Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001542.1 Hibiscus syriacus cultivar Beakdansim tig00003030_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: 113757
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1907 original size:64 final size:64
Alignment explanation
Indices: 1815--1975 Score: 175
Period size: 67 Copynumber: 2.5 Consensus size: 64
1805 TGCACTAAGA
* * *
1815 GTGCATCG-ATCATCAAGTGCATTCGATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGCT-
1 GTGCATCGAAGCATCAAATGCATTCGATGTTTCATAAA-AGCCACAGTGCATCGATGCATGG-TA
1877 G
64 G
* * *
1878 GTGCATCGAAGCATCAAATGCATTCGATGTTTTTTCATAAAATCCTCAGTGCATCGGTGCATGGT
1 GTGCATCGAAGCATCAAATGCATTCGATG---TTTCATAAAAGCCACAGTGCATCGATGCATGGT
*
1943 AT
63 AG
* *
1945 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGAAGCATCAAATGCATTCGATGTT
1976 CAATTTAATT
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
63 8 0.10
64 20 0.24
66 1 0.01
67 51 0.61
68 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGAAGCATCAAATGCATTCGATGTTTCATAAAAGCCACAGTGCATCGATGCATGGTAG
Found at i:18083 original size:27 final size:26
Alignment explanation
Indices: 18052--18109 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
18042 TAGTGAATTA
*
18052 ATTGAAATTGAAGAAA-ATGGGTTTTT
1 ATTGAAA-TGAAGAAATATGAGTTTTT
* *
18078 GATTGATATGATGAAATATGAGTTTTT
1 -ATTGAAATGAAGAAATATGAGTTTTT
18105 ATTGA
1 ATTGA
18110 GGATTACAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.41
Consensus pattern (26 bp):
ATTGAAATGAAGAAATATGAGTTTTT
Found at i:18987 original size:54 final size:53
Alignment explanation
Indices: 18900--19296 Score: 501
Period size: 54 Copynumber: 7.4 Consensus size: 53
18890 CTATGTGTAC
* *
18900 TATCGACACTAAGTGTACAACCCACGTAATTCATAATATGTTTATGAACGATCG
1 TATCGACACTAAGTGTGCAACCCACG-AATTCATAATATGTTTATGAACGACCG
* * *
18954 TATCAACACTAAGTGTGCAACACACAGAATTCATAATATGTTTATGAACGACTG
1 TATCGACACTAAGTGTGCAACCCAC-GAATTCATAATATGTTTATGAACGACCG
* *
19008 TATCGACACTAAGTATGCAACCCACGAAATTCATAATATGTTTATGAATGACCG
1 TATCGACACTAAGTGTGCAACCCACG-AATTCATAATATGTTTATGAACGACCG
* *
19062 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATAAACGACCG
1 TATCGACACTAAGTGTGCAACCCAC-GAATTCATAATATGTTTATGAACGACCG
* * * * * *
19116 TATCTG-CACTAAATATGCAACCCACAAAATTTATAATATGTTTATGAATGATCG
1 TATC-GACACTAAGTGTGCAACCCAC-GAATTCATAATATGTTTATGAACGACCG
* *
19170 TATCGACACTAAGTGTGCAACCCACGGAATTTATAATATGTTTATGAACGACCA
1 TATCGACACTAAGTGTGCAACCCAC-GAATTCATAATATGTTTATGAACGACCG
* **
19224 TATC-AGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACTA
1 TATCGA-CACTAAGTGTGCAACCCACG-AATTCATAATATGTTTATGAACGACCG
* *
19278 TATCGGCACTACGTGTGCA
1 TATCGACACTAAGTGTGCA
19297 TACCAAAGAA
Statistics
Matches: 302, Mismatches: 33, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
53 4 0.01
54 295 0.98
55 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (53 bp):
TATCGACACTAAGTGTGCAACCCACGAATTCATAATATGTTTATGAACGACCG
Found at i:22533 original size:45 final size:45
Alignment explanation
Indices: 22484--23340 Score: 1205
Period size: 45 Copynumber: 19.1 Consensus size: 45
22474 ATAAAAGACT
* * *
22484 AAATGCATAACGGTGCATTATTGGAATGAAAGGATGTCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
*
22529 AAATGCATAACGGTGCATTATTGGCATGAAAGGATGCCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
* *
22574 AAATGCATAACAGTGCATTATCGGCATGAAATGATGCCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
* * * *
22619 AAATGCATAACAGTGCATTATCGTCATGATAGAATGCCATAAAT-
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
* *
22663 ATAATGCATAACGGTGCATTATCAGTATGAAAGGATGCCATAAATG
1 A-AATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
** ** * *
22709 AAATATATAATAGTGCATAATCGACATGAAAGGATGCCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
