGGTTTTCATTT
1 TCTCGTTGCGATTTTCATTT
**
106420 TCTCGTTGCAGATAGTCATTT
1 TCTCGTTGC-GATTTTCATTT
*
106441 TCACGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCATTT
106461 ATCTCGTTGCGA
1 -TCTCGTTGCGA
106473 CTCTTCTGCA
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
14 9 0.13
16 3 0.04
17 3 0.04
19 10 0.14
20 18 0.26
21 26 0.38
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (20 bp):
TCTCGTTGCGATTTTCATTT
Found at i:106594 original size:33 final size:33
Alignment explanation
Indices: 106552--106622 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
106542 AATACTAACT
*
106552 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
* * *
106585 TGAAAATCGCAATAAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
106618 TGAAA
1 TGAAA
106623 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.15, G:0.23, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
Found at i:107027 original size:20 final size:20
Alignment explanation
Indices: 107002--107194 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
106992 CTTTAAAAAT
107002 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
107022 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
107042 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
107063 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
107083 CGCATTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
107103 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
107123 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
107143 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
107163 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
107183 CGCGTTGCGATT
1 CGCGTTGCGATT
107195 CTGTAAAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 132 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:107212 original size:21 final size:20
Alignment explanation
Indices: 107188--107241 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
107178 ATATTCGCGT
107188 TGCGATTCTGTAAAATCGCAA
1 TGCGATT-TGTAAAATCGCAA
** *
107209 TGCGAATTTGTACTATCGCAT
1 TGCG-ATTTGTAAAATCGCAA
107230 TGCGATTT-TAAA
1 TGCGATTTGTAAA
107242 GAATCGCGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 4 0.15
21 18 0.67
22 3 0.11
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (20 bp):
TGCGATTTGTAAAATCGCAA
Found at i:108584 original size:3 final size:3
Alignment explanation
Indices: 108576--108630 Score: 67
Period size: 3 Copynumber: 18.0 Consensus size: 3
108566 GGCCTGGTTG
* *
108576 TAA TAA TAA TAT TAA TAA TAA AAA TATA TAA TAAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA TAA
108622 TAA TAA TAA
1 TAA TAA TAA
108631 AACCGGGATA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 37 0.82
4 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:118669 original size:2 final size:2
Alignment explanation
Indices: 118662--118696 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
118652 GATGTATTAA
118662 AT AT AT 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 AT AT AT A
118697 CTCTTTAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:120117 original size:77 final size:79
Alignment explanation
Indices: 120037--120190 Score: 213
Period size: 82 Copynumber: 1.9 Consensus size: 79
120027 TGACTCGTCT
*
120037 AAAAAAA-T-TCAACTTTGAGTTGTAAAATAAAATTCATCAACACAAATAACTCAAAAATTTTTT
1 AAAAAAATTATCAACTTTGAGTTGTAAAATAAAACTCATCAACACAAATAACTC-AAAATTTTTT
120100 GACTTGACTCGAATA
65 GACTTGACTCGAATA
* * * *
120115 AAAAAAATTAAGTCAACTTTGAGTTGTAAAATAAGACTCGTCAACTCGAATAACTCAAAATTTTT
1 AAAAAAATT-A-TCAACTTTGAGTTGTAAAATAAAACTCATCAACACAAATAACTCAAAATTTTT
*
120180 TGACTCGACTC
64 TGACTTGACTC
120191 CATTAGAACG
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
78 7 0.11
79 1 0.02
81 19 0.29
82 39 0.59
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.31
Consensus pattern (79 bp):
AAAAAAATTATCAACTTTGAGTTGTAAAATAAAACTCATCAACACAAATAACTCAAAATTTTTTG
ACTTGACTCGAATA
Found at i:124536 original size:28 final size:30
Alignment explanation
Indices: 124483--124548 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
124473 TCTATTTTAG
* *
124483 TTTTTGTATTTATAATTAGGGCTCCC-AAT
1 TTTTTATATTTATAATTAGAGCTCCCTAAT
124512 TTTTTATATTTATAATTAGAG-TCCCTAAT
1 TTTTTATATTTATAATTAGAGCTCCCTAAT
*
124541 TTTGTATA
1 TTTTTATA
124549 ATTTCATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.52
Consensus pattern (30 bp):
TTTTTATATTTATAATTAGAGCTCCCTAAT
Found at i:133858 original size:2 final size:2
Alignment explanation
Indices: 133851--133876 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
133841 TCTGTTCTTT
133851 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
133877 CACCTTACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:143253 original size:2 final size:2
Alignment explanation
Indices: 143246--143286 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
143236 TAATTGATTC
143246 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
143287 TTTTTTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:143718 original size:16 final size:16
Alignment explanation
Indices: 143678--143726 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
143668 AATTAAATTC
*
143678 GATTTAATAATTTTATTT
1 GATTTAATAA-TTTA-TG
*
143696 TATTTAATAATTTATG
1 GATTTAATAATTTATG
143712 GATTTAATAATTTAT
1 GATTTAATAATTTAT
143727 AAATTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 15 0.54
17 4 0.14
18 9 0.32
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (16 bp):
GATTTAATAATTTATG
Found at i:143732 original size:16 final size:16
Alignment explanation
Indices: 143697--143732 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
143687 ATTTTATTTT
**
143697 ATTTAATAATTTATGG
1 ATTTAATAATTTATAA
143713 ATTTAATAATTTATAA
1 ATTTAATAATTTATAA
143729 ATTT
1 ATTT
143733 TATTTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
ATTTAATAATTTATAA
Found at i:145622 original size:37 final size:35
Alignment explanation
Indices: 145539--145632 Score: 109
Period size: 37 Copynumber: 2.6 Consensus size: 35
145529 GAAAAAATGA
*
145539 TTGGTAAATGTTTTTTTG-AAAATGGTTTTCAAAGT
1 TTGGTAAATG-TTTTTTGAAAAAAGGTTTTCAAAGT
* *
145574 TTAGTAAATGTTTCTTTGAAAAACAGTTTTTCAAAGT
