Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001067.1 Hibiscus syriacus cultivar Beakdansim tig00002113_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: 101672
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5245 original size:20 final size:20
Alignment explanation
Indices: 5216--5253 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5206 TTTCAAATGG
5216 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
5236 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
5254 GAATAAATTG
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:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:5425 original size:64 final size:66
Alignment explanation
Indices: 5264--5426 Score: 249
Period size: 66 Copynumber: 2.5 Consensus size: 66
5254 GAATAAATTG
* * * * * *
5264 AACATCGAATGCAGTTTATGCATCGATGCACTCTCCATGCATCGATGCACTCTTGGTTTTAATGA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCTAGGTCTTAATCA
5329 A
66 A
*
5330 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACT-TAGG-CTTATTCA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCTAGGTCTTAATCA
5393 A
66 A
5394 AACATCGAATGCATTTTATGCATCGATGCACAC
1 AACATCGAATGCATTTTATGCATCGATGCACAC
5427 TTAGTGCACC
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
64 39 0.43
65 3 0.03
66 48 0.53
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (66 bp):
AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCTAGGTCTTAATCA
A
Found at i:5440 original size:64 final size:65
Alignment explanation
Indices: 5264--5444 Score: 240
Period size: 64 Copynumber: 2.8 Consensus size: 65
5254 GAATAAATTG
* * * * *
5264 AACATCGAATGCAGTTTATGCATCGATGCACTCTCCATGCATCGATGCACTCTTGGTTTTAATGA
1 AACATCGAATGCATTTTATGCATCGATGCACACT-CATGCATCGATGCACTCTAGGTCTTAATCA
5329 A
65 A
* *
5330 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACT-TAGG-CTTATTCA
1 AACATCGAATGCATTTTATGCATCGATGCACAC-TCATGCATCGATGCACTCTAGGTCTTAATCA
5393 A
65 A
* *
5394 AACATCGAATGCATTTTATGCATCGATGCACACTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTTATGCATCGATGCACACTCA-TGCATCGATGCACT
5445 AAGTGTTCCA
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
63 1 0.01
64 52 0.50
65 3 0.03
66 47 0.46
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACACTCATGCATCGATGCACTCTAGGTCTTAATCAA
Found at i:7928 original size:15 final size:14
Alignment explanation
Indices: 7884--7928 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
7874 TAATGGTTAT
*
7884 TTAATTCAAAATAA
1 TTAATTCAAATTAA
7898 TTAAATTCAAATTTAA
1 TT-AATTCAAA-TTAA
7914 TTAATTCAGAATTAA
1 TTAATTCA-AATTAA
7929 AAAACCCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 2 0.07
15 18 0.67
16 7 0.26
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (14 bp):
TTAATTCAAATTAA
Found at i:21032 original size:2 final size:2
Alignment explanation
Indices: 21021--21057 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
21011 GCTCTTTATT
21021 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
21058 GTCGATTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:22239 original size:72 final size:72
Alignment explanation
Indices: 22118--22263 Score: 283
Period size: 72 Copynumber: 2.0 Consensus size: 72
22108 AACTAAGCTT
22118 ATTTATATTTTAATATTAAAAATTAAATGTTTTAAAATTTAAAAATAATATATTTGGGAAAGCCT
1 ATTTATATTTTAATATTAAAAATTAAATGTTTTAAAATTTAAAAATAATATATTTGGGAAAGCCT
22183 AAAAGGA
66 AAAAGGA
*
22190 ATTTATATTTTAATATTAAAAATTAAATGTTTTAAAATTTAAAACTAATATATTTGGGAAAGCCT
1 ATTTATATTTTAATATTAAAAATTAAATGTTTTAAAATTTAAAAATAATATATTTGGGAAAGCCT
22255 AAAAGGA
66 AAAAGGA
22262 AT
1 AT
22264 CGAGTATGAT
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:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (72 bp):
ATTTATATTTTAATATTAAAAATTAAATGTTTTAAAATTTAAAAATAATATATTTGGGAAAGCCT
AAAAGGA
Found at i:22906 original size:10 final size:10
Alignment explanation
Indices: 22886--22920 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
22876 TATATCAATT
22886 TAAACTATAAA
1 TAAA-TATAAA
22897 TAAATATAAA
1 TAAATATAAA
22907 TAAATATAAA
1 TAAATATAAA
22917 TAAA
1 TAAA
22921 CAATAATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 20 0.83
11 4 0.17
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (10 bp):
TAAATATAAA
Found at i:23033 original size:17 final size:17
Alignment explanation
Indices: 23011--23056 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
23001 AAATAATTAA
23011 ATAAATTATTAAAAGTT
1 ATAAATTATTAAAAGTT
* *
23028 ATAAATTATTCGACAGTT
1 ATAAATTATT-AAAAGTT
*
23046 TTAAATTATTA
1 ATAAATTATTA
23057 TAGGGTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (17 bp):
ATAAATTATTAAAAGTT
Found at i:25871 original size:14 final size:14
Alignment explanation
Indices: 25852--25878 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25842 TTACAATCAT