22754 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
* * * * *
22799 AAATGCATAATGGTGCATTATCAGTATGAAATGATTCCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
** * *
22844 AAATATATAACGGTGCATAATCGGCATGAAATGATGCCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
*
22889 AAATGCATAACGGTGCATTATCGGCATGAAAAGATGCCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
** * * *
22934 AAATGCATAACAATGTATTATCGGCATGAAAGAATGTCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
* ** *
22979 AAATGCATAACGTTGCATTATTAGCATGAAAGGATTCCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
* * *
23024 AAATGCATAACGTTGCATTATCGGTATGAAACGATGCCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
* *
23069 AAATGCATAACGGTGCATTATCAGCATG-AATGATGCCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
** *
23113 AAATGCATAATTGTGCATTATTGGCATGAAAGGATGCCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
* * *
23158 AAATGCATAATGGTACATTATCGGCATGAGAGGATGCCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
* *
23203 AAATGCATAACGGTGTATTATCGGTATGAAAGGATGCCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
*
23248 AAATGCATAACGGTGCATTATCGACATGAAAGGATGCCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
* * *
23293 AAATGCATAACGGTGCATTATCGACATAAAAGGATTCCATAAATG
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
23338 AAA
1 AAA
23341 ATAAATTATA
Statistics
Matches: 722, Mismatches: 87, Indels: 6
0.89 0.11 0.01
Matches are distributed among these distances:
44 40 0.06
45 681 0.94
46 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (45 bp):
AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATG
Found at i:22750 original size:22 final size:22
Alignment explanation
Indices: 22724--22795 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
22714 TATAATAGTG
22724 CATAATCGACATGAAAGGATGC
1 CATAATCGACATGAAAGGATGC
*
22746 CATAAAT-GAAATGCATAACGG-TG-
1 CAT-AATCGACATG-A-AA-GGATGC
* *
22769 CATTATCGGCATGAAAGGATGC
1 CATAATCGACATGAAAGGATGC
22791 CATAA
1 CATAA
22796 ATGAAATGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
20 2 0.05
21 4 0.11
22 15 0.39
23 11 0.29
24 4 0.11
25 2 0.05
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (22 bp):
CATAATCGACATGAAAGGATGC
Found at i:30386 original size:22 final size:22
Alignment explanation
Indices: 30356--30435 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 22
30346 TAGGGCAGAT
*
30356 GGAATCGATACCCCCTTGAAGG
1 GGAACCGATACCCCCTTGAAGG
*
30378 GGAACCGATTCCCCCTTTGAAGG
1 GGAACCGATACCCCC-TTGAAGG
* *
30401 GGAACCGAT-TCCCC--GTAGG
1 GGAACCGATACCCCCTTGAAGG
*
30420 GGAATCGATACCCCCT
1 GGAACCGATACCCCCT
30436 GGGGTTCTGG
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
19 12 0.24
20 4 0.08
22 17 0.35
23 16 0.33
ACGTcount: A:0.24, C:0.31, G:0.26, T:0.19
Consensus pattern (22 bp):
GGAACCGATACCCCCTTGAAGG
Found at i:30397 original size:23 final size:22
Alignment explanation
Indices: 30356--30414 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 22
30346 TAGGGCAGAT
* *
30356 GGAATCGATACCCCCTTGAAGG
1 GGAACCGATTCCCCCTTGAAGG
30378 GGAACCGATTCCCCCTTTGAAGG
1 GGAACCGATTCCCCC-TTGAAGG
30401 GGAACCGATTCCCC
1 GGAACCGATTCCCC
30415 GTAGGGGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.24, C:0.32, G:0.25, T:0.19
Consensus pattern (22 bp):
GGAACCGATTCCCCCTTGAAGG
Found at i:32938 original size:11 final size:11
Alignment explanation
Indices: 32924--32953 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
32914 AATTAAGTTT
32924 TAATTTTAAAA
1 TAATTTTAAAA
32935 TAATTTTAAAA
1 TAATTTTAAAA
*
32946 CAATTTTA
1 TAATTTTA
32954 CAAAGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:37112 original size:54 final size:54
Alignment explanation
Indices: 37025--37364 Score: 432
Period size: 54 Copynumber: 6.3 Consensus size: 54
37015 CTATGTGTAC