1 TTGGTAAATGTTT-TTTGAAAAA-AGGTTTTCAAAGT
* *
145611 TTGGTAGATGTTTGTTGAAAAA
1 TTGGTAAATGTTTTTTGAAAAA
145633 TGATAATGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
34 3 0.06
35 13 0.26
36 12 0.24
37 22 0.44
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (35 bp):
TTGGTAAATGTTTTTTGAAAAAAGGTTTTCAAAGT
Found at i:147301 original size:19 final size:22
Alignment explanation
Indices: 147277--147317 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 22
147267 ATGAACATGC
147277 ATACATG-AT-AATTAT-TATG
1 ATACATGCATAAATTATATATG
147296 ATACATGCATAAATTATATATG
1 ATACATGCATAAATTATATATG
147318 TTCATATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 2 0.11
21 6 0.32
22 4 0.21
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (22 bp):
ATACATGCATAAATTATATATG
Found at i:147423 original size:8 final size:8
Alignment explanation
Indices: 147410--147444 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
147400 AAGAGAAATG
147410 ACATGAAC
1 ACATGAAC
147418 ACATGAAC
1 ACATGAAC
147426 ACATGAAC
1 ACATGAAC
147434 ACATGAA-
1 ACATGAAC
147441 ACAT
1 ACAT
147445 AAGAATAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.15
8 23 0.85
ACGTcount: A:0.51, C:0.23, G:0.11, T:0.14
Consensus pattern (8 bp):
ACATGAAC
Found at i:148384 original size:35 final size:36
Alignment explanation
Indices: 148338--148430 Score: 127
Period size: 35 Copynumber: 2.6 Consensus size: 36
148328 GAAAAAATGA
*
148338 TTGGTAAATGTTTTTTTGAAAATAG-TTTTCAAAGT
1 TTGGTAAATGTTTTTTTGAAAACAGTTTTTCAAAGT
*
148373 TTGGTAAATGTTTCTTTGAAAAACAGTTTTTCAAAGT
1 TTGGTAAATGTTTTTTTG-AAAACAGTTTTTCAAAGT
* *
148410 TTGGTATATG-TTTATTGAAAA
1 TTGGTAAATGTTTTTTTGAAAA
148431 ATGATAATGG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
35 21 0.41
36 11 0.22
37 19 0.37
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.46
Consensus pattern (36 bp):
TTGGTAAATGTTTTTTTGAAAACAGTTTTTCAAAGT
Found at i:148413 original size:37 final size:35
Alignment explanation
Indices: 148338--148431 Score: 127
Period size: 37 Copynumber: 2.6 Consensus size: 35
148328 GAAAAAATGA
*
148338 TTGGTAAATGTTTTTTTG-AAAATAGTTTTCAAAGT
1 TTGGTAAATG-TTTTTTGAAAAACAGTTTTCAAAGT
148373 TTGGTAAATGTTTCTTTGAAAAACAGTTTTTCAAAGT
1 TTGGTAAATGTTT-TTTGAAAAACAG-TTTTCAAAGT
* *
148410 TTGGTATATGTTTATTGAAAAA
1 TTGGTAAATGTTTTTTGAAAAA
148432 TGATAATGGG
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
34 3 0.06
35 14 0.26
36 14 0.26
37 22 0.42
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (35 bp):
TTGGTAAATGTTTTTTGAAAAACAGTTTTCAAAGT
Found at i:149990 original size:652 final size:652
Alignment explanation
Indices: 148249--150222 Score: 3452
Period size: 652 Copynumber: 3.0 Consensus size: 652
148239 GGGTGCTACA
148249 CCCAACTTAACCAAGCGCCACGCCGTGACATTATTCGATTGACAAGTATTGTTAAGTTCAAAGTT
1 CCCAACTTAACCAAGCGCCACGCCGTGACATTATTCGATTGACAAGTATTGTTAAGTTCAAAGTT
** *
148314 TGGCAACTGACTTTGAAAAAATGATTGGTAAATGTTTTTTTGAAAATAGTTTTCAAAGTTTGGTA
66 TGGCAACCAACTTTGAAAAAATGATTGGTAAATGTTTTTTTGAAAATGGTTTTCAAAGTTTGGTA
* * *
148379 AATGTTTCTTTGAAAAACAGTTTTTCAAAGTTTGGTATATGTTTATTGAAAAATGATAATGGGAT
131 AATATTTCTTTGAAAAACAGTTTTTCAAAGTTTGGTAGATGTTTGTTGAAAAATGATAATGGGAT
*
148444 AATCACAATTAATCCACAGACTTTAGGGTATTTACAAGATTAAGTCCTTAAGCTTCAACTATAAA
196 AATCACAATTAATCCATAGACTTTAGGGTATTTACAAGATTAAGTCCTTAAGCTTCAACTATAAA
*
148509 TACCTTAGCTCATTTAGCTTCAAAATCATCCCAAAATCATTTCTTTCTCCCAATACTAGAGAGTT
261 TACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAATCATTTCTTTCTCCCAATACTAGAGAGTT
*
148574 TTCTTGTGAGTAGTGAGTGTTTTGTAAACACATGTAAATTTTCTCTCTTT-AAAAAGATCTGCAG
326 TTCTTGTGAGTAGAGAGTGTTTTGTAAACACATGTAAATTTTCTCTCTTTAAAAAAGATCTGCAG
* **
148638 CAGTCCGGAGACGTAGGCACAATTGGATGAACTCTGTTATCAATTTCATGTATTATTTTTCCGCT
391 CAGTCCGGAGACGTAGGCACAATTGGATGAACTCCGTTATCAATTTCGGGTATTATTTTTCCGCT
*
148703 TTTATTTCGCATTCTCACTAATCTGGTTATAGGGAAAATACTTGTTACTCGTTTATTTCCCAACA
456 TTTATTTCGCATTCTCACTAATCTGGTTATAGGAAAAATACTTGTTACTCGTTTATTTCCCAACA
* * *
148768 TTTGGGGTATGTCTAATGCCGATCATTGTCATGCCACTGATAAAGAGGAAATTTGGAAGACTTTG
521 GTTGGGGTATGTCTAATGCCGATCATTGTCATGCCACTGATAAAGAGGAGATTTGGAAGACTCTG
* * *
148833 CGGAAGAATTTCAAGCTTGGGAGAAATATTTATGCACCTACTATCATTTCTCATTATACAGTAGT
586 CGGAAGAATTTCAGGCTTGGGAGAAATGTTTCTGCACCTACTATCATTTCTCATTATACAGTAGT
148898 GC
651 GC
* *
148900 CCCAACTTAACCAAGCGCCACGCTGTGATATTATTCGATTGACAAGTATTGTTAAGTTCAAAGTT
1 CCCAACTTAACCAAGCGCCACGCCGTGACATTATTCGATTGACAAGTATTGTTAAGTTCAAAGTT
*
148965 TGGCAACCAACTTTGAAAAAATGATTGGTAAATGTTTTTTT-TAAATGGTTTTCAAAGTTTGGTA
66 TGGCAACCAACTTTGAAAAAATGATTGGTAAATGTTTTTTTGAAAATGGTTTTCAAAGTTTGGTA
149029 AATATTTCCTTT-AAAAACAGTTTTTCAAAGTTTGGTAGATGTTTGTTGAAAAATGATAATGGGA
131 AATATTT-CTTTGAAAAACAGTTTTTCAAAGTTTGGTAGATGTTTGTTGAAAAATGATAATGGGA
* *
149093 TAATCACAATTAATCCATAGGCTTTAGGGTATTTACAAGATTAAGCCCTTAAGCTTCAACTATAA
195 TAATCACAATTAATCCATAGACTTTAGGGTATTTACAAGATTAAGTCCTTAAGCTTCAACTATAA
*
149158 ATACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAATCATTTCTTTC-CCCTAATACTATAGAG
260 ATACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAATCATTTCTTTCTCCC-AATACTAGAGAG
* * * *
149222 TTTTATTGTGAGTAGCGAGTGTTTTGTAAACACCTGTAATTTTTCTCTCTTTAAAAAAGATCTGC
324 TTTTCTTGTGAGTAGAGAGTGTTTTGTAAACACATGTAAATTTTCTCTCTTTAAAAAAGATCTGC
* *
149287 AGCAGTCCGGAGACGTAGGCACAATTGGCTGAACTCCGTTATCAATTTCGGGTATTATTTTTTCG
389 AGCAGTCCGGAGACGTAGGCACAATTGGATGAACTCCGTTATCAATTTCGGGTATTATTTTTCCG
149352 CTTTTATTTCGCATTCTCACTAATCTGGTTATAGGAAAAATACTTGTTACTCGTTTATTTCCCAA
454 CTTTTATTTCGCATTCTCACTAATCTGGTTATAGGAAAAATACTTGTTACTCGTTTATTTCCCAA
*
149417 CAGTTGGGGTATGTCTAATGTCGATCATTGTCATGCCACTGATAAAGAGGAGATTTGGAAGACTC
519 CAGTTGGGGTATGTCTAATGCCGATCATTGTCATGCCACTGATAAAGAGGAGATTTGGAAGACTC
149482 TGCGGAAGAATTTCAGGCTTGGGAGAAATGTTTCTGCACCTACTATCATTTCTCATTATACAGTA
584 TGCGGAAGAATTTCAGGCTTGGGAGAAATGTTTCTGCACCTACTATCATTTCTCATTATACAGTA
149547 GTGC
649 GTGC
149551 CCCAACTTAACCAAGCGCCACGCCGTGACATTATTCGATTGACAAGTATTGTTAAGTTCAAAGTT
1 CCCAACTTAACCAAGCGCCACGCCGTGACATTATTCGATTGACAAGTATTGTTAAGTTCAAAGTT
* *
149616 TGGCAACCAACTTTGAAAAAATGATTGGTAAATATTTTTTTGAAAATGGTTTTCAAAGTTTAGTA
66 TGGCAACCAACTTTGAAAAAATGATTGGTAAATGTTTTTTTGAAAATGGTTTTCAAAGTTTGGTA
* * *
149681 AATATTTCTTTGAAAAACAATTTTTCAAAGTTTGATAGATGTTTGTTGAAAAATGATAATGAGAT
