Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014410.1 Kokia drynarioides strain JFW-HI SEQ_129448, 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: 41002
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:71 original size:10 final size:10
Alignment explanation
Indices: 56--80 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
46 TGAGTTTATT
56 AATAATAATA
1 AATAATAATA
66 AATAATAATA
1 AATAATAATA
76 AATAA
1 AATAA
81 AAAAATAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AATAATAATA
Found at i:988 original size:29 final size:29
Alignment explanation
Indices: 937--1194 Score: 263
Period size: 29 Copynumber: 8.8 Consensus size: 29
927 GGAGGTTCCT
* ** *
937 AAACTGTCCGAAAATTTAATTTTTACCCTT
1 AAACT-TCCAAAAATTCCATTTTTACCCTC
* * *
967 GAACTTCCAAATATTCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
***
997 AAACTTTTGAAAATTCCATTTTTACCC-C
1 AAACTTCCAAAAATTCCATTTTTACCCTC
* * *
1025 TGAACTTCAAAAAATTTCATTTTTTA-CCTC
1 -AAACTTCCAAAAATTCCA-TTTTTACCCTC
1055 GAAACTTCC-AAAATTCCATTTTTA-CCTC
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
* *
1083 TAAACTTCAAAAAATTCCATTTTTACACTC
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
* *
1113 GAACTTCCAAAAATTCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
*
1143 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCTC
1172 AAACTTCCAAAAATTCCATTTTT
1 AAACTTCCAAAAATTCCATTTTT
1195 CCCCCGGATG
Statistics
Matches: 190, Mismatches: 31, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
28 17 0.09
29 104 0.55
30 69 0.36
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.37
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCTC
Found at i:1029 original size:59 final size:58
Alignment explanation
Indices: 937--1199 Score: 280
Period size: 59 Copynumber: 4.5 Consensus size: 58
927 GGAGGTTCCT
* ** * * * * *
937 AAACTGTCCGAAAATTTAATTTTTACCCTTGAACTTCCAAATATTCCATTTTTAACCCTA
1 AAACT-TCCAAAAATTCCATTTTTACCCCTAAACTTCAAAAAATTCCATTTTT-ACCCTC
*** * *
997 AAACTTTTGAAAATTCCATTTTTACCCCTGAACTTCAAAAAATTTCATTTTTTA-CCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCAAAAAATTCCA-TTTTTACCCTC
* *
1055 GAAACTTCC-AAAATTCCATTTTTACCTCTAAACTTCAAAAAATTCCATTTTTACACTC
1 -AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCAAAAAATTCCATTTTTACCCTC
* * *
1113 GAACTTCCAAAAATTCCATTTTTGA-CCCTAAAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTT-ACCCCT-AAACTTCAAAAAATTCCATTTTTACCCTC
*
1172 AAACTTCCAAAAATTCCATTTTTCCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCC
1200 GGATGTCTAA
Statistics
Matches: 174, Mismatches: 22, Indels: 15
0.82 0.10 0.07
Matches are distributed among these distances:
57 13 0.07
58 58 0.33
59 93 0.53
60 10 0.06
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.37
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCAAAAAATTCCATTTTTACCCTC
Found at i:2850 original size:27 final size:27
Alignment explanation
Indices: 2810--2870 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
2800 AATAAGATCG
* *
2810 AATTCTAA-TTAAA-TAATAAAAATAT
1 AATTTTAATTTAAATTAATAAAAAAAT
2835 AAGTTTTAATTTAAATTAATAAAAAAAT
1 AA-TTTTAATTTAAATTAATAAAAAAAT
2863 AATTTTAA
1 AATTTTAA
2871 AATATTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 5 0.16
27 11 0.35
28 13 0.42
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