* * *
37025 TATCAGCACTAAGTGTGCAACCCAC-GAAATTCATAATATGTTTATGAATGACTG
1 TATCGGCACTAAGTGTGCAACCCACAG-AATTCATAATATGTTTATGAACGACCG
* *
37079 TATTGGCACTAAGTGTGCAACCCACAAAATTCATAATATGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * * * *
37133 TATCGGCACTAAGTGTGCAACTCACAGAACTCATAATTTGTTTATGAACGGCCA
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * * *
37187 TATCGACACTAAGTGTTG-AACCCACATAATTTATAATATGTTTATGAACGATCG
1 TATCGGCACTAAGTG-TGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * * * *
37241 TATCGACACTAAGTGTGCAACCCATAGAATTTATAAAATGTTTATGAATGACCG
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * *
37295 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGATCG
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* *
37349 TATCGACACTACGTGT
1 TATCGGCACTAAGTGT
37365 TCACCCCAAA
Statistics
Matches: 247, Mismatches: 36, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
53 2 0.01
54 243 0.98
55 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (54 bp):
TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
Found at i:38011 original size:15 final size:15
Alignment explanation
Indices: 37991--38020 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
37981 TAATCTACAC
*
37991 CAACCACTGCAACAA
1 CAACCAATGCAACAA
38006 CAACCAATGCAACAA
1 CAACCAATGCAACAA
38021 TCTATACAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.37, G:0.07, T:0.07
Consensus pattern (15 bp):
CAACCAATGCAACAA
Found at i:39024 original size:32 final size:31
Alignment explanation
Indices: 38988--39071 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 31
38978 TTGACATGAA
38988 ACATGTCATATCATCACTTTATACGACATGCC
1 ACATG-CATATCATCACTTTATACGACATGCC
* * *
39020 ACATGCTATATCATTACTTTATATGACATGCT
1 ACATGC-ATATCATCACTTTATACGACATGCC
*
39052 ACATGCCACATCATCACTTT
1 ACATG-CATATCATCACTTT
39072 GAGTAACGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
31 1 0.02
32 43 0.96
33 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.35
Consensus pattern (31 bp):
ACATGCATATCATCACTTTATACGACATGCC
Found at i:47908 original size:11 final size:11
Alignment explanation
Indices: 47902--47935 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
47892 ATTTTTTTCA
47902 TTGTTTTTTTT
1 TTGTTTTTTTT
47913 TTGTTTTTTTT
1 TTGTTTTTTTT
47924 TTGTTTTTTTT
1 TTGTTTTTTTT
47935 T
1 T
47936 AATTATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (11 bp):
TTGTTTTTTTT
Found at i:47919 original size:22 final size:22
Alignment explanation
Indices: 47894--47935 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
47884 TTTATTCTAT
47894 TTTTTTCATTGTTTTTTTTTTG
1 TTTTTTCATTGTTTTTTTTTTG
**
47916 TTTTTTTTTTGTTTTTTTTT
1 TTTTTTCATTGTTTTTTTTT
47936 AATTATGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.02, C:0.02, G:0.07, T:0.88
Consensus pattern (22 bp):
TTTTTTCATTGTTTTTTTTTTG
Found at i:47934 original size:12 final size:12
Alignment explanation
Indices: 47873--47935 Score: 58
Period size: 12 Copynumber: 5.4 Consensus size: 12
47863 TGTACTTATG
*
47873 TTTTTTTATTTT
1 TTTTTTTGTTTT
* * *
47885 TTATTCTATTTT
1 TTTTTTTGTTTT
**
47897 TTTCATTG-TTT
1 TTTTTTTGTTTT
47908 TTTTTTTG-TTT
1 TTTTTTTGTTTT
47919 TTTTTTTGTTTT
1 TTTTTTTGTTTT
47931 TTTTT
1 TTTTT
47936 AATTATGTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
11 20 0.49
12 21 0.51
ACGTcount: A:0.06, C:0.03, G:0.05, T:0.86
Consensus pattern (12 bp):
TTTTTTTGTTTT
Found at i:49619 original size:21 final size:21
Alignment explanation
Indices: 49595--49634 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
49585 TTCAACTTTG
49595 CATTAGCAT-ATATACATTATA
1 CATTA-CATGATATACATTATA
*
49616 CATTACATGGTATACATTA
1 CATTACATGATATACATTA
49635 CATCTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (21 bp):
CATTACATGATATACATTATA