25852 TTAAAAAATAATTC
1 TTAAAAAATAATTC
25866 TTAAAAAATAATT
1 TTAAAAAATAATT
25879 TAATCTGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAAAAATAATTC
Found at i:32033 original size:35 final size:35
Alignment explanation
Indices: 31975--32113 Score: 206
Period size: 35 Copynumber: 3.9 Consensus size: 35
31965 TGAATAAGAA
* *
31975 GAACGAAAGTAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
* *
32010 GAACAAAAGGAAGCATCGACACTTTCGATTCAAGAA
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAG-T
*
32046 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
* *
32081 GAACGGAAGGAAGCATCAACACTTTCGATTCAA
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAA
32114 TTGTTAATTT
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
35 61 0.66
36 32 0.34
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.19
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
Found at i:32091 original size:71 final size:71
Alignment explanation
Indices: 31970--32113 Score: 252
Period size: 71 Copynumber: 2.0 Consensus size: 71
31960 GAAGGTGAAT
* *
31970 AAGAAGAACGAAAGTAAGCATCGGCACTTTCGATTCAAGTGAACAAAAGGAAGCATCGACACTTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAAAAGGAAGCATCAACACTTT
32035 CGATTC
66 CGATTC
**
32041 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCAACACTTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAAAAGGAAGCATCAACACTTT
32106 CGATTC
66 CGATTC
32112 AA
1 AA
32114 TTGTTAATTT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (71 bp):
AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAAAAGGAAGCATCAACACTTT
CGATTC
Found at i:36714 original size:11 final size:11
Alignment explanation
Indices: 36675--36723 Score: 61
Period size: 10 Copynumber: 4.8 Consensus size: 11
36665 GAACGCTGGA
36675 AACCGGTTTTG
1 AACCGGTTTTG
36686 -ACCGG-TTT-
1 AACCGGTTTTG
*
36694 AACTGGTTTTG
1 AACCGGTTTTG
36705 AACCGGTTTTG
1 AACCGGTTTTG
36716 -ACCGGTTT
1 AACCGGTTT
36724 GACCGGTCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 7 0.21
10 16 0.48
11 10 0.30
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.39
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:36726 original size:9 final size:10
Alignment explanation
Indices: 36676--36730 Score: 69
Period size: 9 Copynumber: 5.6 Consensus size: 10
36666 AACGCTGGAA
36676 ACCGGTTTTG
1 ACCGGTTTTG
*
36686 ACCGG-TTTA
1 ACCGGTTTTG
*
36695 ACTGGTTTTG
1 ACCGGTTTTG
36705 AACCGGTTTTG
1 -ACCGGTTTTG
36716 ACCGG-TTTG
1 ACCGGTTTTG
36725 ACCGGT
1 ACCGGT
36731 CACGACCCGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 16 0.42
10 13 0.34
11 9 0.24
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:36773 original size:18 final size:18
Alignment explanation
Indices: 36750--36784 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
36740 TTTACCCGTT
36750 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
36768 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
36785 AGTGCTATTA
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:0.17, C:0.49, G:0.23, T:0.11
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:36784 original size:13 final size:13
Alignment explanation
Indices: 36743--36773 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
36733 CGACCCGTTT
36743 ACCCGTTGACCCG
1 ACCCGTTGACCCG
36756 ACCCGTTGACCCG
1 ACCCGTTGACCCG
36769 ACCCG
1 ACCCG
36774 ACCCGTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.48, G:0.23, T:0.13
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:36846 original size:29 final size:29
Alignment explanation
Indices: 36786--36851 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
36776 CCGTTGACCA
* *** *
36786 GTGCTATTATGGGAATTAATTCGGTTTTG
1 GTGCTATTATGAGAATTAATTCGAAATGG
36815 GTGCTATTATGAGAATTAATTCGAAATGG
1 GTGCTATTATGAGAATTAATTCGAAATGG
36844 GTGCTATT
1 GTGCTATT
36852 TTGGTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (29 bp):
GTGCTATTATGAGAATTAATTCGAAATGG
Found at i:36860 original size:29 final size:28
Alignment explanation
Indices: 36786--36860 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
36776 CCGTTGACCA
*** *
36786 GTGCTATTATGGGAATTAATTCGGTTTTG
1 GTGCTATTAT-GGAATTAATTCGAAATGG
36815 GTGCTATTATGAGAATTAATTCGAAATGG
1 GTGCTATTATG-GAATTAATTCGAAATGG
*
36844 GTGCTATTTTGGTAATT
1 GTGCTATTATGG-AATT
36861 TTTTTTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 2 0.05
29 37 0.95
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (28 bp):
GTGCTATTATGGAATTAATTCGAAATGG
Found at i:37618 original size:24 final size:24
Alignment explanation
Indices: 37586--37654 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
37576 ATAGTTTATC
*
37586 TGATTTTTGACCTGGATTCTGATA
1 TGATATTTGACCTGGATTCTGATA