AATTTTAATTTAAATTAATAAAAAAAT
Found at i:4652 original size:30 final size:32
Alignment explanation
Indices: 4618--4681 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 32
4608 GTTTATTTTC
*
4618 TTTATAATTTTTAA-AGGATTAAATTA-AATT
1 TTTATAATTTTTAAGAGGATTAAAATATAATT
* *
4648 TTTATTATTTTTAAGGGGATTAAAATATAATT
1 TTTATAATTTTTAAGAGGATTAAAATATAATT
4680 TT
1 TT
4682 ATCTTTACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 13 0.45
31 10 0.34
32 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (32 bp):
TTTATAATTTTTAAGAGGATTAAAATATAATT
Found at i:9588 original size:67 final size:67
Alignment explanation
Indices: 9470--9602 Score: 212
Period size: 67 Copynumber: 2.0 Consensus size: 67
9460 ATTACACCGT
* *
9470 GCAATCAGCCTAACATACTAGCTAAAAGAGTGAACGAGATTCAATTCAAACACCAAATCAGAGCT
1 GCAACCAGCCTAACATACTAGCTAAAAGAGTGAACGAGACTCAATTCAAACACCAAATCAGAGCT
9535 CA
66 CA
* * * *
9537 GCAACCAGCCTAACATATTAGCTAAAAGAGTGAACGGGACTCAGTTTAAACACCAAATCAGAGCT
1 GCAACCAGCCTAACATACTAGCTAAAAGAGTGAACGAGACTCAATTCAAACACCAAATCAGAGCT
9602 C
66 C
9603 CATGTTTATA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.18
Consensus pattern (67 bp):
GCAACCAGCCTAACATACTAGCTAAAAGAGTGAACGAGACTCAATTCAAACACCAAATCAGAGCT
CA
Found at i:14588 original size:23 final size:23
Alignment explanation
Indices: 14562--14629 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
14552 TTCATTTAAC
*
14562 TTAATCAAACATGTTGACGAACA
1 TTAATCAAACATGTTCACGAACA
* * *
14585 TTAAACGAACATGTTCATGAACA
1 TTAATCAAACATGTTCACGAACA
*
14608 TATAATTGAAA-ATGTTCACGAA
1 T-TAA-TCAAACATGTTCACGAA
14630 TAATATTAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
23 20 0.57
24 13 0.37
25 2 0.06
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (23 bp):
TTAATCAAACATGTTCACGAACA
Found at i:16726 original size:29 final size:29
Alignment explanation
Indices: 16684--16754 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 29
16674 ATCAGAGTTG
* *
16684 AAAATGAGACTTTTTGAATACCCGGGGGT
1 AAAATGATAATTTTTGAATACCCGGGGGT
* * *
16713 AAAAT-AGTAA-TTTTGGATTCTCGGGGGT
1 AAAATGA-TAATTTTTGAATACCCGGGGGT
16741 AAAATGATAATTTT
1 AAAATGATAATTTT
16755 GGGAAATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
28 24 0.71
29 10 0.29
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (29 bp):
AAAATGATAATTTTTGAATACCCGGGGGT
Found at i:16874 original size:29 final size:29
Alignment explanation
Indices: 16705--16936 Score: 79
Period size: 29 Copynumber: 7.9 Consensus size: 29
16695 TTTTGAATAC
*
16705 CCGGGGGTAAAAT-AGTAA-TTTTGG-ATT
1 CCGGGGGTAAAATGA-TAATTTTTGGAAAT
*
16732 CTCGGGGGTAAAATGATAATTTTGGGAAATT
1 C-CGGGGGTAAAATGATAATTTTTGGAAA-T
** * * * *
16763 TTGGGGTTTAAAATG-GAA-TTTTAGACAT
1 CCGGGG-GTAAAATGATAATTTTTGGAAAT
* * *
16791 CCGAGGGTAAAACGATAATTTTTAGAAAAAT
1 CCGGGGGTAAAATGATAATTTTT-G-GAAAT
* * *
16822 -C-GGGATACAAAAAGA-AATTTTTTGGACAT
1 CCGGGGGT--AAAATGATAA-TTTTTGGAAAT
**
16851 CCGGGGGTAAAATGATAATTTTTGAGAGTT
1 CCGGGGGTAAAATGATAATTTTTG-GAAAT
* ** * **
16881 TC-GGGGTAAAAAAATAAGTTTTAGGAGGT
1 CCGGGGGTAAAATGATAA-TTTTTGGAAAT
*
16910 TCGGGGGTAAAAAT-ATAATTTTTGGAA
1 CCGGGGGT-AAAATGATAATTTTTGGAA
16937 GTTTTGAGGT
Statistics
Matches: 150, Mismatches: 35, Indels: 38
0.67 0.16 0.17
Matches are distributed among these distances:
27 7 0.05
28 21 0.14