Found at i:50500 original size:17 final size:18
Alignment explanation
Indices: 50461--50507 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
50451 TGTTTATGAG
50461 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
50479 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
50496 GGAATTGGAATC
1 GGAATTGGAATC
50508 CAATTCCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:51160 original size:27 final size:28
Alignment explanation
Indices: 51079--51173 Score: 165
Period size: 28 Copynumber: 3.4 Consensus size: 28
51069 CCCGAACCCG
* *
51079 ACCCGACTCAAATATCACACTTAAAAAA
1 ACCCGACCCGAATATCACACTTAAAAAA
51107 ACCCGACCCGAATATCACACTTAAAAAA
1 ACCCGACCCGAATATCACACTTAAAAAA
51135 ACCCGACCCGAATATCACACTT-AAAAA
1 ACCCGACCCGAATATCACACTTAAAAAA
51162 ACCCGACCCGAA
1 ACCCGACCCGAA
51174 CAAAATAAAG
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 17 0.26
28 48 0.74
ACGTcount: A:0.45, C:0.34, G:0.07, T:0.14
Consensus pattern (28 bp):
ACCCGACCCGAATATCACACTTAAAAAA
Found at i:53180 original size:77 final size:77
Alignment explanation
Indices: 53097--53439 Score: 439
Period size: 77 Copynumber: 4.5 Consensus size: 77
53087 ATCTCACTTG
* * *
53097 AGATTG-TTTTTCTTTAAAAAAAAATTTCTCTCGCTTGAGACAATTTTTACTCGAAAGAAGACAT
1 AGATTGTTTTTTC-TTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCGAAAGAAGACAT
53161 TTCATTTCACTCA
65 TTCATTTCACTCA
* * * * *
53174 AGATTGTTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGATAGTTTTTACTTGAAATAAGATATT
1 AGATTGTTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCGAAAGAAGACATT
53239 TCATTTCACTCA
66 TCATTTCACTCA
* * ** * *
53251 AGATTG-TTTTTCTTAAAATAAGATTTTTCTCGCTTGAGACCGTTTTTTACTCGAAATAAGATAT
1 AGATTGTTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGA-CAATTTTTACTCGAAAGAAGACAT
*
53315 TTCATTTAACTCA
65 TTCATTTCACTCA
* * *
53328 AGATTGTTTTTTCTTAAAACAAGATTTGTATCGCTTGACACAATTTTTACTCGAAAGAATACATT
1 AGATTGTTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCGAAAGAAGACATT
*
53393 TCATTTCACTAA
66 TCATTTCACTCA
*
53405 AGATTG----TT-TTAAAACAAGATTTATCTCGCTTGAGA
1 AGATTGTTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGA
53440 TTGTTTCACT
Statistics
Matches: 234, Mismatches: 29, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
72 24 0.10
73 2 0.01
76 31 0.13
77 142 0.61
78 35 0.15
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (77 bp):
AGATTGTTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCGAAAGAAGACATT
TCATTTCACTCA
Found at i:53477 original size:39 final size:39
Alignment explanation
Indices: 53420--53982 Score: 815
Period size: 39 Copynumber: 14.5 Consensus size: 39
53410 GTTTTAAAAC
*
53420 AAGA-TTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * * * *
53458 AAGATTTCATCTTGCTTGAGATAGTTTCAATTGAAATAT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
53497 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* *
53536 AAGATTTCATCTCGCTTGAGATAGTTTCACTTGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * *
53575 AAGATTTCATCTCACTTGAGATAGTTTCACTCGAAATAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* *
53614 AAGATTTCATTTCGCTTGAGATAGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * *
53653 AAGATTTCATTTCGCTTGAGATAGTTTCACTTGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
53692 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
53731 AAGATTTTATCTCCCTTGAGATAGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * *
53770 AAGATTTCATCTCACTTGAGATAGTTTCACTTGAAACAT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
53809 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * *
53848 AAGATTTTATCTCACTTGAGATTGTTTCACTTGAAATAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
53887 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * *
53926 AATATTTTATCTCACTTGAGATATTTTCACTCGAAACTG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
53965 AAGA-TTTATCTCACTTGA
1 AAGATTTTATCTCGCTTGA
53983 TATTGTTTTT
Statistics
Matches: 477, Mismatches: 47, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
38 18 0.04
39 459 0.96
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
Found at i:54255 original size:135 final size:136
Alignment explanation
Indices: 54006--54380 Score: 479
Period size: 135 Copynumber: 2.8 Consensus size: 136
53996 AAAACAAACT
* * * * *
54006 ACGCCTCGCTTGAGGGATCATCATTTCGAATAAAGAGTTCATAATGAGAAGAACTCATCCGACAG
1 ACGCCTCGCTTGAGGGATTAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAG
* * **
54071 A-ATGAGAAGAAGTTCATAATGAGAAGAGCTTGTTTGACCTATCGTTCGA-TCACGACATTTCAA
66 AGA-GAGAAGAAGTTCATAATGAGAATAGCTTGTTCGACCTATCACTCGATTCACGACATTTCAA
54134 ATCAGTG
130 ATCAGTG
* * *
54141 ATGCCTCGCTTGAGGGATTAACCTTTCAAATAGATAGTTCATAATGAGAAGAACTCATCCGATAG
1 ACGCCTCGCTTGAGGGATTAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAG
* * *
54206 AGGGAGAAGAAGTTCATAATGAGAATAGCTTGTTCGACCTATCACTCGATTCATGGCATTTCAAA
66 AGAGAGAAGAAGTTCATAATGAGAATAGCTTGTTCGACCTATCACTCGATTCACGACATTTCAAA
54271 TCAGTG
131 TCAGTG
* * ** * *
54277 ACACGC-CGCTTGAGGGATTGACATTTCCGATGGAGAGTTCATAATGAGAAGAACTCATTCGAT-
1 ACGC-CTCGCTTGAGGGATTAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCCGATA
* * * *
54340 GAGATAGAACAAGTTCATAATGAGAATAACTTGTTCAACCT
65 GAGAGAGAAGAAGTTCATAATGAGAATAGCTTGTTCGACCT
54381 TATTTCAATC
Statistics
Matches: 208, Mismatches: 29, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
135 136 0.65
136 71 0.34
137 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (136 bp):
ACGCCTCGCTTGAGGGATTAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAG
AGAGAGAAGAAGTTCATAATGAGAATAGCTTGTTCGACCTATCACTCGATTCACGACATTTCAAA
TCAGTG
Found at i:55977 original size:17 final size:16
Alignment explanation
Indices: 55953--56023 Score: 56
Period size: 17 Copynumber: 4.2 Consensus size: 16
55943 TGTACTTATG
55953 TTTATTTTATTTTTTA
1 TTTATTTTATTTTTTA
*
55969 TTCTATTTT-TGTTTTCA
1 TT-TATTTTAT-TTTTTA
*
55986 TTGTTTTTTATTTTTT-
1 TT-TATTTTATTTTTTA
56002 TATTATTGTTATTTTATTA
1 T-TTATT-TTATTTT-TTA
56021 TTT
1 TTT
56024 TAATTATGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
16 7 0.16
17 30 0.70
18 5 0.12
19 1 0.02
ACGTcount: A:0.15, C:0.03, G:0.04, T:0.77
Consensus pattern (16 bp):
TTTATTTTATTTTTTA
Found at i:56033 original size:22 final size:21
Alignment explanation
Indices: 55985--56034 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
55975 TTTTGTTTTC
*
55985 ATTGTTTTTTATTTTTTTATT
1 ATTGTTTTTTATTTTTTAATT
56006 ATTGTTATTTTATTATTTTAATT
1 ATTGTT-TTTTATT-TTTTAATT
56029 A-TGTTT
1 ATTGTTT
56035 ATTAATTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 7 0.27
22 11 0.42
23 8 0.31
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (21 bp):
ATTGTTTTTTATTTTTTAATT
Found at i:56037 original size:23 final size:22
Alignment explanation
Indices: 55985--56030 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
55975 TTTTGTTTTC
*
55985 ATTGTT-TTTTATTTTTTTATT
1 ATTGTTATTTTATTTTTTAATT
56006 ATTGTTATTTTATTATTTTAATT
1 ATTGTTATTTTATT-TTTTAATT
56029 AT
1 AT
56031 GTTTATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.27
22 7 0.32
23 9 0.41
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (22 bp):
ATTGTTATTTTATTTTTTAATT
Found at i:56038 original size:9 final size:8
Alignment explanation
Indices: 55954--56038 Score: 59
Period size: 9 Copynumber: 10.4 Consensus size: 8
55944 GTACTTATGT
55954 TTATTTTA
1 TTATTTTA
55962 TT-TTTTA
1 TTATTTTA
*
55969 TTCTATTT-
1 TTAT-TTTA
*
55977 TTGTTTTCA
1 TTATTTT-A
*
55986 TTGTTTT-
1 TTATTTTA
*
55993 TTATTTTT
1 TTATTTTA
*
56001 TTATTATTG
1 TTATT-TTA
56010 TTATTTTA
1 TTATTTTA
56018 TTATTTTAA
1 TTATTTT-A
56027 TTATGTTTA