* * * *
37610 TGATATTTGATCTGAATTTTTATA
1 TGATATTTGACCTGGATTCTGATA
* * *
37634 TGATACTTGACATGGACTCTG
1 TGATATTTGACCTGGATTCTG
37655 TTTTGTACTT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.45
Consensus pattern (24 bp):
TGATATTTGACCTGGATTCTGATA
Found at i:43925 original size:11 final size:11
Alignment explanation
Indices: 43886--43934 Score: 61
Period size: 10 Copynumber: 4.8 Consensus size: 11
43876 GAACGCTGGA
43886 AACCGGTTTTG
1 AACCGGTTTTG
43897 -ACCGG-TTT-
1 AACCGGTTTTG
*
43905 AACTGGTTTTG
1 AACCGGTTTTG
43916 AACCGGTTTTG
1 AACCGGTTTTG
43927 -ACCGGTTT
1 AACCGGTTT
43935 GACCGGTCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 7 0.21
10 16 0.48
11 10 0.30
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.39
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:43937 original size:9 final size:10
Alignment explanation
Indices: 43887--43941 Score: 69
Period size: 9 Copynumber: 5.6 Consensus size: 10
43877 AACGCTGGAA
43887 ACCGGTTTTG
1 ACCGGTTTTG
*
43897 ACCGG-TTTA
1 ACCGGTTTTG
*
43906 ACTGGTTTTG
1 ACCGGTTTTG
43916 AACCGGTTTTG
1 -ACCGGTTTTG
43927 ACCGG-TTTG
1 ACCGGTTTTG
43936 ACCGGT
1 ACCGGT
43942 CACGACCCGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 16 0.42
10 13 0.34
11 9 0.24
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:43995 original size:18 final size:18
Alignment explanation
Indices: 43974--44008 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
43964 CCGACCCGTT
43974 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
43992 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
44009 AGTGCTATTA
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:0.17, C:0.49, G:0.23, T:0.11
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:44008 original size:13 final size:13
Alignment explanation
Indices: 43954--43997 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
43944 CGACCCGTTT
*
43954 ACCCGTTTACCCG
1 ACCCGTTGACCCG
43967 ACCCGTTGACCCG
1 ACCCGTTGACCCG
43980 ACCCGTTGACCCG
1 ACCCGTTGACCCG
43993 ACCCG
1 ACCCG
43998 ACCCGTTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.16, C:0.48, G:0.20, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:44008 original size:26 final size:26
Alignment explanation
Indices: 43944--44008 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
43934 TGACCGGTCA
* *
43944 CGACCCGTTTACCCGTTTACCCGACC
1 CGACCCGTTGACCCGTTGACCCGACC
43970 CGTTGACCC---GACCCGTTGACCCGACC
1 C---GACCCGTTGACCCGTTGACCCGACC
43996 CGACCCGTTGACC
1 CGACCCGTTGACC
44009 AGTGCTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
23 5 0.16
26 21 0.68
29 5 0.16
ACGTcount: A:0.15, C:0.46, G:0.20, T:0.18
Consensus pattern (26 bp):
CGACCCGTTGACCCGTTGACCCGACC
Found at i:44070 original size:29 final size:29
Alignment explanation
Indices: 44010--44075 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
44000 CCGTTGACCA
* *** *
44010 GTGCTATTATGGGAATTAATTCGGTTTTG
1 GTGCTATTATGAGAATTAATTCGAAATGG
44039 GTGCTATTATGAGAATTAATTCGAAATGG
1 GTGCTATTATGAGAATTAATTCGAAATGG
44068 GTGCTATT
1 GTGCTATT
44076 TTGGTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (29 bp):
GTGCTATTATGAGAATTAATTCGAAATGG
Found at i:44084 original size:29 final size:28
Alignment explanation
Indices: 44010--44084 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
44000 CCGTTGACCA
*** *
44010 GTGCTATTATGGGAATTAATTCGGTTTTG
1 GTGCTATTAT-GGAATTAATTCGAAATGG
44039 GTGCTATTATGAGAATTAATTCGAAATGG
1 GTGCTATTATG-GAATTAATTCGAAATGG
*
44068 GTGCTATTTTGGTAATT
1 GTGCTATTATGG-AATT
44085 TTTTTAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 2 0.05
29 37 0.95
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (28 bp):
GTGCTATTATGGAATTAATTCGAAATGG
Found at i:44843 original size:24 final size:24
Alignment explanation
Indices: 44811--44879 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
44801 ATAGTTTATC
*
44811 TGATTTTTGACCTGGATTCTGATA
1 TGATATTTGACCTGGATTCTGATA
* * * *
44835 TGATATTTGATCTGAATTTTTATA
1 TGATATTTGACCTGGATTCTGATA
* * *
44859 TGATACTTGACATGGACTCTG
1 TGATATTTGACCTGGATTCTG
44880 TTTTGTACTT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.45
Consensus pattern (24 bp):
TGATATTTGACCTGGATTCTGATA
Found at i:52620 original size:16 final size:16
Alignment explanation
Indices: 52599--52633 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
52589 GGTATTACCC
52599 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
52615 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
52631 GAC
1 GAC
52634 ATGTAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.37
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:52648 original size:16 final size:16
Alignment explanation
Indices: 52629--52664 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