131 AATATTTCTTTGAAAAACAGTTTTTCAAAGTTTGGTAGATGTTTGTTGAAAAATGATAATGGGAT
*
149746 AATCACAATTAATCTATAGACTTTAGGGTATTTACAAGATTAAGTCCTTAAGCTTCAACTATAAA
196 AATCACAATTAATCCATAGACTTTAGGGTATTTACAAGATTAAGTCCTTAAGCTTCAACTATAAA
149811 TACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAATCATTTCTTTCTCCCAATACTAGAGAGTT
261 TACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAATCATTTCTTTCTCCCAATACTAGAGAGTT
* *
149876 TTCTTGTGAGTAGAGAGTGTTTTGTAAACACTTGTAAATTTTCTCTCTTTAAAAAAGATCAGCAG
326 TTCTTGTGAGTAGAGAGTGTTTTGTAAACACATGTAAATTTTCTCTCTTTAAAAAAGATCTGCAG
* * *
149941 CAGTCTGGAGACGTAGGCACAATTGGTTGAACTCCGTTATCAATTTCGGGTATTATTTTTCCGTT
391 CAGTCCGGAGACGTAGGCACAATTGGATGAACTCCGTTATCAATTTCGGGTATTATTTTTCCGCT
150006 TTTATTTCGCATTCTCACTAATCTGGTTATAGGAAAAATACTTGTTACTCGTTTATTTCCCAACA
456 TTTATTTCGCATTCTCACTAATCTGGTTATAGGAAAAATACTTGTTACTCGTTTATTTCCCAACA
* * * *
150071 GTTGGGGTATGTTTAATGCCGATCATTGTCATGCCATTAATAAAGATGAGATTTGGAAGACTCTG
521 GTTGGGGTATGTCTAATGCCGATCATTGTCATGCCACTGATAAAGAGGAGATTTGGAAGACTCTG
* *
150136 CGGAAGAATTTCAGGATTGGGAGAAATGTTTCTGCACCTACTATCATTTCTCATTCTACAGTAGT
586 CGGAAGAATTTCAGGCTTGGGAGAAATGTTTCTGCACCTACTATCATTTCTCATTATACAGTAGT
150201 GC
651 GC
*
150203 CCCAACTTAACCAAGTGCCA
1 CCCAACTTAACCAAGCGCCA
150223 TTCGATTGGC
Statistics
Matches: 1257, Mismatches: 60, Indels: 11
0.95 0.05 0.01
Matches are distributed among these distances:
649 3 0.00
650 245 0.19
651 476 0.38
652 530 0.42
653 3 0.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (652 bp):
CCCAACTTAACCAAGCGCCACGCCGTGACATTATTCGATTGACAAGTATTGTTAAGTTCAAAGTT
TGGCAACCAACTTTGAAAAAATGATTGGTAAATGTTTTTTTGAAAATGGTTTTCAAAGTTTGGTA
AATATTTCTTTGAAAAACAGTTTTTCAAAGTTTGGTAGATGTTTGTTGAAAAATGATAATGGGAT
AATCACAATTAATCCATAGACTTTAGGGTATTTACAAGATTAAGTCCTTAAGCTTCAACTATAAA
TACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAATCATTTCTTTCTCCCAATACTAGAGAGTT
TTCTTGTGAGTAGAGAGTGTTTTGTAAACACATGTAAATTTTCTCTCTTTAAAAAAGATCTGCAG
CAGTCCGGAGACGTAGGCACAATTGGATGAACTCCGTTATCAATTTCGGGTATTATTTTTCCGCT
TTTATTTCGCATTCTCACTAATCTGGTTATAGGAAAAATACTTGTTACTCGTTTATTTCCCAACA
GTTGGGGTATGTCTAATGCCGATCATTGTCATGCCACTGATAAAGAGGAGATTTGGAAGACTCTG
CGGAAGAATTTCAGGCTTGGGAGAAATGTTTCTGCACCTACTATCATTTCTCATTATACAGTAGT
GC
Found at i:159443 original size:14 final size:14
Alignment explanation
Indices: 159424--159452 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
159414 TATATATATA
159424 TGTGTGTGTGTGTT
1 TGTGTGTGTGTGTT
159438 TGTGTGTGTGTGTT
1 TGTGTGTGTGTGTT
159452 T
1 T
159453 AACATGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.41, T:0.59
Consensus pattern (14 bp):
TGTGTGTGTGTGTT
Found at i:162991 original size:3 final size:3
Alignment explanation
Indices: 162983--163031 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
162973 CAAGTTATTA
*
162983 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
163031 A
1 A
163032 CAATTATCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:164437 original size:131 final size:131
Alignment explanation
Indices: 164203--164483 Score: 418
Period size: 131 Copynumber: 2.1 Consensus size: 131
164193 CATGGGATAA
* * *
164203 TAATACATTTAATCTTTAATACTTACATATTCTTTCAATTTGATCCTAATTTTATATAATTCAGT
1 TAATACATTTAATCTTTAATACTTACATATTCTTTCAATATGATCCTAATTCTATATAATTCAAT
** * *
164268 AAATTGTCCCTTTACATTTACAAAACCTAAAAATTCAACCCTCATTTTAAGAACATAAAACATCT
66 AAATTCACCCTTTACATCTACAAAACCTAAAAATTCAACCCTCATTTTAAAAACATAAAACATCT
164333 C
131 C
** * *
164334 TAATACATTTAATCTTTAATACTTGTATATTCTTTCAGTATGGTCCTAATTCTATATAATTCAAT
1 TAATACATTTAATCTTTAATACTTACATATTCTTTCAATATGATCCTAATTCTATATAATTCAAT
* * * *
164399 AAATTCACCCTTTACATCTATAAAACCTATAGATTCAACCCTCATTTTAAAAATATAAAACATCT
66 AAATTCACCCTTTACATCTACAAAACCTAAAAATTCAACCCTCATTTTAAAAACATAAAACATCT
164464 C
131 C
*
164465 TAATACAATTAATCTTTAA
1 TAATACATTTAATCTTTAA
164484 ATATAATAAT
Statistics
Matches: 134, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
131 134 1.00
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.40
Consensus pattern (131 bp):
TAATACATTTAATCTTTAATACTTACATATTCTTTCAATATGATCCTAATTCTATATAATTCAAT
AAATTCACCCTTTACATCTACAAAACCTAAAAATTCAACCCTCATTTTAAAAACATAAAACATCT
C
Found at i:166581 original size:27 final size:27
Alignment explanation
Indices: 166543--166596 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
166533 TAATATGAAA
166543 CATTTTGAGATGATAAGGAGAATGTTT
1 CATTTTGAGATGATAAGGAGAATGTTT
166570 CATTTTGAGATGATAAGGAGAATGTTT
1 CATTTTGAGATGATAAGGAGAATGTTT
166597 TGAAGCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (27 bp):
CATTTTGAGATGATAAGGAGAATGTTT
Found at i:170413 original size:22 final size:22
Alignment explanation
Indices: 170388--170429 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
170378 AAGCTGATGA
170388 TCATCTGAGTCGGACGTTAATT
1 TCATCTGAGTCGGACGTTAATT
170410 TCATCTGAGTCGGACGTTAA
1 TCATCTGAGTCGGACGTTAA
170430 CTTGCTCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (22 bp):
TCATCTGAGTCGGACGTTAATT
Found at i:171851 original size:31 final size:32
Alignment explanation
Indices: 171790--171859 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
171780 AATTTTAAAG
* * *
171790 TTATAAAATGAATAATTAAATTTATCAAATTA
1 TTATAAAATGAATAATTAAAATGATAAAATTA
*
171822 TTATAAAAT-AATTATTAAAATGATAAAATTA
1 TTATAAAATGAATAATTAAAATGATAAAATTA
*
171853 CTATAAA
1 TTATAAA
171860 TAGCCCTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 24 0.73
32 9 0.27
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (32 bp):
TTATAAAATGAATAATTAAAATGATAAAATTA
Found at i:172730 original size:13 final size:13
Alignment explanation
Indices: 172712--172736 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
172702 TTGGATACTG
172712 ATACTTTGGGTAC
1 ATACTTTGGGTAC
172725 ATACTTTGGGTA
1 ATACTTTGGGTA
172737 TGTTGGCCTT
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:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (13 bp):
ATACTTTGGGTAC
Found at i:177686 original size:2 final size:2
Alignment explanation
Indices: 177679--177709 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
177669 ATAGATCGGT
177679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