1 TTAT-TTTA
56036 TTA
1 TTA
56039 ATTGTTTTGA
Statistics
Matches: 65, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
7 16 0.25
8 20 0.31
9 26 0.40
10 3 0.05
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (8 bp):
TTATTTTA
Found at i:58129 original size:2 final size:2
Alignment explanation
Indices: 58116--58204 Score: 160
Period size: 2 Copynumber: 44.0 Consensus size: 2
58106 ATTAAAATGA
*
58116 AT AT AT AC 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
58158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
58201 AT AT
1 AT AT
58205 GATTAATGAG
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 82 0.98
3 2 0.02
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58582 original size:70 final size:69
Alignment explanation
Indices: 58483--58634 Score: 234
Period size: 70 Copynumber: 2.2 Consensus size: 69
58473 CTTAAAAAAA
* *
58483 TTAATTATTTTTTTAAGACATTATCAGTTTTAAAGTTAAATAAATTAA-TTTTGGCCTCTAACTT
1 TTAATTA-TTTTTTAAGACATTACCAGTTTTAAAGTTAAATAAATTAAGTCTT-GCCTCTAA-TT
58547 TTTTGGT
63 TTTTGGT
*
58554 TTAATTATTTTTTAAGACATTACCAGTTTTAAAGTTAAATAACTTAAGTCTTGCCTCTAATTTTT
1 TTAATTATTTTTTAAGACATTACCAGTTTTAAAGTTAAATAAATTAAGTCTTGCCTCTAATTTTT
58619 TGGT
66 TGGT
*
58623 TTAATTACTTTT
1 TTAATTATTTTT
58635 GAAATTAGTG
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
69 20 0.26
70 46 0.61
71 10 0.13
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (69 bp):
TTAATTATTTTTTAAGACATTACCAGTTTTAAAGTTAAATAAATTAAGTCTTGCCTCTAATTTTT
TGGT
Found at i:60758 original size:31 final size:31
Alignment explanation
Indices: 60723--60847 Score: 146
Period size: 31 Copynumber: 4.0 Consensus size: 31
60713 GATCCTCGGT
* *
60723 AACTGTCCATAGGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
**
60754 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
60785 TACTGTCCATAT-TTCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* *
60816 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
60848 TACCCTCAAC
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
30 4 0.05
31 49 0.62
32 22 0.28
33 4 0.05
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:65591 original size:30 final size:30
Alignment explanation
Indices: 65557--65628 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
65547 CCCGAAAGAC
65557 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
65587 CTATCCAGAGGTCATAAATATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
65617 CTGTCCATAGGT
1 CTATCCAGAGGT
65629 TCCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:65650 original size:31 final size:31
Alignment explanation
Indices: 65615--65739 Score: 139
Period size: 31 Copynumber: 4.0 Consensus size: 31
65605 TATCCTCGGT
* *
65615 AACTGTCCATAGGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
**
65646 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
65677 TACTGTCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
*
65708 ATTA-TGTCCATATGTTCCGTAGAACATAGGTA
1 A--ACTGTCCATATGTTCCGAAGAACATAGGTA
65740 TACCCTCAAC
Statistics
Matches: 79, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
30 3 0.04
31 50 0.63
32 22 0.28
33 4 0.05
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:66828 original size:18 final size:18
Alignment explanation
Indices: 66805--66839 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
66795 TTCATTTAGG
66805 GGGGAATCGATACCCCCA
1 GGGGAATCGATACCCCCA
66823 GGGGAATCGATACCCCC
1 GGGGAATCGATACCCCC
66840 TGAACATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.29, T:0.11
Consensus pattern (18 bp):
GGGGAATCGATACCCCCA
Found at i:71395 original size:22 final size:22
Alignment explanation
Indices: 71370--71413 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
71360 TTTTAATATT
71370 TCTTTAAAAATAAAGACACCAA
1 TCTTTAAAAATAAAGACACCAA