52619 TGTTTTTAAC
52629 CTGACATGTAAATGAT
1 CTGACATGTAAATGAT
* *
52645 CTGACTTGTTAATGAT
1 CTGACATGTAAATGAT
52661 CTGA
1 CTGA
52665 TCTGATATTT
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:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (16 bp):
CTGACATGTAAATGAT
Found at i:53092 original size:21 final size:21
Alignment explanation
Indices: 53067--53120 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
53057 TTTACATTAT
**
53067 GGTTTATGGTTTAGTGTTTAG
1 GGTTTATGGTTTAAAGTTTAG
*
53088 TGTTTATGGTTTAAAGTTTAG
1 GGTTTATGGTTTAAAGTTTAG
*
53109 GGTTTAGGGTTT
1 GGTTTATGGTTT
53121 CTTTAAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (21 bp):
GGTTTATGGTTTAAAGTTTAG
Found at i:53280 original size:13 final size:13
Alignment explanation
Indices: 53270--53296 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53260 TACATATTAT
53270 ATAAAATTATTTA
1 ATAAAATTATTTA
53283 ATAAAATTATTTA
1 ATAAAATTATTTA
53296 A
1 A
53297 ATGTAAATTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:53306 original size:15 final size:14
Alignment explanation
Indices: 53270--53312 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
53260 TACATATTAT
53270 ATAAAATTATTT-A
1 ATAAAATTATTTAA
53283 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
53297 ATGTAAATTATATAA
1 AT-AAAATTATTTAA
53312 A
1 A
53313 ACATGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:53419 original size:20 final size:19
Alignment explanation
Indices: 53394--53431 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
53384 TTTCATATTA
*
53394 ATTTTATTTGCATGATTAGT
1 ATTTTAGTTGCATG-TTAGT
53414 ATTTTAGTTGCATGTTAG
1 ATTTTAGTTGCATGTTAG
53432 GTTAATTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.24, C:0.05, G:0.18, T:0.53
Consensus pattern (19 bp):
ATTTTAGTTGCATGTTAGT
Found at i:53627 original size:14 final size:14
Alignment explanation
Indices: 53605--53671 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 14
53595 GTCATTTACA
53605 TTAGGGTTTATGGT
1 TTAGGGTTTATGGT
*
53619 TTAGTGTTTA-GTGT
1 TTAGGGTTTATG-GT
* *
53633 TTAGTGTTTTTGGT
1 TTAGGGTTTATGGT
** *
53647 TTAAAGTTTATGAT
1 TTAGGGTTTATGGT
53661 TTAGGGTTTAT
1 TTAGGGTTTAT
53672 ATAAACTATA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
13 1 0.02
14 41 0.95
15 1 0.02
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:53629 original size:21 final size:20
Alignment explanation
Indices: 53605--53670 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 20
53595 GTCATTTACA
* *
53605 TTAGGGTTTATGGTTTAGTGT
1 TTAGAGTTTATGATTTAG-GT
* * *
53626 TTAGTGTTTAGTGTTTTTGGT
1 TTAGAGTTTA-TGATTTAGGT
*
53647 TTAAAGTTTATGATTTAGGGT
1 TTAGAGTTTATGATTTA-GGT
53668 TTA
1 TTA
53671 TATAAACTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
20 5 0.14
21 25 0.69
22 6 0.17
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (20 bp):
TTAGAGTTTATGATTTAGGT
Found at i:53700 original size:9 final size:9
Alignment explanation
Indices: 53688--53729 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
53678 TATATAAGTA
*
53688 ATATACTTT
1 ATATAGTTT
53697 ATATAGTTT
1 ATATAGTTT
53706 ATATA-TATAT
1 ATATAGT-T-T
53716 ATATAGTTT
1 ATATAGTTT
53725 ATATA
1 ATATA
53730 TATTATACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
8 1 0.03
9 20 0.69
10 7 0.24
11 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (9 bp):
ATATAGTTT
Found at i:53720 original size:19 final size:20
Alignment explanation
Indices: 53696--53747 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
53686 TAATATACTT
53696 TATATAGTTTATATATA-TA
1 TATATAGTTTATATATATTA
53715 TATATAGTTTATATATATTA
1 TATATAGTTTATATATATTA
* *
53735 TACATGGTTTATA
1 TATATAGTTTATA
53748 CATACATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (20 bp):
TATATAGTTTATATATATTA
Found at i:53770 original size:13 final size:13
Alignment explanation
Indices: 53760--53786 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53750 TACATATTAT
53760 ATAAAATTATTTA
1 ATAAAATTATTTA
53773 ATAAAATTATTTA
1 ATAAAATTATTTA
53786 A
1 A
53787 ATGTAAATTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:53796 original size:15 final size:14
Alignment explanation
Indices: 53760--53802 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
53750 TACATATTAT
53760 ATAAAATTATTT-A
1 ATAAAATTATTTAA
53773 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
53787 ATGTAAATTATATAA
1 AT-AAAATTATTTAA
53802 A
1 A
53803 ACATGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:54440 original size:30 final size:30
Alignment explanation
Indices: 54406--54470 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
54396 GAAAAAAAGT
54406 AATATGATTACTTTTTAAATGTAATTAA-AA
1 AATATGATTACTTTTTAAATGTAA-TAATAA
*