29 60 0.40
30 32 0.21
31 30 0.20
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.31
Consensus pattern (29 bp):
CCGGGGGTAAAATGATAATTTTTGGAAAT
Found at i:16885 original size:60 final size:60
Alignment explanation
Indices: 16781--16933 Score: 143
Period size: 60 Copynumber: 2.6 Consensus size: 60
16771 TAAAATGGAA
* * * *
16781 TTTTAGACATCCGAGGGTAAAACGATAATTTTT-AGAAAAATCGGGATACAAAAAGA-AATT
1 TTTTGGACATCCGGGGGTAAAATGATAATTTTTGAGAAAAATCGGGATA-AAAAA-ATAAGT
*** *
16841 TTTTGGACATCCGGGGGTAAAATGATAATTTTTGAG-AGTTTCGGGGTAAAAAAATAAGT
1 TTTTGGACATCCGGGGGTAAAATGATAATTTTTGAGAAAAATCGGGATAAAAAAATAAGT
* ** *
16900 TTTAGGAGGTTCGGGGGTAAAAAT-ATAATTTTTG
1 TTTTGGACATCCGGGGGT-AAAATGATAATTTTTG
16934 GAAGTTTTGA
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
58 1 0.01
59 32 0.41
60 43 0.55
61 2 0.03
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.31
Consensus pattern (60 bp):
TTTTGGACATCCGGGGGTAAAATGATAATTTTTGAGAAAAATCGGGATAAAAAAATAAGT
Found at i:16928 original size:59 final size:59
Alignment explanation
Indices: 16852--17105 Score: 227
Period size: 58 Copynumber: 4.4 Consensus size: 59
16842 TTTGGACATC
* * *
16852 CGGGGGT-AAAATGATAATTTTTGAG-AGTTTCGGGGTAAAAAAATAAGTTTTAGGAGGTT
1 CGGGGGTAAAAAT-ATAATTTTTGAGAAGTTTCGAGGTAAAAAAAGAA-TTTTAGGAAGTT
* * ** *
16911 CGGGGGTAAAAATATAATTTTTG-GAAGTTTTGAGGTCAAAATGGAATTTTTGGAAGTT
1 CGGGGGTAAAAATATAATTTTTGAGAAGTTTCGAGGTAAAAAAAGAATTTTAGGAAGTT
* * * **
16969 CGAGGGTAAAAATATAATTTTT-AGAAGTTT-TAGGATCAAAATGGAATTTTTA-GAAGTT
1 CGGGGGTAAAAATATAATTTTTGAGAAGTTTCGAGG-TAAAAAAAGAA-TTTTAGGAAGTT
* * * * *
17027 TGGGGGTAAAAATGTAATTTTAG-GAAGTTTCGAGG-ATAAAATAGAATTTTTGGAAGTT
1 CGGGGGTAAAAATATAATTTTTGAGAAGTTTCGAGGTA-AAAAAAGAATTTTAGGAAGTT
* *
17085 CGAGGCTAAAAATATAATTTT
1 CGGGGGTAAAAATATAATTTT
17106 CAAAAGTTTT
Statistics
Matches: 163, Mismatches: 23, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
57 7 0.04
58 112 0.69
59 39 0.24
60 5 0.03
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (59 bp):
CGGGGGTAAAAATATAATTTTTGAGAAGTTTCGAGGTAAAAAAAGAATTTTAGGAAGTT
Found at i:16952 original size:29 final size:29
Alignment explanation
Indices: 16859--17105 Score: 200
Period size: 29 Copynumber: 8.4 Consensus size: 29
16849 ATCCGGGGGT
*
16859 AAAATGATAATTTTT-GAGAGTTTCGGGGTA
1 AAAAT-ATAATTTTTGGA-AGTTTCGAGGTA
* * * *
16889 AAAAAATAAGTTTTAGG-AGGTTCGGGGGTA
1 AAAATATAA-TTTTTGGAAGTTTC-GAGGTA
* *
16919 AAAATATAATTTTTGGAAGTTTTGAGGTC
1 AAAATATAATTTTTGGAAGTTTCGAGGTA
**
16948 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
1 AAAATATAATTTTTGGAAGTTTCGA-GGTA
* * *
16977 AAAATATAATTTTTAGAAGTTT-TAGGATC
1 AAAATATAATTTTTGGAAGTTTCGAGG-TA
** * * *
17006 AAAATGGAATTTTTAGAAGTTTGGGGGTA
1 AAAATATAATTTTTGGAAGTTTCGAGGTA
* *
17035 AAAATGTAATTTTAGGAAGTTTCGAGG-A
1 AAAATATAATTTTTGGAAGTTTCGAGGTA
*
17063 TAAAATAGAATTTTTGGAAG-TTCGAGGCTA
1 -AAAATATAATTTTTGGAAGTTTCGAGG-TA
17093 AAAATATAATTTT
1 AAAATATAATTTT
17106 CAAAAGTTTT
Statistics
Matches: 174, Mismatches: 32, Indels: 23
0.76 0.14 0.10
Matches are distributed among these distances:
28 14 0.08
29 128 0.74
30 31 0.18
31 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.35
Consensus pattern (29 bp):
AAAATATAATTTTTGGAAGTTTCGAGGTA
Found at i:16981 original size:58 final size:59
Alignment explanation