177710 TAAGAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:179780 original size:11 final size:11
Alignment explanation
Indices: 179764--179797 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
179754 TTATCACACC
179764 AAATTCTCTCA
1 AAATTCTCTCA
179775 AAATTCTCT-A
1 AAATTCTCTCA
*
179785 AATTTCTCTCA
1 AAATTCTCTCA
179796 AA
1 AA
179798 TACTATCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (11 bp):
AAATTCTCTCA
Found at i:179853 original size:13 final size:14
Alignment explanation
Indices: 179825--179853 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
179815 ATATTTTATA
179825 ATATTTTTACTATT
1 ATATTTTTACTATT
179839 ATATTTTTACT-TT
1 ATATTTTTACTATT
179852 AT
1 AT
179854 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Found at i:182068 original size:24 final size:24
Alignment explanation
Indices: 182021--182075 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
182011 ACATGCGCAA
*
182021 GACGACGACAACGACGACGACGAC
1 GACGATGACAACGACGACGACGAC
* ** *
182045 GATGATGACAACGATTACGTCGAC
1 GACGATGACAACGACGACGACGAC
182069 GACGATG
1 GACGATG
182076 GTGATGATGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.29, T:0.11
Consensus pattern (24 bp):
GACGATGACAACGACGACGACGAC
Found at i:186012 original size:51 final size:50
Alignment explanation
Indices: 185907--186034 Score: 148
Period size: 51 Copynumber: 2.5 Consensus size: 50
185897 CCCTACGTGG
* * * * * **
185907 CGTATAACGCGCTGCAAGGGCCGCGTTATACCCACGTGGCACCAGCTCAC
1 CGTATAACGCGGTGCAGGGGGCGCGCTATACCCACGTGACACCAAATCAC
* * *
185957 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCAT
1 CGTATAACGCGGTGCAGGGGGCGCGCTATA-CCCACGTGACACCAAATCAC
*
186008 CGTATAACGCGGTGCAGGGAGCGCGCT
1 CGTATAACGCGGTGCAGGGGGCGCGCT
186035 TTACTGCTAA
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
50 25 0.38
51 40 0.62
ACGTcount: A:0.21, C:0.32, G:0.31, T:0.16
Consensus pattern (50 bp):
CGTATAACGCGGTGCAGGGGGCGCGCTATACCCACGTGACACCAAATCAC
Found at i:187079 original size:37 final size:39
Alignment explanation
Indices: 186994--187079 Score: 90
Period size: 37 Copynumber: 2.3 Consensus size: 39
186984 ATTAAACCTT
* *
186994 TTTTATATTTTAAATTTTGTAAAAAAAATTATGTAAATA
1 TTTTATAATTTAAATTTTGTAAAAAAAATTATATAAATA
* * *
187033 --TTATGAATTT-AATTTTTTTAAGAAAA-TATATAAATA
1 TTTTAT-AATTTAAATTTTGTAAAAAAAATTATATAAATA
187069 TTTTATAATTT
1 TTTTATAATTT
187080 GTAATATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
36 9 0.23
37 22 0.56
38 8 0.21
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (39 bp):
TTTTATAATTTAAATTTTGTAAAAAAAATTATATAAATA
Found at i:187243 original size:18 final size:19
Alignment explanation
Indices: 187220--187263 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
187210 ACAGTAATCC
*
187220 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTA
187238 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
187258 TATTCC
1 TATTCC
187264 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:187251 original size:20 final size:20
Alignment explanation
Indices: 187226--187263 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
187216 ATCCTATTCC
*
187226 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
187246 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
187264 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:187563 original size:13 final size:13
Alignment explanation
Indices: 187545--187571 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
187535 TTACAGACGC
187545 GCATATGAAGACT
1 GCATATGAAGACT
187558 GCATATGAAGACT
1 GCATATGAAGACT
187571 G
1 G
187572 TTCAACTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:188190 original size:20 final size:21
Alignment explanation
Indices: 188157--188197 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
188147 TTTTTCCGTC
*
188157 TTCTTTTTCCATTTTTTGTTTG
1 TTCTTTTT-CATTTTATGTTTG
188179 TTCTTTTT-ATTTTATGTTT
1 TTCTTTTTCATTTTATGTTT
188198 TCTCAATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.07, C:0.10, G:0.07, T:0.76
Consensus pattern (21 bp):
TTCTTTTTCATTTTATGTTTG
Found at i:191521 original size:20 final size:23
Alignment explanation
Indices: 191484--191529 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
191474 TGTGATTTTA
191484 TTTTTATTTTTATATATTAT-AT
1 TTTTTATTTTTATATATTATCAT
191506 TTTTTATTTTT-T-TATTATCAT
1 TTTTTATTTTTATATATTATCAT
191527 TTT
1 TTT
191530 ATGAATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.26
21 6 0.26
22 11 0.48
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTTATTTTTATATATTATCAT
Found at i:191770 original size:18 final size:16
Alignment explanation
Indices: 191743--191779 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
191733 TTTAAACTTA
191743 TAATTATATATATTTT
1 TAATTATATATATTTT
191759 TAATTATATATATTTT
1 TAATTATATATATTTT
191775 TAATT
1 TAATT
191780 TTAATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TAATTATATATATTTT
Found at i:205071 original size:2 final size:2
Alignment explanation
Indices: 205064--205135 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
205054 AATAATTTAG
205064 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
205106 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
205136 CATTTTAATA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:209605 original size:28 final size:28
Alignment explanation
Indices: 209565--209619 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
209555 TAATTGAAAT
209565 ATTACATCGTCGAGTCAATGCTTAAAAC
1 ATTACATCGTCGAGTCAATGCTTAAAAC
209593 ATTACATCGTCGAGTCAATGCTTAAAA
1 ATTACATCGTCGAGTCAATGCTTAAAA
209620 GCAATGACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (28 bp):
ATTACATCGTCGAGTCAATGCTTAAAAC
Found at i:211561 original size:24 final size:24
Alignment explanation
Indices: 211533--211591 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
211523 ATGAGTTATT
211533 TGGCATTGAAAACA-CATCACGTTA
1 TGGCATTGAAAACATC-TCACGTTA
* **
211557 TGGCA-GGGTAACATCTCACGTTA
1 TGGCATTGAAAACATCTCACGTTA
211580 TGGCATTGAAAA
1 TGGCATTGAAAA
211592 TACCATTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (24 bp):
TGGCATTGAAAACATCTCACGTTA
Found at i:228637 original size:30 final size:30
Alignment explanation