54436 AATATGATTACTTTTTAAATGTTATAATAA
1 AATATGATTACTTTTTAAATGTAATAATAA
54466 AATAT
1 AATAT
54471 TTATTATGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 3 0.09
30 30 0.91
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (30 bp):
AATATGATTACTTTTTAAATGTAATAATAA
Found at i:54592 original size:22 final size:23
Alignment explanation
Indices: 54556--54600 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
54546 TAATGCAAAG
54556 GAAAATTAATATAGTTTAATTTA
1 GAAAATTAATATAGTTTAATTTA
54579 GAAAATT-ATATAGTTTAATTTA
1 GAAAATTAATATAGTTTAATTTA
54601 TATAAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (23 bp):
GAAAATTAATATAGTTTAATTTA
Found at i:54793 original size:21 final size:22
Alignment explanation
Indices: 54769--54829 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 22
54759 TGCATTTACA
54769 TTAGGGTTTATGGTTTAGGA-T
1 TTAGGGTTTATGGTTTAGGAGT
** * *
54790 TTAGTATTTTTGGTTTA-AAGT
1 TTAGGGTTTATGGTTTAGGAGT
*
54811 TTAGGGTTTAGGGTTTAGG
1 TTAGGGTTTATGGTTTAGG
54830 TTTCTATAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (22 bp):
TTAGGGTTTATGGTTTAGGAGT
Found at i:54932 original size:20 final size:20
Alignment explanation
Indices: 54909--54949 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
54899 TATATAAGTA
* *
54909 ATTTACTTTATATAGTTTAT
1 ATTTACTATACATAGTTTAT
*
54929 ATTTACTATACATGGTTTAT
1 ATTTACTATACATAGTTTAT
54949 A
1 A
54950 CTACGTGTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (20 bp):
ATTTACTATACATAGTTTAT
Found at i:55149 original size:64 final size:63
Alignment explanation
Indices: 55077--55195 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 63
55067 GCATAATGTT
**
55077 TTTATAATTTATAATTTAT-TACTTATAT-TAGTTATACATACATATATATACTATATTAATATA
1 TTTATAATTTATAAACTATATA-TTATATATAGTT-TACATACATATATATA-TATATTAATATA
55140 A
63 A
* *
55141 TTTATAATTTATAAACTATATATTTTATATAGTTTATATACATATATATATATAT
1 TTTATAATTTATAAACTATATATTATATATAGTTTACATACATATATATATATAT
55196 ATAGAAAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
63 5 0.10
64 37 0.76
65 7 0.14
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (63 bp):
TTTATAATTTATAAACTATATATTATATATAGTTTACATACATATATATATATATTAATATAA
Found at i:55189 original size:57 final size:58
Alignment explanation
Indices: 55079--55198 Score: 131
Period size: 57 Copynumber: 2.1 Consensus size: 58
55069 ATAATGTTTT
* *
55079 TATAATTTATAATTTATTACTTATATTAGTTATACATACATATATATACTATAT-TA-A
1 TATAATTTATAATTTATAACTTATATTA-TTATACATACATATACATACTATATATATA
* **
55136 TATAATTTATAATTTATAAACTATATATT-TTATATAGTTTATATACATA-TATATATATA
1 TATAATTTATAATTTAT-AACT-TATATTATTATACA-TACATATACATACTATATATATA
55195 TATA
1 TATA
55199 GAAAATTAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
57 28 0.53
58 14 0.26
59 11 0.21
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (58 bp):
TATAATTTATAATTTATAACTTATATTATTATACATACATATACATACTATATATATA
Found at i:55438 original size:20 final size:20
Alignment explanation
Indices: 55386--55462 Score: 88
Period size: 19 Copynumber: 4.0 Consensus size: 20
55376 TAAAATCTAA
*
55386 TTCTCAATTTCCCTCCAAAAT
1 TTCTCAATTTCCCT-CTAAAT
*
55407 TT-TCTA-TTCCCTCTAAAT
1 TTCTCAATTTCCCTCTAAAT
55425 TTCTCAATTTCCCTCTAAA-
1 TTCTCAATTTCCCTCTAAAT
* *
55444 TTATCAATTTCCCTATAAA
1 TTCTCAATTTCCCTCTAAA
55463 AAAATTTCAC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
18 7 0.14
19 26 0.53
20 14 0.29
21 2 0.04
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (20 bp):
TTCTCAATTTCCCTCTAAAT
Found at i:55456 original size:39 final size:39
Alignment explanation
Indices: 55386--55462 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
55376 TAAAATCTAA
* * *
55386 TTCTCAATTTCCCTCCAAAATTTTCTATTCCCTCTAAAT
1 TTCTCAATTTCCCTCCAAAATTATCAATTCCCTATAAAT
*
55425 TTCTCAATTTCCCT-CTAAATTATCAATTTCCCTATAAA
1 TTCTCAATTTCCCTCCAAAATTATCAA-TTCCCTATAAA
55463 AAAATTTCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 9 0.27
39 24 0.73
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (39 bp):
TTCTCAATTTCCCTCCAAAATTATCAATTCCCTATAAAT
Found at i:55531 original size:2 final size:2
Alignment explanation
Indices: 55524--55716 Score: 90
Period size: 2 Copynumber: 99.0 Consensus size: 2
55514 ACTTTGAATA
55524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
55565 A- AT AT AA AT -T AT AGT TT AT AC AT AT AT AGT TT AC AT AT AT AGT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT A-T
* * * *
55608 TT AT AT AT AT AGT -T CAT AT AA AC AT A- AT TT AT AT AT AT A- ACT
1 AT AT AT AT AT A-T AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
55650 -T AT A- AT A- AT -T AT AT AGT TT AT A- AT AT AA AT AT AGT TT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT
*
55689 AT AT AA ACT A- AT AT -T AT AT AT AT -T AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