Indices: 16899--17144 Score: 304
Period size: 58 Copynumber: 4.2 Consensus size: 59
16889 AAAAAATAAG
* * * *
16899 TTTTAGGAGGTTCGGGGGTAAAAATATAATTTTTGGAAGTTTTGAGG-TCAAAATGGAA
1 TTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTTGAGGATCAAAATGGAA
16957 TTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTT-AGGATCAAAATGGAA
1 TTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTTGAGGATCAAAATGGAA
* * * * * *
17015 TTTTTAGAAGTTTGGGGGTAAAAATGTAA-TTTTAGGAAGTTTCGAGGAT-AAAATAGAA
1 TTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTA-GAAGTTTTGAGGATCAAAATGGAA
* * * *
17073 TTTTTGGAAGTTCGAGGCTAAAAATATAATTTTCAAAAGTTTTG-GGGTCAAAAATGGAA
1 TTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTTGAGGATC-AAAATGGAA
17132 TTTTTGGATAGTT
1 TTTTTGGA-AGTT
17145 TAAGGACCTC
Statistics
Matches: 161, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
57 11 0.07
58 121 0.75
59 25 0.16
60 4 0.02
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (59 bp):
TTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTTGAGGATCAAAATGGAA
Found at i:17026 original size:87 final size:86
Alignment explanation
Indices: 16899--17144 Score: 258
Period size: 87 Copynumber: 2.8 Consensus size: 86
16889 AAAAAATAAG
* * * * * *
16899 TTTTAGGAGGTTCGGGGGTAAAAATATAATTTTTGGAAGTTTTGAGGTCAAAATGGAATTTTTGG
1 TTTTA-GAAGTTCGAGGATAAAAATAGAATTTTTAGAAGTTTTGGGGTCAAAATGGAATTTTTGG
* *
16964 AAGTTCGAGGGTAAAAATATAAT
65 AAGTTCGAGGAT-AAAATAGAAT
** * * * * * *
16987 TTTTAGAAGTTTTAGGATCAAAATGGAATTTTTAGAAGTTTGGGGGTAAAAATGTAATTTTAGGA
1 TTTTAGAAGTTCGAGGATAAAAATAGAATTTTTAGAAGTTTTGGGGTCAAAATGGAATTTTTGGA
17052 AGTTTCGAGGATAAAATAGAAT
66 AG-TTCGAGGATAAAATAGAAT
* * * * *
17074 TTTTGGAAGTTCGAGGCTAAAAATATAATTTTCAAAAGTTTTGGGGTCAAAAATGGAATTTTTGG
1 TTTTAGAAGTTCGAGGATAAAAATAGAATTTTTAGAAGTTTTGGGGTC-AAAATGGAATTTTTGG
17139 ATAGTT
65 A-AGTT
17145 TAAGGACCTC
Statistics
Matches: 126, Mismatches: 29, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
87 94 0.75
88 30 0.24
89 2 0.02
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (86 bp):
TTTTAGAAGTTCGAGGATAAAAATAGAATTTTTAGAAGTTTTGGGGTCAAAATGGAATTTTTGGA
AGTTCGAGGATAAAATAGAAT
Found at i:17074 original size:116 final size:118
Alignment explanation
Indices: 16912--17145 Score: 348
Period size: 116 Copynumber: 2.0 Consensus size: 118
16902 TAGGAGGTTC
* * * *
16912 GGGGGTAAAAATATAATTTTTGGAAGTTTTGAGGTCAAAATGGAATTTTTGGAAGTTCGAGGGTA
1 GGGGGTAAAAATATAATTTTAGGAAGTTTCGAGGTCAAAATAGAATTTTTGGAAGTTCGAGGCTA
* *
16977 AAAATATAATTTTTAGAAGTTTTAGGATC-AAAATGGAATTTTTAGA-AGTTT
66 AAAATATAATTTTCAAAAGTTTTAGGATCAAAAATGGAATTTTTAGATAGTTT
*
17028 GGGGGTAAAAATGTAATTTTAGGAAGTTTCGAGGAT-AAAATAGAATTTTTGGAAGTTCGAGGCT
1 GGGGGTAAAAATATAATTTTAGGAAGTTTCGAGG-TCAAAATAGAATTTTTGGAAGTTCGAGGCT
* * *
17092 AAAAATATAATTTTCAAAAGTTTTGGGGTCAAAAATGGAATTTTTGGATAGTTT
65 AAAAATATAATTTTCAAAAGTTTTAGGATCAAAAATGGAATTTTTAGATAGTTT
17146 AAGGACCTCC
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
116 83 0.79
117 17 0.16
118 5 0.05
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.36
Consensus pattern (118 bp):
GGGGGTAAAAATATAATTTTAGGAAGTTTCGAGGTCAAAATAGAATTTTTGGAAGTTCGAGGCTA
AAAATATAATTTTCAAAAGTTTTAGGATCAAAAATGGAATTTTTAGATAGTTT
Found at i:18939 original size:14 final size:15
Alignment explanation