Indices: 228601--228667 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
228591 AAGTGAATCG
*
228601 TGGTTCAAACCGATTTTGCCGGTTTTCAGC
1 TGGTTCAAACCGATTTTACCGGTTTTCAGC
** *
228631 TGGTTCACCCCGATTTTACTGGTTTTCAGC
1 TGGTTCAAACCGATTTTACCGGTTTTCAGC
*
228661 CGGTTCA
1 TGGTTCA
228668 TTGCTAGTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.15, C:0.25, G:0.22, T:0.37
Consensus pattern (30 bp):
TGGTTCAAACCGATTTTACCGGTTTTCAGC
Found at i:232088 original size:41 final size:41
Alignment explanation
Indices: 232043--232123 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
232033 TAAGATTGTA
* *
232043 TTCGTGTTTGTTTGTTTGTTTTTGAAAGTGTTCATGTTCGG
1 TTCGTGTTTGTTTATTTATTTTTGAAAGTGTTCATGTTCGG
* *
232084 TTCGTGTTTTTTTATTTATTTTTGAAGGTGTTCATGTTCG
1 TTCGTGTTTGTTTATTTATTTTTGAAAGTGTTCATGTTCG
232124 TTTATTTAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.11, C:0.07, G:0.23, T:0.58
Consensus pattern (41 bp):
TTCGTGTTTGTTTATTTATTTTTGAAAGTGTTCATGTTCGG
Found at i:232190 original size:24 final size:24
Alignment explanation
Indices: 232146--232230 Score: 118
Period size: 24 Copynumber: 3.6 Consensus size: 24
232136 TATCGAACGC
* *
232146 GTTCGTTT-AATGTTCGTGAACAT
1 GTTCGTTTAAATGTTTGCGAACAT
*
232169 GTTCTTTTAAATGTTTGCGAACAT
1 GTTCGTTTAAATGTTTGCGAACAT
*
232193 GTTCTTTTAAATGTTTGCGAACAT
1 GTTCGTTTAAATGTTTGCGAACAT
*
232217 GTTCGTTTATATGT
1 GTTCGTTTAAATGT
232231 AAATTTAACG
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
23 7 0.12
24 49 0.88
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (24 bp):
GTTCGTTTAAATGTTTGCGAACAT
Found at i:232503 original size:12 final size:12
Alignment explanation
Indices: 232486--232532 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
232476 ATATAAAAAA
*
232486 TAAACGAGCCTC
1 TAAACGAGCTTC
* *
232498 TAAACGAACTTA
1 TAAACGAGCTTC
*
232510 TAAATGAGCTTC
1 TAAACGAGCTTC
232522 TAAACGAGCTT
1 TAAACGAGCTT
232533 GTTTGTGAAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (12 bp):
TAAACGAGCTTC
Found at i:242232 original size:12 final size:12
Alignment explanation
Indices: 242196--242233 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
242186 ATGATTATGA
242196 TTATT-ATTTTT
1 TTATTAATTTTT
*
242207 ATTATTAATCTTT
1 -TTATTAATTTTT
242220 TTATTAATTTTT
1 TTATTAATTTTT
242232 TT
1 TT
242234 TCCTTTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (12 bp):
TTATTAATTTTT
Found at i:248882 original size:63 final size:64
Alignment explanation
Indices: 248751--248903 Score: 238
Period size: 63 Copynumber: 2.4 Consensus size: 64
248741 GTACCGATAC
* **
248751 AAAGGGCAAT-GGTTCGAATACCTTTCTTGACACAAATTTTTTTCCCATATGCTAGCTGAACTGG
1 AAAGGGC-ATGGGTTCGAATCCCACTCTTGACACAAATTTTTTTCCCATATGCTAGCTGAACTGG
*
248815 AAAGGGCATGGGTTCGAATCCCACTCTTGACAC-AATTTTTTTCCCATATGCTAGTTGAACTGG
1 AAAGGGCATGGGTTCGAATCCCACTCTTGACACAAATTTTTTTCCCATATGCTAGCTGAACTGG
*
248878 AAAGGGCATGGGTTCAAATCCCACTC
1 AAAGGGCATGGGTTCGAATCCCACTC
248904 AAATAAATGC
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
63 56 0.67
64 27 0.33
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (64 bp):
AAAGGGCATGGGTTCGAATCCCACTCTTGACACAAATTTTTTTCCCATATGCTAGCTGAACTGG
Found at i:255891 original size:49 final size:49
Alignment explanation
Indices: 255828--255927 Score: 166
Period size: 49 Copynumber: 2.0 Consensus size: 49
255818 TTGTCACGTA
*
255828 GAGGTGATCGGTTTATTTAAATAATATTTTTTATTTAAACTCACTCGTC
1 GAGGTGATCGGTTTACTTAAATAATATTTTTTATTTAAACTCACTCGTC
*
255877 GAGGTGA-CGAGTTTACTTAAATAATATTTTTTATTTAAACTCGCTCGTC
1 GAGGTGATCG-GTTTACTTAAATAATATTTTTTATTTAAACTCACTCGTC
255926 GA
1 GA
255928 CTGACGAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 2 0.04
49 46 0.96
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (49 bp):
GAGGTGATCGGTTTACTTAAATAATATTTTTTATTTAAACTCACTCGTC
Found at i:257602 original size:2 final size:2
Alignment explanation
Indices: 257595--257619 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
257585 GACAGCCATT
257595 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
257620 TTAATCCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:269932 original size:25 final size:26
Alignment explanation
Indices: 269882--269933 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
269872 ATTATTATTT
* *
269882 AAAATTTATTATTATTAAAAATATGA
1 AAAATATATTATTATTAAAAACATGA
269908 AAAATATA-TATT-TTAAAAACCATGA
1 AAAATATATTATTATTAAAAA-CATGA
269933 A
1 A
269934 TCAATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 7 0.30
25 9 0.39
26 7 0.30
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (26 bp):
AAAATATATTATTATTAAAAACATGA
Found at i:273080 original size:16 final size:16
Alignment explanation
Indices: 273059--273091 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
273049 TAATAAATAA
*
273059 ACGAACATAAACGAAC
1 ACGAACATAAACAAAC
273075 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
273091 A
1 A
273092 AACAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.24, G:0.09, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:273194 original size:24 final size:26
Alignment explanation
Indices: 273161--273209 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
273151 AAATGATAAC
*
273161 CGAACGTAAAC-A-AACACAAACAAA
1 CGAACATAAACAACAACACAAACAAA
273185 CGAACATAAACGAACAACACAAACA
1 CGAACATAAAC-AACAACACAAACA
273210 CAAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 10 0.48
26 1 0.05
27 10 0.48
ACGTcount: A:0.61, C:0.27, G:0.08, T:0.04
Consensus pattern (26 bp):
CGAACATAAACAACAACACAAACAAA
Found at i:273504 original size:26 final size:26
Alignment explanation
Indices: 273469--273519 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
273459 CTGTTCGAAC
*
273469 ATAAATGAACG-AACATAAACGAACAT
1 ATAAACGAACGTAA-ATAAACGAACAT
*
273495 ATAAACGAACGTAAATGAACGAACA
1 ATAAACGAACGTAAATAAACGAACA
273520 AGTCCTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.57, C:0.16, G:0.14, T:0.14
Consensus pattern (26 bp):
ATAAACGAACGTAAATAAACGAACAT
Found at i:278381 original size:104 final size:105
Alignment explanation
Indices: 278190--278416 Score: 327
Period size: 104 Copynumber: 2.2 Consensus size: 105
278180 CCTCTAGGCG
* * * *
278190 ACCTTCATAGGTCG-TCAAGTCCTCCAAACGTTCAAGCATTGGTTTCCTATATTTCTCATAAGTA