55717 TTTTTCAATT
Statistics
Matches: 143, Mismatches: 25, Indels: 46
0.67 0.12 0.21
Matches are distributed among these distances:
1 14 0.10
2 121 0.85
3 8 0.06
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:55626 original size:13 final size:13
Alignment explanation
Indices: 55529--55646 Score: 89
Period size: 13 Copynumber: 8.8 Consensus size: 13
55519 GAATAATATA
*
55529 TATATATATA-TA
1 TATATATATAGTT
*
55541 TATATATATA-TA
1 TATATATATAGTT
55553 TATATATATA-TT
1 TATATATATAGTT
*
55565 AATATAAATTATAGTT
1 --TATATA-TATAGTT
55581 TATACATATATAGTT
1 TAT--ATATATAGTT
*
55596 TACATATATAGTT
1 TATATATATAGTT
55609 TATATATATAGTT
1 TATATATATAGTT
* * *
55622 CATATAAACATAATT
1 --TATATATATAGTT
55637 TATATATATA
1 TATATATATA
55647 ACTTATAATA
Statistics
Matches: 88, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
12 23 0.26
13 30 0.34
14 8 0.09
15 23 0.26
16 4 0.05
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (13 bp):
TATATATATAGTT
Found at i:62700 original size:13 final size:13
Alignment explanation
Indices: 62666--62700 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
62656 CTGAAATAAT
62666 TAAATAAATAAAA
1 TAAATAAATAAAA
*
62679 TGAATAAATAAAA
1 TAAATAAATAAAA
*
62692 TAAAAAAAT
1 TAAATAAAT
62701 TGGTAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:62828 original size:13 final size:13
Alignment explanation
Indices: 62810--62836 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
62800 AACTATATGT
62810 ATATGTTTTCAAA
1 ATATGTTTTCAAA
62823 ATATGTTTTCAAA
1 ATATGTTTTCAAA
62836 A
1 A
62837 CTATATTATA
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:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
ATATGTTTTCAAA
Found at i:62880 original size:111 final size:109
Alignment explanation
Indices: 62746--62989 Score: 309
Period size: 111 Copynumber: 2.2 Consensus size: 109
62736 AAAACAATAT
* *
62746 AAAATGTTTTCAAAAATTATATATATTATATATGTTTTCAAAAACCG-TTTTAAAAACTATAT-G
1 AAAATATTTTCAAAAA--CTATATA-T-TATATGTTTTCAAAAACCGCTTTTAAAAA-TATATAG
*
62809 TATATGTTTTCAAAAT-ATGTTTTCAAAACTATAT-TATATACGTTTTC-A
61 TATATGTTTTCAAAATCAT-TTTTAAAAACTATATAT-TATACGTTTTCAA
* *
62857 AAAATCATTTTTTAAAAACTATATATTATATGTTTTCAAAAACCGTCTTTTAAAAATATATATTA
1 AAAAT-A-TTTTCAAAAACTATATATTATATGTTTTCAAAAACCG-CTTTTAAAAATATATAGTA
*
62922 TATGTTTTCAAAATCATTTTTAAAAACTATATATTATATGTTTTCAA
63 TATGTTTTCAAAATCATTTTTAAAAACTATATATTATACGTTTTCAA
62969 AAAATATTTTCAAAAACTATA
1 AAAATATTTTCAAAAACTATA
62990 CCATATATAT
Statistics
Matches: 118, Mismatches: 7, Indels: 17
0.83 0.05 0.12
Matches are distributed among these distances:
109 19 0.16
110 20 0.17
111 61 0.52
112 9 0.08
113 9 0.08
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.44
Consensus pattern (109 bp):
AAAATATTTTCAAAAACTATATATTATATGTTTTCAAAAACCGCTTTTAAAAATATATAGTATAT
GTTTTCAAAATCATTTTTAAAAACTATATATTATACGTTTTCAA
Found at i:62947 original size:73 final size:72
Alignment explanation
Indices: 62746--62999 Score: 271
Period size: 73 Copynumber: 3.4 Consensus size: 72
62736 AAAACAATAT
* * ** *
62746 AAAATGTTTTCAAAAATTATATATATTATATATGTTTTCAAAAACCGTTTTAAAAACTATAT-GT
1 AAAACGTTTTC-AAAA--ATATATA-TATATATGTTTTCAAAATCATTTTTAAAAACTATATATT
62810 ATATGTTTTCA
62 ATATGTTTTCA
* * *
62821 AAATATGTTTTCAAAACTATAT-TATATACGTTTTCAAAAATCATTTTTTAAAAACTATATATTA
1 AAA-ACGTTTTCAAAAATATATATATATATGTTTTC-AAAATCA-TTTTTAAAAACTATATATTA
62885 TATGTTTTCA
63 TATGTTTTCA
*
62895 AAAACCGTCTTTTAAAAATATATAT-TATATGTTTTCAAAATCATTTTTAAAAACTATATATTAT
1 AAAA-CGT-TTTCAAAAATATATATATATATGTTTTCAAAATCATTTTTAAAAACTATATATTAT
62959 ATGTTTTCAA
64 ATGTTTTC-A
** *
62969 AAAATATTTTCAAAAACTATACCATATATAT
1 AAAACGTTTTCAAAAA-TATA-TATATATAT
63000 CTTCAAAAAC
Statistics
Matches: 154, Mismatches: 14, Indels: 22
0.81 0.07 0.12
Matches are distributed among these distances:
71 12 0.08
72 13 0.08
73 55 0.36
74 31 0.20
75 34 0.22
76 9 0.06
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (72 bp):
AAAACGTTTTCAAAAATATATATATATATGTTTTCAAAATCATTTTTAAAAACTATATATTATAT
GTTTTCA
Found at i:62987 original size:37 final size:37
Alignment explanation
Indices: 62746--62989 Score: 218
Period size: 35 Copynumber: 6.6 Consensus size: 37
62736 AAAACAATAT
* *
62746 AAAATGTTTTCAAAAATTATATATATTATATATGTTTTCAA
1 AAAATATTTTCAAAAA--CTATATA-T-TATATGTTTTCAA
*** *
62787 AAACCGTTTT-AAAAACTATAT-GTATATGTTTTCAA
1 AAAATATTTTCAAAAACTATATATTATATGTTTTCAA
* * *
62822 AATATGTTTTC-AAAACTATAT-TATATACGTTTTC-A
1 AAAATATTTTCAAAAACTATATAT-TATATGTTTTCAA
*
62857 AAAATCATTTTTTAAAAACTATATATTATATGTTTTCAA
1 AAAAT-A-TTTTCAAAAACTATATATTATATGTTTTCAA
* *
62896 AAACCGTCTTTT-AAAAA-TATATATTATATGTTTTC--
1 AAA--ATATTTTCAAAAACTATATATTATATGTTTTCAA
*
62931 AAAATCATTTTTAAAAACTATATATTATATGTTTTCAA