Indices: 18916--18944 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
18906 AATTTGGACA
18916 TGTAATTTGGACTTT
1 TGTAATTTGGACTTT
18931 TGTAA-TTGGACTTT
1 TGTAATTTGGACTTT
18945 ATAATAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (15 bp):
TGTAATTTGGACTTT
Found at i:18989 original size:11 final size:11
Alignment explanation
Indices: 18977--19040 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
18967 AAAAAAAATT
18977 AATTTAAATTTA
1 AATTT-AATTTA
18989 AATTTAATTTA
1 AATTTAATTTA
*
19000 AATTCAAATTTA
1 AATT-TAATTTA
* * *
19012 AAATAAATCTA
1 AATTTAATTTA
**
19023 AATTTAAAATA
1 AATTTAATTTA
19034 AATTTAA
1 AATTTAA
19041 AAGGGGCCAG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
11 30 0.68
12 14 0.32
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:18995 original size:17 final size:17
Alignment explanation
Indices: 18981--19041 Score: 86
Period size: 17 Copynumber: 3.6 Consensus size: 17
18971 AAAATTAATT
**
18981 TAAATTTAAATTTAATT
1 TAAATTTAAATTTAAAA
*
18998 TAAATTCAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
19015 TAAATCTAAATTTAAAA
1 TAAATTTAAATTTAAAA
19032 TAAATTTAAA
1 TAAATTTAAA
19042 AGGGGCCAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:19765 original size:158 final size:158
Alignment explanation
Indices: 19477--19817 Score: 540
Period size: 158 Copynumber: 2.2 Consensus size: 158
19467 CTTCAACCTG
*
19477 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCAAGCGTTGGTTCGATT
1 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCAAGCGTGGGTTCGATT
* * * *
19542 TGGTCTTCTTCTCTATGTCTCATTAGGAAGATGATCGCGTCGTTTGTTTCAATCCGCTTCTCTGT
66 TGGTCTTCTTCTCTATATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCGCTTCTCTGT
19607 ATCTCATCAGGAAGACGAATTTGGTCCA
131 ATCTCATCAGGAAGACGAATTTGGTCCA
* * * *
19635 CTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTTACATCGAGCGTGGGTTTGATT
1 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCAAGCGTGGGTTCGATT
* **
19700 TGGTCTTCTTTTC-AGTATCTCATCAGGAAGATGACCTTGTCATTTGTTTCAATCCGCTTCTCTG
66 TGGTCTTCTTCTCTA-TATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCGCTTCTCTG
*
19764 TATTTCATCAGGAAGACGAATTTGGTCCA
130 TATCTCATCAGGAAGACGAATTTGGTCCA
*
19793 CTTCTCAGTAACTCATCAGGAAGCT
1 CTTCTCAGTATCTCATCAGGAAGCT
19818 AACCATTTTA
Statistics
Matches: 167, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
157 1 0.01
158 166 0.99
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.35
Consensus pattern (158 bp):
CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCAAGCGTGGGTTCGATT
TGGTCTTCTTCTCTATATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCGCTTCTCTGT
ATCTCATCAGGAAGACGAATTTGGTCCA
Found at i:19996 original size:206 final size:206
Alignment explanation
Indices: 19635--20523 Score: 962
Period size: 206 Copynumber: 4.2 Consensus size: 206
19625 ATTTGGTCCA
* * * *
19635 CTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTTACATCGAGCGTGGGTTTGATT
1 CTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGATTTGATT
* * * *
19700 TGGTCTTCTTTTCAGTATCTCATCAGGAAGATGACCTTGTCATTTGTTTCAATCCGCTTCTCTGT
66 TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCATTTATTTCAATCCGCTTCTCTAT
* *
19765 ATTTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTAACTCATCAGGAAGCTAACCATTTTATT