1 ACCTCCATAGGTCGCTCAAGTCCTCCAAACGATCAAGCATTGGTTTCCTATACTTCCCATAAGTA
278254 ACAGTGATTACCTAAATAGGTAATTAGACTTTTAGTTGAA
66 ACAGTGATTACCTAAATAGGTAATTAGACTTTTAGTTGAA
** *
278294 ACCTCCATAGGTCGCT-AAGTCCTCTGAACGATCAAGCATTGGTTTCCTTTACTTCCCATAAGTA
1 ACCTCCATAGGTCGCTCAAGTCCTCCAAACGATCAAGCATTGGTTTCCTATACTTCCCATAAGTA
* *
278358 ACAGTGATTATCTATATCA-GTAATTAGACTTTTAGTTGAA
66 ACAGTGATTACCTAAAT-AGGTAATTAGACTTTTAGTTGAA
*
278398 ACTTCCATAGGTCGC-CAAG
1 ACCTCCATAGGTCGCTCAAG
278417 ACATCCCGAC
Statistics
Matches: 110, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
104 108 0.98
105 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (105 bp):
ACCTCCATAGGTCGCTCAAGTCCTCCAAACGATCAAGCATTGGTTTCCTATACTTCCCATAAGTA
ACAGTGATTACCTAAATAGGTAATTAGACTTTTAGTTGAA
Found at i:294180 original size:31 final size:31
Alignment explanation
Indices: 294142--294294 Score: 265
Period size: 31 Copynumber: 5.0 Consensus size: 31
294132 GGGTCGAGGG
294142 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
294173 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
294204 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
294235 TTACCTATGTTCTTCGGGACATA-GGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
294265 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
294295 GTCCTTCGGG
Statistics
Matches: 118, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
30 26 0.22
31 92 0.78
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:298501 original size:30 final size:30
Alignment explanation
Indices: 298444--298593 Score: 227
Period size: 30 Copynumber: 5.0 Consensus size: 30
298434 CAAGGGTCGG
298444 GTTACCTATGTTCTTCGGGAC--ATGGACT
1 GTTACCTATGTTCTTCGGGACATATGGACT
298472 GTTTACCTA-GTTCTTCGGGACATATGGACT
1 G-TTACCTATGTTCTTCGGGACATATGGACT
298502 GTTTACCTATGTTCTTCGGGACATATGGACT
1 G-TTACCTATGTTCTTCGGGACATATGGACT
298533 GTTACCTATGTTCTTCGGGACATATGGACT
1 GTTACCTATGTTCTTCGGGACATATGGACT
* *
298563 GTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTACCTATGTTCTTCGGGA-CATATGGACT
298593 G
1 G
298594 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 2, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
28 13 0.11
29 7 0.06
30 72 0.63
31 23 0.20
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (30 bp):
GTTACCTATGTTCTTCGGGACATATGGACT
Found at i:299797 original size:32 final size:32
Alignment explanation
Indices: 299761--299840 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 32
299751 TCGTATTAAA
* *
299761 AATATATTTTATATAATTTGTAT-TTTTAATTT
1 AATATATTTTATATAATATGT-TCTATTAATTT
* * *
299793 AATATATTTTAAAAAATATGTTCGTATTATTTT
1 AATATATTTTATATAATATGTTC-TATTAATTT
299826 AATATATTTTATATA
1 AATATATTTTATATA
299841 TTCATATTTC
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
31 1 0.03
32 18 0.46
33 20 0.51
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (32 bp):
AATATATTTTATATAATATGTTCTATTAATTT
Found at i:299798 original size:74 final size:73
Alignment explanation
Indices: 299673--299822 Score: 219
Period size: 74 Copynumber: 2.0 Consensus size: 73
299663 ATTTGAACTA
* * *
299673 TATATTCGTATTAAAAAATAGTTTACATAATTTGTATTTTTTAGTTAATATATTTTGAAATATAT
1 TATATTCGTATTAAAAAATAGTTTACATAATTTGTATTTTTAAGTTAATATATTTTAAAAAATAT
*
299738 ATTTGTAT
66 ATTCGTAT
* * *
299746 TATATTCGTATTAAAAATATATTTTATATAATTTGTATTTTTAATTTAATATATTTTAAAAAATA
1 TATATTCGTATTAAAAA-ATAGTTTACATAATTTGTATTTTTAAGTTAATATATTTTAAAAAATA
*
299811 TGTTCGTAT
65 TATTCGTAT
299820 TAT
1 TAT
299823 TTTAATATAT
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
73 17 0.25
74 51 0.75
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (73 bp):
TATATTCGTATTAAAAAATAGTTTACATAATTTGTATTTTTAAGTTAATATATTTTAAAAAATAT
ATTCGTAT
Found at i:301247 original size:276 final size:277
Alignment explanation
Indices: 300752--301305 Score: 1060
Period size: 276 Copynumber: 2.0 Consensus size: 277
300742 TGTAATATCC
300752 CATTTTTGTCGAGTGAGTTGTATGTAAATGAGTTAGGATGGTATATATATATATATATTGGAATA
1 CATTTTTGTCGAGTGAGTTGTATGTAAATGAGTTAGGATGG-ATATATATATATATATTGGAATA
300817 TTCAGCAAATGTGAAAGCGCGTGGGCTTTGTTCATTTTCCGTTATTGGCCACTTTTTTTCTATTC
65 TTCAGCAAATGTGAAAGCGCGTGGGCTTTGTTCATTTTCCGTTATTGGCCACTTTTTTTCTATTC
300882 TTATTTATTTTCAATAGTTCAAACTGAGTCCACCGGTTACTGCTCCACTCCACTTCCTTTTTCAC
130 TTATTTATTTTCAATAGTTCAAACTGAGTCCACCGGTTACTGCTCCACTCCACTTCCTTTTTCAC
300947 TCTCTCTTTTAAATTAGGTACATTATATTTTGAAATTAGTGACCAAAATAGATAAAATATAAGAT
195 TCTCTCTTTTAAATTAGGTACATTATATTTTGAAATTAGTGACCAAAATAGATAAAATATAAGAT
301012 CACTGTGTAATTAACCCT
260 CACTGTGTAATTAACCCT
301030 CATTTTTGTCGAGTGAGTTGTATGTAAATGAGTTAGGATGG-TATATATATATATATTGGAATAT
1 CATTTTTGTCGAGTGAGTTGTATGTAAATGAGTTAGGATGGATATATATATATATATTGGAATAT
301094 TCAGCAAATGTGAAAGCGCGTGGGCTTTGTTCATTTTCCGTTATTGGCCACTTTTTTTCTATTCT
66 TCAGCAAATGTGAAAGCGCGTGGGCTTTGTTCATTTTCCGTTATTGGCCACTTTTTTTCTATTCT
301159 TATTTATTTTCAATA-TTCAAAACTGAGTCCA-CGGTTACTGCTCCCACTCCACTTCCTTTTTCA
131 TATTTATTTTCAATAGTTC-AAACTGAGTCCACCGGTTACTGCT-CCACTCCACTTCCTTTTTCA
301222 CTCTCTCTTTTAAATTAGGTACATTATATTTTGAAATTAGTGACCAAAATAGATAAAATATAAGA
194 CTCTCTCTTTTAAATTAGGTACATTATATTTTGAAATTAGTGACCAAAATAGATAAAATATAAGA
301287 TCACTGTGTAATTAACCCT
259 TCACTGTGTAATTAACCCT
301306 AATTATTATT
Statistics
Matches: 274, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
275 14 0.05
276 219 0.80
278 41 0.15
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (277 bp):
CATTTTTGTCGAGTGAGTTGTATGTAAATGAGTTAGGATGGATATATATATATATATTGGAATAT
TCAGCAAATGTGAAAGCGCGTGGGCTTTGTTCATTTTCCGTTATTGGCCACTTTTTTTCTATTCT
TATTTATTTTCAATAGTTCAAACTGAGTCCACCGGTTACTGCTCCACTCCACTTCCTTTTTCACT
CTCTCTTTTAAATTAGGTACATTATATTTTGAAATTAGTGACCAAAATAGATAAAATATAAGATC
ACTGTGTAATTAACCCT
Found at i:302029 original size:27 final size:28
Alignment explanation
Indices: 301994--302058 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 28
301984 TCGGGCCGGA
301994 ATATATATTTAAATTAAA-AATATAAAT
1 ATATATATTTAAATTAAATAATATAAAT
* *
302021 ATATATATTTTAATTAAATTAATTTAAAT
1 ATATATATTTAAATTAAA-TAATATAAAT
302050 ATTATATAT
1 A-TATATAT
302059 ATAATAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 17 0.52
29 9 0.27
30 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
ATATATATTTAAATTAAATAATATAAAT