71392 TCTTTAAAAATAAAGACACCAA
1 TCTTTAAAAATAAAGACACCAA
71414 AAATCTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.18, G:0.05, T:0.23
Consensus pattern (22 bp):
TCTTTAAAAATAAAGACACCAA
Found at i:71422 original size:23 final size:22
Alignment explanation
Indices: 71374--71422 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
71364 AATATTTCTT
** *
71374 TAAAAATAAAGACACCAATCTT
1 TAAAAATAAAGACACCAAAATC
71396 TAAAAATAAAGACACCAAAAATC
1 TAAAAATAAAGACACC-AAAATC
71419 TAAA
1 TAAA
71423 TTTATATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.61, C:0.16, G:0.04, T:0.18
Consensus pattern (22 bp):
TAAAAATAAAGACACCAAAATC
Found at i:73863 original size:19 final size:18
Alignment explanation
Indices: 73841--73896 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
73831 ATATGTTAAA
73841 AATTATAAAATAATATTAT
1 AATTAT-AAATAATATTAT
* *
73860 AATT-TACA-AATATTAA
1 AATTATAAATAATATTAT
*
73876 AACTTATAATTAATATTAT
1 AA-TTATAAATAATATTAT
73895 AA
1 AA
73897 ACATAACAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 9 0.31
17 4 0.14
18 3 0.10
19 13 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTATAAATAATATTAT
Found at i:79786 original size:28 final size:28
Alignment explanation
Indices: 79727--79786 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
79717 TGTTATAGTG
* *
79727 TTTTTAATGTTTATAACATTAATTATAT
1 TTTTTAATATTTATAACATTAAATATAT
79755 TTTTTAATATTTATAA-ATTATAATATCAT
1 TTTTTAATATTTATAACATTA-AATAT-AT
79784 TTT
1 TTT
79787 AGAAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 4 0.14
28 19 0.68
29 5 0.18
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTTTAATATTTATAACATTAAATATAT
Found at i:80146 original size:14 final size:16
Alignment explanation
Indices: 80127--80160 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
80117 TATTATAAGC
80127 ATAACA-AAAAA-ATT
1 ATAACATAAAAACATT
80141 ATAACATAAAAACATT
1 ATAACATAAAAACATT
80157 ATAA
1 ATAA
80161 AAATTTATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 5 0.28
16 7 0.39
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.24
Consensus pattern (16 bp):
ATAACATAAAAACATT
Found at i:80146 original size:46 final size:46
Alignment explanation
Indices: 80064--80152 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
80054 TATAAATTTA
* *
80064 TAATTAATATTAGAAACATAACAAAAACATCGTAACAAAAAAAATT
1 TAATTAATATTAGAAACATAACAAAAAAATCATAACAAAAAAAATT
* * * * *
80110 TAATTAGTATTATAAGCATAACAAAAAAATTATAACATAAAAA
1 TAATTAATATTAGAAACATAACAAAAAAATCATAACAAAAAAA
80153 CATTATAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.61, C:0.09, G:0.04, T:0.26
Consensus pattern (46 bp):
TAATTAATATTAGAAACATAACAAAAAAATCATAACAAAAAAAATT
Found at i:80504 original size:30 final size:30
Alignment explanation
Indices: 80463--80521 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
80453 TCGAATTCAT
*
80463 GAGTCAAATTGACATTTTATCTAAAGTTTA
1 GAGTCAAATTGACATTTCATCTAAAGTTTA
* * *
80493 GAGTTAAATTGATATTTCATCTATAGTTT
1 GAGTCAAATTGACATTTCATCTAAAGTTT
80522 TGGGATCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (30 bp):
GAGTCAAATTGACATTTCATCTAAAGTTTA
Found at i:80634 original size:30 final size:31
Alignment explanation
Indices: 80593--80670 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 31
80583 CTAACTGTTC
* * *
80593 AGTGACTAAAATGTAACAAAT-GATAGCATA
1 AGTGACCAAAATATAACAAATCAATAGCATA
* * * *
80623 GGTGACCAAAATTTAATAAATCAATAGCGTA
1 AGTGACCAAAATATAACAAATCAATAGCATA
*
80654 AGTGACCGAAATATAAC
1 AGTGACCAAAATATAAC
80671 TTTTCAGAAT
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
30 17 0.46
31 20 0.54
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.23
Consensus pattern (31 bp):
AGTGACCAAAATATAACAAATCAATAGCATA
Found at i:92269 original size:24 final size:24
Alignment explanation