131 ATCTCATCAGGAAAACGAATTTGGTCCACTTCTCAGTAACTCATCAGGAAGCTAACCATTTTATT
*
19830 GCTTCAACCTG
196 GCTTCGACCTG
19841 CTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGATTTGATT
1 CTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGATTTGATT
*
19906 TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTATTTCAATCCGCTTCTCTAT
66 TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCATTTATTTCAATCCGCTTCTCTAT
* * * *
19971 ATCTCATCATGAAAACGATTTTGGTCCACTTCTCAGTATCTCATTAGGAAGCTAACCATTTTATT
131 ATCTCATCAGGAAAACGAATTTGGTCCACTTCTCAGTAACTCATCAGGAAGCTAACCATTTTATT
*
20036 GCTTCGACCCG
196 GCTTCGACCTG
* * * * * * *
20047 TTTCTCAGTATCTCATTAGGAAGCTAGGATTCGAAGATTTGCTTACCTCGAGCATGGGTTTGATT
1 CTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGATTTGATT
* * * * * *
20112 TGGTTTTTTTTCTCAGTATCTCATTAGGAAGATGACCGTGCCATTTGTTTTAATCCGCTTCTCTA
66 TGG-TCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCATTTATTTCAATCCGCTTCTCTA
* * * * * **
20177 TATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTTTCAGTGTCTCATCAGGAAGCT
130 TATCTCATCAGGAA---AACGA----A-T--TTGGTCC-ACTTCTCAGTAACTCATCAGGAAGCT
** * * *
20242 GAGGTTGGAAGATTTGTTCGCATTGAGTTGGTA--TA
184 -A------ACCA-TT-TT---ATTG-CTTCG-ACCTG
*
20277 CTTCTCTGTATCTCATCAGGAA-CATAGGGTTCGAAGATTTGCTCACATCGAGCGT-GAGTTTGA
1 CTTCTCAGTATCTCATCAGGAAGC-TAGGGTTCGAAGATTTGCTCACATCGAGCGTGGA-TTTGA
* * *
20340 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTATTTCAATCCGCTTTTCT
64 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCATTTATTTCAATCCGCTTCTCT
* * * * * * *
20405 GTATCTTATCAGGAAGACGAATTTGGTCCACTTATCAGCATA-TCATCAAGAAACTAACCATTTT
129 ATATCTCATCAGGAAAACGAATTTGGTCCACTTCTCAGTA-ACTCATCAGGAAGCTAACCATTTT
20469 ATTGCTTCGACCTG
193 ATTGCTTCGACCTG
* * *
20483 CTTCTTAGTGTCTCATCAGGAAG-TTGAGGTTCGAAGATTTG
1 CTTCTCAGTATCTCATCAGGAAGCTAG-GGTTCGAAGATTTG
20524 TTCGCATTGA
Statistics
Matches: 565, Mismatches: 85, Indels: 66
0.79 0.12 0.09
Matches are distributed among these distances:
204 1 0.00
205 5 0.01
206 288 0.51
207 67 0.12
209 2 0.00
210 6 0.01
211 2 0.00
215 1 0.00
217 6 0.01
218 40 0.07
219 6 0.01
221 1 0.00
222 1 0.00
225 2 0.00
226 5 0.01
227 2 0.00
229 66 0.12
230 60 0.11
231 3 0.01
232 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (206 bp):
CTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGATTTGATT
TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCATTTATTTCAATCCGCTTCTCTAT
ATCTCATCAGGAAAACGAATTTGGTCCACTTCTCAGTAACTCATCAGGAAGCTAACCATTTTATT
GCTTCGACCTG
Found at i:20679 original size:39 final size:39
Alignment explanation
Indices: 20636--20805 Score: 139
Period size: 39 Copynumber: 4.4 Consensus size: 39
20626 GTTGACGATG
* * * *
20636 ATTTGCCCCAAGCTCGGGGTAAGATATCGAATGGCTGTA
1 ATTTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTGTA
* * * * *** * * *
20675 ATTTGCCTCTGGCTCGAGGTAAGAGAT-TGGTTGATGATG
1 ATTTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTG-TA
*
20714 ATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCT-TCA
1 ATTTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTGT-A
20753 ATTTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCT-TCA
1 ATTTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTGT-A
* *
20792 ATCTGTCCCAGGCT
1 ATTTGCCCCAGGCT
20806 AAAGGTAAGA
Statistics