Found at i:305742 original size:2 final size:2
Alignment explanation
Indices: 305735--305771 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
305725 TCATAAAATA
* *
305735 AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
305772 ATTTTACATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:307635 original size:19 final size:19
Alignment explanation
Indices: 307611--307666 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
307601 CAAATCGAAC
307611 ACGAACATATTCAAAAATA
1 ACGAACATATTCAAAAATA
* *
307630 ACGAACATGAATCAAACAT-
1 ACGAACAT-ATTCAAAAATA
*
307649 --GAACATATTCTAAAATA
1 ACGAACATATTCAAAAATA
307666 A
1 A
307667 AGAAATGAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
16 7 0.24
17 6 0.21
19 8 0.28
20 8 0.28
ACGTcount: A:0.55, C:0.16, G:0.07, T:0.21
Consensus pattern (19 bp):
ACGAACATATTCAAAAATA
Found at i:307653 original size:36 final size:35
Alignment explanation
Indices: 307603--307675 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 35
307593 ATATTAAACA
* *
307603 AATCGAACACGAACATATTCAAAAATAACGAACATG
1 AATCAAACACGAACATATTCAAAAATAAAGAA-ATG
* *
307639 AATCAAACATGAACATATTCTAAAATAAAGAAATG
1 AATCAAACACGAACATATTCAAAAATAAAGAAATG
307674 AA
1 AA
307676 CATAAACGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
35 5 0.15
36 28 0.85
ACGTcount: A:0.56, C:0.15, G:0.10, T:0.19
Consensus pattern (35 bp):
AATCAAACACGAACATATTCAAAAATAAAGAAATG
Found at i:311843 original size:3 final size:3
Alignment explanation
Indices: 311830--311859 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
311820 ATAACACTTG
*
311830 TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
311860 GTTATCCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:313527 original size:42 final size:43
Alignment explanation
Indices: 313465--313750 Score: 277
Period size: 42 Copynumber: 6.7 Consensus size: 43
313455 AAGTCTTTAT
* *
313465 TTTTTTCAAT-TCTA-TCTTTTACCTTTCTAATCGATGCCCT-TAA
1 TTTTTTCAATCTC-ACT-TTTTACCTTTATAATTGA-GCCCTCTAA
* *
313508 -TTTTTCAATCTCACTTTTTATCTTTGTAATTGATG-CCTCTAA
1 TTTTTTCAATCTCACTTTTTACCTTTATAATTGA-GCCCTCTAA
* *
313550 TTTTTT-AATCACACTTTTTACCTTTATAATTGAGGCCTCTAA
1 TTTTTTCAATCTCACTTTTTACCTTTATAATTGAGCCCTCTAA
* * * * * *
313592 TTTTTTTAATCACATTTTTTACCATTATGATTGAGGCCTCTAA
1 TTTTTTCAATCTCACTTTTTACCTTTATAATTGAGCCCTCTAA
* *
313635 GTTTTTTCAATCTCACTTTCTACCTTTATAATTGAAGCCGT-TAA
1 -TTTTTTCAATCTCACTTTTTACCTTTATAATTG-AGCCCTCTAA
*
313679 -TTTTT-AATCTCACTTTTTACCTTTATAATTGAGGCC-CTAA
1 TTTTTTCAATCTCACTTTTTACCTTTATAATTGAGCCCTCTAA
* * *
313719 GTTTTTTCAAACTCACTTTCTATCTTTATAAT
1 -TTTTTTCAATCTCACTTTTTACCTTTATAAT
313751 AGAGGGCCCT
Statistics
Matches: 208, Mismatches: 23, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
40 6 0.03
41 29 0.14
42 77 0.37
43 62 0.30
44 30 0.14
45 4 0.02
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.49
Consensus pattern (43 bp):
TTTTTTCAATCTCACTTTTTACCTTTATAATTGAGCCCTCTAA
Found at i:313611 original size:43 final size:42
Alignment explanation
Indices: 313481--313771 Score: 304
Period size: 43 Copynumber: 6.9 Consensus size: 42
313471 CAATTCTATC
* * * *
313481 TTTTACCTTTCTAATCGATGCC-CTTAATTTTTCAATCTCACT
1 TTTTACCTTTATAATTGAGGCCTC-TAATTTTTTAATCTCACT
* * * *
313523 TTTTATCTTTGTAATTGATGCCTCTAATTTTTTAATCACACT
1 TTTTACCTTTATAATTGAGGCCTCTAATTTTTTAATCTCACT
* *
313565 TTTTACCTTTATAATTGAGGCCTCTAATTTTTTTAATCACATT
1 TTTTACCTTTATAATTGAGGCCTCTAA-TTTTTTAATCTCACT
* *
313608 TTTTACCATTATGATTGAGGCCTCTAAGTTTTTTCAATCTCACT
1 TTTTACCTTTATAATTGAGGCCTCTAA-TTTTTT-AATCTCACT
* *
313652 TTCTACCTTTATAATTGAAGCCGT-TAA-TTTTTAATCTCACT
1 TTTTACCTTTATAATTGAGGCC-TCTAATTTTTTAATCTCACT
*
313693 TTTTACCTTTATAATTGAGGCC-CTAAGTTTTTTCAAACTCACT
1 TTTTACCTTTATAATTGAGGCCTCTAA-TTTTTT-AATCTCACT
* * * *
313736 TTCTATCTTTATAATAGAGGGCC-CTAGTTTTTTAAT
1 TTTTACCTTTATAATTGA-GGCCTCTAATTTTTTAAT
313772 TTCATAAAAT
Statistics
Matches: 214, Mismatches: 26, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
40 3 0.01
41 29 0.14
42 71 0.33
43 75 0.35
44 35 0.16
45 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.48
Consensus pattern (42 bp):
TTTTACCTTTATAATTGAGGCCTCTAATTTTTTAATCTCACT
Found at i:313768 original size:85 final size:85
Alignment explanation
Indices: 313465--313771 Score: 313
Period size: 85 Copynumber: 3.6 Consensus size: 85
313455 AAGTCTTTAT
* * * *
313465 TTTTTTCAAT-TCTATCTTT-TACCTTTCTAATCGATGCC-CTTAATTTTTCAATCTCACTTTTT
1 TTTTTTCAATCTC-A-CTTTCTACCTTTATAATTGAGGCCGC-T-ATTTTTTAATCTCACTTTTT
* * *
313527 ATCTTTGTAATTGATGCCTCTAA-
62 ACCTTTATAATTGAGGCCTCTAAG
* * * * *
313550 TTTTTT-AATCACACTTTTTACCTTTATAATTGAGGCCTCTAATTTTTTTAATCACATTTTTTAC
1 TTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGCCGCT-A-TTTTTTAATCTCACTTTTTAC
* *
313614 CATTATGATTGAGGCCTCTAAG
64 CTTTATAATTGAGGCCTCTAAG
* * *
313636 TTTTTTCAATCTCACTTTCTACCTTTATAATTGAAGCCGTTAATTTTTAATCTCACTTTTTACCT
1 TTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGCCGCTATTTTTTAATCTCACTTTTTACCT
313701 TTATAATTGAGGCC-CTAAG
66 TTATAATTGAGGCCTCTAAG
* * *
313720 TTTTTTCAAACTCACTTTCTATCTTTATAATAGAGGGCC-CTAGTTTTTTAAT
1 TTTTTTCAATCTCACTTTCTACCTTTATAATTGA-GGCCGCTA-TTTTTTAAT
313772 TTCATAAAAT
Statistics
Matches: 186, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
83 4 0.02
84 61 0.33
85 85 0.46
86 7 0.04
87 29 0.16
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (85 bp):
TTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGCCGCTATTTTTTAATCTCACTTTTTACCT
TTATAATTGAGGCCTCTAAG
Found at i:313768 original size:128 final size:129
Alignment explanation
Indices: 313508--313768 Score: 334
Period size: 128 Copynumber: 2.0 Consensus size: 129
313498 ATGCCCTTAA
* * * *
313508 TTTTTCAATCTCACTTTTTATCTTTGTAATTGATGCCTCTAATTTTTTAATCACACTTTTTACCT
1 TTTTTCAATCTCACTTTCTACCTTTATAATTGAAGCCTCTAATTTTTTAATCACACTTTTTACCT
* * * * * *
313573 TTATAATTGAGGCCTCTAATTTTTTTAATCACATTTTTTACCATTATGATTGAGGCCTCTAAGT
66 TTATAATTGAGGCCTCTAATTTTTTCAAACACACTTTCTACCATTATAATAGAGGCCTCTAAGT
*
313637 TTTTTCAATCTCACTTTCTACCTTTATAATTGAAGCCGT-TAA-TTTTTAATCTCACTTTTTACC
1 TTTTTCAATCTCACTTTCTACCTTTATAATTGAAGCC-TCTAATTTTTTAATCACACTTTTTACC
* * *
313700 TTTATAATTGAGGCC-CTAAGTTTTTTCAAACTCACTTTCTATCTTTATAATAGAGGGCC-CT-A