1 AAAAT-ATTTTCAAAAACTATATATTATATGTTTTCAA
62969 AAAATATTTTCAAAAACTATA
1 AAAATATTTTCAAAAACTATA
62990 CCATATATAT
Statistics
Matches: 171, Mismatches: 18, Indels: 32
0.77 0.08 0.14
Matches are distributed among these distances:
33 1 0.01
34 4 0.02
35 43 0.25
36 28 0.16
37 37 0.22
38 35 0.20
39 9 0.05
40 5 0.03
41 9 0.05
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.44
Consensus pattern (37 bp):
AAAATATTTTCAAAAACTATATATTATATGTTTTCAA
Found at i:62997 original size:37 final size:35
Alignment explanation
Indices: 62767--63008 Score: 227
Period size: 37 Copynumber: 6.6 Consensus size: 35
62757 AAAAATTATA
***
62767 TATATTATATATGTTTTCAAAAACCGTTTTAAAAAC
1 TATA-TATATATGTTTTCAAAAAATATTTTAAAAAC
* * * *
62803 TATATGTATATGTTTTCAAAATATGTTTTCAAAAC
1 TATATATATATGTTTTCAAAAAATATTTTAAAAAC
* *
62838 TATATTATATACGTTTTCAAAAATCATTTTTTAAAAAC
1 TATA-TATATATGTTTTCAAAAA--ATATTTTAAAAAC
* *
62876 TATATATTATATGTTTTCAAAAACCGTCTTTTAAAAA-
1 TATATA-TATATGTTTTCAAAAA--ATATTTTAAAAAC
*
62913 TATATATTATATGTTTTCAAAATCAT-TTTTAAAAAC
1 TATATA-TATATGTTTTCAAAA-AATATTTTAAAAAC
62949 TATATATTATATGTTTTCAAAAAATATTTTCAAAAAC
1 TATATA-TATATGTTTTCAAAAAATATTTT-AAAAAC
* * *
62986 TATACCATATATATCTTCAAAAA
1 TATA-TATATATGTTTTCAAAAA
63009 CTATATATAT
Statistics
Matches: 177, Mismatches: 20, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
35 41 0.23
36 46 0.26
37 48 0.27
38 42 0.24
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.43
Consensus pattern (35 bp):
TATATATATATGTTTTCAAAAAATATTTTAAAAAC
Found at i:63660 original size:19 final size:20
Alignment explanation
Indices: 63620--63664 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
63610 AAGAAAAAGA
*
63620 AAAAAAATAAAGATGCATAT
1 AAAAAAATAAAGAAGCATAT
63640 AAAAAAATAAA-AAGACA-AT
1 AAAAAAATAAAGAAG-CATAT
63659 AAAAAA
1 AAAAAA
63665 TATCGGTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (20 bp):
AAAAAAATAAAGAAGCATAT
Found at i:64673 original size:29 final size:29
Alignment explanation
Indices: 64618--64674 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
64608 TTTTTTCTAA
* * * *
64618 TTTTAAGTTTATAATTATATTATTTCTTT
1 TTTTAAATTTAGAATTATAGTAATTCTTT
*
64647 TTTTAAATTTAGAATTATGGTAATTCTT
1 TTTTAAATTTAGAATTATAGTAATTCTT
64675 ATTTATATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTTAAATTTAGAATTATAGTAATTCTTT
Found at i:65048 original size:45 final size:45
Alignment explanation
Indices: 64984--65074 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
64974 AGAGTGATTC
*
64984 ATTAACTATTCGATTTCTTGTCAAGTTTCTTAACAAATGGAGTAA
1 ATTAACTATTCGATTTCTTGTCAAGTTTCTTAACAAATGAAGTAA
65029 ATTAACTATTCGATTTCTTGTCAAGTTTCTTAACAAATGAAGTAA
1 ATTAACTATTCGATTTCTTGTCAAGTTTCTTAACAAATGAAGTAA
65074 A
1 A
65075 GTGAACAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (45 bp):
ATTAACTATTCGATTTCTTGTCAAGTTTCTTAACAAATGAAGTAA
Found at i:65834 original size:24 final size:23
Alignment explanation
Indices: 65788--65839 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
65778 TTAGTTCATG
*
65788 TTTTATTTTAATATTTTTAAATA
1 TTTTAATTTAATATTTTTAAATA
* *
65811 TTTTAATTTATTATTTGTTTAATA
1 TTTTAATTTAATATTT-TTAAATA
65835 TTTTA
1 TTTTA
65840 CATTGTCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTAATTTAATATTTTTAAATA
Found at i:68917 original size:58 final size:58
Alignment explanation
Indices: 68855--68970 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
68845 AATCATACAT
*
68855 CATTTGCGCACTTAATCATGCAATTATAAGGACCAAAAAGTCATGTACCAATAGCAAG
1 CATTTGCGCACTTAATCATGCAATTATAAGGACCAAAAAGTCAAGTACCAATAGCAAG
68913 CATTTGCGCACTTAATCATGCAATTATAAGGACCAAAAAGTCAAGTACCAATAGCAAG
1 CATTTGCGCACTTAATCATGCAATTATAAGGACCAAAAAGTCAAGTACCAATAGCAAG
68971 TATACAATTG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.23
Consensus pattern (58 bp):
CATTTGCGCACTTAATCATGCAATTATAAGGACCAAAAAGTCAAGTACCAATAGCAAG
Found at i:71373 original size:17 final size:17
Alignment explanation
Indices: 71346--71378 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
71336 TCCTCTTTAG
71346 AAAAGATCAAT-ACATC
1 AAAAGATCAATCACATC
71362 AAAAGCATCAATCACAT
1 AAAAG-ATCAATCACAT
71379 AGATCATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.55, C:0.21, G:0.06, T:0.18
Consensus pattern (17 bp):
AAAAGATCAATCACATC
Found at i:71663 original size:73 final size:74
Alignment explanation
Indices: 71582--71736 Score: 303
Period size: 74 Copynumber: 2.1 Consensus size: 74
71572 AAAGGAAATG
71582 AAGAGAAAG-AAAAAAGTTTCAGTCATGGGAGAAAGCTTAAGAGAATTTTGGGAGAAAAGATAGA
1 AAGAGAAAGAAAAAAAGTTTCAGTCATGGGAGAAAGCTTAAGAGAATTTTGGGAGAAAAGATAGA
71646 ATTTGTGAA
66 ATTTGTGAA
71655 AAGAGAAAGAAAAAAAGTTTCAGTCATGGGAGAAAGCTTAAGAGAATTTTGGGAGAAAAGATAGA
1 AAGAGAAAGAAAAAAAGTTTCAGTCATGGGAGAAAGCTTAAGAGAATTTTGGGAGAAAAGATAGA
71720 ATTTGTGAA
66 ATTTGTGAA