Indices: 92215--92306 Score: 143
Period size: 23 Copynumber: 3.9 Consensus size: 24
92205 GTGCCACATA
*
92215 TTTGTCCCAAAGGACCACATA-GT
1 TTTGTCCCGAAGGACCACATAGGT
92238 TTTGTCCCGAAGGACCACATAGGT
1 TTTGTCCCGAAGGACCACATAGGT
*
92262 TTTTTCCCGAAGGACCACATAGG-
1 TTTGTCCCGAAGGACCACATAGGT
*
92285 TTTGTCTCGAAGGACCACATAG
1 TTTGTCCCGAAGGACCACATAG
92307 AACCCTTGAC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
23 40 0.62
24 24 0.38
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (24 bp):
TTTGTCCCGAAGGACCACATAGGT
Found at i:92487 original size:14 final size:14
Alignment explanation
Indices: 92463--92510 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
92453 TACACATATT
92463 CACAT-ATCACATC
1 CACATAATCACATC
92476 CACATAATCACATC
1 CACATAATCACATC
* *
92490 CACATAATCATATA
1 CACATAATCACATC
92504 CACATAA
1 CACATAA
92511 CCATCAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 5 0.16
14 27 0.84
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (14 bp):
CACATAATCACATC
Found at i:95176 original size:5 final size:5
Alignment explanation
Indices: 95166--95193 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
95156 ACTTTCTTTC
95166 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
95194 CATATCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:103113 original size:21 final size:21
Alignment explanation
Indices: 103080--103159 Score: 142
Period size: 21 Copynumber: 3.8 Consensus size: 21
103070 TTAAAAATAT
103080 TAAAGGAAGTATCGATATTCAC
1 TAAAGG-AGTATCGATATTCAC
103102 TAAAGGAGTATCGATATTCAC
1 TAAAGGAGTATCGATATTCAC
103123 TAAAGGAGTATCGATATTCAC
1 TAAAGGAGTATCGATATTCAC
*
103144 TAAAGGAGTATTGATA
1 TAAAGGAGTATCGATA
103160 CTCCCTATAC
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
21 51 0.89
22 6 0.11
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (21 bp):
TAAAGGAGTATCGATATTCAC
Found at i:104937 original size:20 final size:20
Alignment explanation
Indices: 104912--104951 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
104902 TGAATAGTAT
*
104912 AATATTAAATTATGTTTTTA
1 AATATTAAATTATGGTTTTA
*
104932 AATATTACATTATGGTTTTA
1 AATATTAAATTATGGTTTTA
104952 TGTGATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (20 bp):
AATATTAAATTATGGTTTTA
Found at i:106350 original size:22 final size:22
Alignment explanation
Indices: 106322--106365 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
106312 ATGAGAGATT
106322 CAGAATGTATCCAATAGTGTTA
1 CAGAATGTATCCAATAGTGTTA
106344 CAGAATGTATCCAATAGTGTTA
1 CAGAATGTATCCAATAGTGTTA
106366 AAGCATGCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (22 bp):
CAGAATGTATCCAATAGTGTTA
Found at i:111694 original size:32 final size:33
Alignment explanation
Indices: 111600--111694 Score: 122
Period size: 32 Copynumber: 2.9 Consensus size: 33
111590 TACGCAAGGG
*
111600 AGTACCTTAGGGCCTAAGAGCCTACCCAA-GAA
1 AGTACCTTGGGGCCTAAGAGCCTACCCAAGGAA
* * *
111632 AGTACCTTGGGACCTTATAGCCTACCCAAGGAA
1 AGTACCTTGGGGCCTAAGAGCCTACCCAAGGAA
* *
111665 A-TGCCTTGGGGCCTCAGAGCCTACCCAAGG
1 AGTACCTTGGGGCCTAAGAGCCTACCCAAGG
111695 TCACCTTAGG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
32 50 0.93
33 4 0.07
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.18
Consensus pattern (33 bp):
AGTACCTTGGGGCCTAAGAGCCTACCCAAGGAA
Found at i:112766 original size:25 final size:24
Alignment explanation
Indices: 112721--112775 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
112711 GATATTTTAA
*
112721 TTCA-TTTTACACTTTAGGGGTAT
1 TTCAGTTTTACACTTTAAGGGTAT
* *
112744 TTTAGTTTTCACAGTTTAAGGGTAT
1 TTCAGTTTT-ACACTTTAAGGGTAT
112769 TTCAGTT
1 TTCAGTT
112776 ATTTCCTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 3 0.12
24 4 0.15
25 19 0.73
ACGTcount: A:0.22, C:0.11, G:0.18, T:0.49
Consensus pattern (24 bp):
TTCAGTTTTACACTTTAAGGGTAT
Done.