65 TTTATAATTGAGGCCTCTAA-TTTTTTCAAACACACTTTCTACCATTATAATAGA-GGCCTCTAA
313762 GT
128 GT
313764 TTTTT
1 TTTTT
313769 AATTTCATAA
Statistics
Matches: 115, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
127 12 0.10
128 62 0.54
129 40 0.35
130 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.48
Consensus pattern (129 bp):
TTTTTCAATCTCACTTTCTACCTTTATAATTGAAGCCTCTAATTTTTTAATCACACTTTTTACCT
TTATAATTGAGGCCTCTAATTTTTTCAAACACACTTTCTACCATTATAATAGAGGCCTCTAAGT
Found at i:315926 original size:16 final size:17
Alignment explanation
Indices: 315905--315938 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
315895 ATGGTGTATT
*
315905 ATTTAATATA-AAAATA
1 ATTTAAAATATAAAATA
315921 ATTTAAAATATAAAATA
1 ATTTAAAATATAAAATA
315938 A
1 A
315939 AAATAGAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATATAAAATA
Found at i:317364 original size:21 final size:21
Alignment explanation
Indices: 317334--317413 Score: 81
Period size: 21 Copynumber: 3.9 Consensus size: 21
317324 GTGATTTTTT
317334 CCAAAAAGGATCGATCCCTTA
1 CCAAAAAGGATCGATCCCTTA
**** *
317355 GGGGAAAGGATCGATCCTTTA
1 CCAAAAAGGATCGATCCCTTA
*
317376 CCAAAAAGGATCGATCCCTCA
1 CCAAAAAGGATCGATCCCTTA
* *
317397 CC-GAAAGGATCAATCCC
1 CCAAAAAGGATCGATCCC
317414 AAACTCTTTG
Statistics
Matches: 46, Mismatches: 13, Indels: 1
0.77 0.22 0.02
Matches are distributed among these distances:
20 13 0.28
21 33 0.72
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (21 bp):
CCAAAAAGGATCGATCCCTTA
Found at i:317458 original size:21 final size:20
Alignment explanation
Indices: 317434--317506 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 20
317424 TTGTGCAATG
317434 GATCGATCCCTCGAGAGAAAT
1 GATCGATCCCTCGAGA-AAAT
*
317455 GATCAATCCCTCGAGAAAAT
1 GATCGATCCCTCGAGAAAAT
* * * *
317475 GATTGATCCCTCTAAATAAAG
1 GATCGATCCCTCGAGA-AAAT
317496 GATCGATCCCT
1 GATCGATCCCT
317507 TCCTTGTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
GATCGATCCCTCGAGAAAAT
Found at i:331443 original size:119 final size:119
Alignment explanation
Indices: 331232--331469 Score: 467
Period size: 119 Copynumber: 2.0 Consensus size: 119
331222 CCTTTAGAAT
331232 ATATAAGCTACCAGGATCGTCATCGAAAAAAGGTATTTTATTGTTGATTAGGCGGTTTCACCTAA
1 ATATAAGCTACCAGGATCGTCATCGAAAAAAGGTATTTTATTGTTGATTAGGCGGTTTCACCTAA
*
331297 TGTTGATGTATGTAAAAACTGTGGTGGTTGAAAATTGTGCATATAAGCCATTGA
66 TGTTGATATATGTAAAAACTGTGGTGGTTGAAAATTGTGCATATAAGCCATTGA
331351 ATATAAGCTACCAGGATCGTCATCGAAAAAAGGTATTTTATTGTTGATTAGGCGGTTTCACCTAA
1 ATATAAGCTACCAGGATCGTCATCGAAAAAAGGTATTTTATTGTTGATTAGGCGGTTTCACCTAA
331416 TGTTGATATATGTAAAAACTGTGGTGGTTGAAAATTGTGCATATAAGCCATTGA
66 TGTTGATATATGTAAAAACTGTGGTGGTTGAAAATTGTGCATATAAGCCATTGA
331470 TGAATTTTGG
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 118 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (119 bp):
ATATAAGCTACCAGGATCGTCATCGAAAAAAGGTATTTTATTGTTGATTAGGCGGTTTCACCTAA
TGTTGATATATGTAAAAACTGTGGTGGTTGAAAATTGTGCATATAAGCCATTGA
Found at i:333152 original size:15 final size:15
Alignment explanation
Indices: 333132--333165 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
333122 CAATCAAATT
333132 CTTCCCTCTTGCCGA
1 CTTCCCTCTTGCCGA
333147 CTTCCCTCTTGCCGA
1 CTTCCCTCTTGCCGA
333162 CTTC
1 CTTC
333166 TGATACTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.47, G:0.12, T:0.35
Consensus pattern (15 bp):
CTTCCCTCTTGCCGA
Found at i:339235 original size:20 final size:19
Alignment explanation
Indices: 339189--339240 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
339179 CAACGCGATT
* *
339189 AGAAATCGCAACGTTGAAA
1 AGAAATCGCAACGATCAAA
339208 AGAAATCGCAACGATCAAA
1 AGAAATCGCAACGATCAAA
339227 AGAAAATCGCAACG
1 AG-AAATCGCAACG
339241 CGATATTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (19 bp):
AGAAATCGCAACGATCAAA
Found at i:339273 original size:42 final size:42
Alignment explanation
Indices: 339226--339327 Score: 163
Period size: 40 Copynumber: 2.5 Consensus size: 42
339216 CAACGATCAA
339226 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
*
339268 CAGAAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
*
339308 AAGAAAAATCGCAATGCGAT
1 AAG-AAAATCGCAACGCGAT
339328 TAAGAAAATG
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
40 25 0.46
41 13 0.24
42 16 0.30
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.16
Consensus pattern (42 bp):
AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
Found at i:339276 original size:20 final size:20
Alignment explanation
Indices: 339227--339336 Score: 116
Period size: 20 Copynumber: 5.3 Consensus size: 20
339217 AACGATCAAA
339227 AGAAAATCGCAACGCGATATTCC
1 AGAAAATCGCAACGCG--ATT-C
*
339250 A-AGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATTC
339269 AGAAAATCGCAACGCGATTCC
1 AGAAAATCGCAACGCGATT-C
* *
339290 A-AGAATCGCAACGCGATTA
1 AGAAAATCGCAACGCGATTC
* *
339309 AGAAAAATCGCAATGCGATTA
1 AG-AAAATCGCAACGCGATTC
339330 AGAAAAT
1 AGAAAAT
339337 GAGTAAATTC
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.04
20 40 0.52
21 20 0.26
22 13 0.17
23 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (20 bp):
AGAAAATCGCAACGCGATTC
Found at i:339442 original size:6 final size:6
Alignment explanation
Indices: 339431--339472 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
339421 GACACGTATT
339431 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
339473 CGAACCGAGA
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:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:339952 original size:5 final size:5
Alignment explanation
Indices: 339944--339984 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
339934 CCGTCTCGTC
339944 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG
339985 TGGTAATACG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.27
Consensus pattern (5 bp):
TCGGG
Found at i:339973 original size:6 final size:6
Alignment explanation
Indices: 339947--339988 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
339937 TCTCGTCTCG
339947 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
339989 AATACGTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.00, C:0.17, G:0.55, T:0.29
Consensus pattern (6 bp):
GGTCGT
Done.