71729 AAGAGAAA
1 AAGAGAAA
71737 ATGAATGGTT
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 9 0.11
74 72 0.89
ACGTcount: A:0.48, C:0.04, G:0.27, T:0.21
Consensus pattern (74 bp):
AAGAGAAAGAAAAAAAGTTTCAGTCATGGGAGAAAGCTTAAGAGAATTTTGGGAGAAAAGATAGA
ATTTGTGAA
Found at i:83796 original size:37 final size:37
Alignment explanation
Indices: 83706--83810 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 37
83696 ATTAATCTTC
*
83706 AATAAGAAATACTCAAATTTCTTATGAAACCTTTAAT
1 AATAAAAAATACTCAAATTTCTTATGAAACCTTTAAT
* * *
83743 AA-GAAAAATACCCAAATTTCTTATGAAACTTTTAAT
1 AATAAAAAATACTCAAATTTCTTATGAAACCTTTAAT
83779 AATAAAAAATACTCAAATTTCTTATGAAACCT
1 AATAAAAAATACTCAAATTTCTTATGAAACCT
83811 AAATTGGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 32 0.53
37 28 0.47
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (37 bp):
AATAAAAAATACTCAAATTTCTTATGAAACCTTTAAT
Found at i:85744 original size:16 final size:16
Alignment explanation
Indices: 85725--85755 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
85715 TCTTAATTAA
85725 AGTTAATTTCAGTTTC
1 AGTTAATTTCAGTTTC
*
85741 AGTTAATTTTAGTTT
1 AGTTAATTTCAGTTT
85756 GGTTTGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (16 bp):
AGTTAATTTCAGTTTC
Found at i:85803 original size:16 final size:16
Alignment explanation
Indices: 85784--85825 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
85774 ATTACTTTTG
85784 GTTCAAGTTATTTTAA
1 GTTCAAGTTATTTTAA
* *
85800 GTTCAAATTATTTTTA
1 GTTCAAGTTATTTTAA
85816 GTTCAAGTTA
1 GTTCAAGTTA
85826 CATTTGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (16 bp):
GTTCAAGTTATTTTAA
Found at i:87622 original size:23 final size:26
Alignment explanation
Indices: 87578--87627 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 26
87568 TATTAATGAT
*
87578 ATAAAATTCTTATATGGATAGATACAA
1 ATAAAATTCTTATA-GGATAGACACAA
87605 ATAAAATT-TTATA-G-TAGACACAA
1 ATAAAATTCTTATAGGATAGACACAA
87628 TTAGTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 8 0.36
24 1 0.05
26 5 0.23
27 8 0.36
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (26 bp):
ATAAAATTCTTATAGGATAGACACAA
Found at i:87816 original size:46 final size:46
Alignment explanation
Indices: 87749--87845 Score: 158
Period size: 46 Copynumber: 2.1 Consensus size: 46
87739 GGACAAATAT
* *
87749 ATTTGGTGGATTGGTCAAACTACATTTGGTTAATTCGTCAAGCTAC
1 ATTTGGTGGATTGGCCAAACTACATTTGGTCAATTCGTCAAGCTAC
* *
87795 ATTTGGTTGATTGGCCAAACTACATTTGGTCAATTGGTCAAGCTAC
1 ATTTGGTGGATTGGCCAAACTACATTTGGTCAATTCGTCAAGCTAC
87841 ATTTG
1 ATTTG
87846 ATCAATTGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (46 bp):
ATTTGGTGGATTGGCCAAACTACATTTGGTCAATTCGTCAAGCTAC
Found at i:87859 original size:23 final size:23
Alignment explanation
Indices: 87749--87859 Score: 132
Period size: 23 Copynumber: 4.8 Consensus size: 23
87739 GGACAAATAT
** *
87749 ATTTGGTGGATTGGTCAAACTAC
1 ATTTGGTCAATTGGTCAAGCTAC
* *
87772 ATTTGGTTAATTCGTCAAGCTAC
1 ATTTGGTCAATTGGTCAAGCTAC
** * *
87795 ATTTGGTTGATTGGCCAAACTAC
1 ATTTGGTCAATTGGTCAAGCTAC
87818 ATTTGGTCAATTGGTCAAGCTAC
1 ATTTGGTCAATTGGTCAAGCTAC
*
87841 ATTTGATCAATTGGTCAAG
1 ATTTGGTCAATTGGTCAAG
87860 TTGTCCATCT
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 75 1.00
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (23 bp):
ATTTGGTCAATTGGTCAAGCTAC
Found at i:94690 original size:40 final size:40
Alignment explanation
Indices: 94646--94739 Score: 170
Period size: 40 Copynumber: 2.4 Consensus size: 40
94636 ATGATTCCAC
*
94646 GAATACAAGCATATTGTTTATATGGTTTATATGTGTACAT
1 GAATACAAGCATATTGTTTATATGGGTTATATGTGTACAT
*
94686 GAATACAAGCATATTGTTTATATGGGTTCTATGTGTACAT
1 GAATACAAGCATATTGTTTATATGGGTTATATGTGTACAT
94726 GAATACAAGCATAT
1 GAATACAAGCATAT
94740 GTCTATGTGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (40 bp):
GAATACAAGCATATTGTTTATATGGGTTATATGTGTACAT
Found at i:95025 original size:23 final size:22
Alignment explanation
Indices: 94963--95036 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 22
94953 ATATCGAGGG
* * *
94963 TTCTACGTGGTCCTTCGGGATAA
1 TTCTACG-CGTCCTTCGGGACAT
*
94986 TTCTACGCGATCATTCGGGACAT
1 TTCTACGCG-TCCTTCGGGACAT
95009 TTCTACGCCGTCCTTCGGGACAT
1 TTCTACG-CGTCCTTCGGGACAT
95032 TTCTA
1 TTCTA
95037 TGTAGAACTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
22 1 0.02
23 41 0.93
24 2 0.05
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.34
Consensus pattern (22 bp):
TTCTACGCGTCCTTCGGGACAT
Found at i:95215 original size:2 final size:2
Alignment explanation
Indices: 95208--95255 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
95198 GTTGATAATG
95208 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
95250 AT AT AT
1 AT AT AT
95256 GCTTTTGTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.