Matches: 103, Mismatches: 25, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
38 5 0.05
39 95 0.92
40 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
ATTTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTGTA
Found at i:20756 original size:78 final size:78
Alignment explanation
Indices: 20614--20779 Score: 208
Period size: 78 Copynumber: 2.1 Consensus size: 78
20604 CCGTGATCGG
* * * * * *
20614 GGTAGGAGTTTGGTTGACGATGATTTGCCCCAAGCTCGGGGTAAGATATCGAATGGCTGTAATTT
1 GGTAAGAGATTGGTTGACGATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGTAATTT
* *
20679 GCCTCTGGCTCGA
66 GCCCCAGGCTCGA
* *
20692 GGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCT-TCAATT
1 GGTAAGAGATTGGTTGACGATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGT-AATT
*
20756 TGCCCCAGGCTCGG
65 TGCCCCAGGCTCGA
*
20770 GGTAAAAGAT
1 GGTAAGAGAT
20780 CAAATGGCTT
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
77 1 0.01
78 74 0.99
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (78 bp):
GGTAAGAGATTGGTTGACGATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGTAATTT
GCCCCAGGCTCGA
Found at i:20812 original size:117 final size:117
Alignment explanation
Indices: 20636--20857 Score: 313
Period size: 117 Copynumber: 1.9 Consensus size: 117
20626 GTTGACGATG
* * * * * **
20636 ATTTGCCCCAAGCTCGGGGTAAGATATCGAATGGCTGTAATTTGCCTCTGGCTCGAGGTAAGAGA
1 ATTTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGTAATCTGCCTCAGGCTAAAGGTAAGAGA
*
20701 TTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTTCA
66 TTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTTCA
*
20753 ATTTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCT-TCAATCTGTCC-CAGGCTAAAGGTAAGA
1 ATTTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGT-AATCTG-CCTCAGGCTAAAGGTAAGA
* *
20816 GATTGGTTGATGATGATCTGCCCCAAGTTCGGGGTAAGAGAT
64 GATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGAT
20858 TGGTTAATGA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
116 1 0.01
117 89 0.97
118 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (117 bp):
ATTTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGTAATCTGCCTCAGGCTAAAGGTAAGAGA
TTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTTCA
Found at i:20813 original size:39 final size:39
Alignment explanation
Indices: 20714--20818 Score: 129
Period size: 39 Copynumber: 2.7 Consensus size: 39
20704 GTTGATGATG
***
20714 ATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTTCA
1 ATCTGCCCCAGGCTAAAGGTAAAAGATCAAATGGCTTCA
* ***
20753 ATTTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTTCA
1 ATCTGCCCCAGGCTAAAGGTAAAAGATCAAATGGCTTCA
* *
20792 ATCTGTCCCAGGCTAAAGGTAAGAGAT
1 ATCTGCCCCAGGCTAAAGGTAAAAGAT
20819 TGGTTGATGA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.22
Consensus pattern (39 bp):
ATCTGCCCCAGGCTAAAGGTAAAAGATCAAATGGCTTCA
Found at i:20835 original size:39 final size:39
Alignment explanation
Indices: 20792--20869 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
20782 AATGGCTTCA
* * *
20792 ATCTGTCCCAGGCTAAAGGTAAGAGATTGGTTGATGATG
1 ATCTGCCCCAAGCTAAAGGTAAGAGATTGGTTAATGATG
* ***
20831 ATCTGCCCCAAGTTCGGGGTAAGAGATTGGTTAATGATG
1 ATCTGCCCCAAGCTAAAGGTAAGAGATTGGTTAATGATG
20870 TAGCTTCACT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.28
Consensus pattern (39 bp):
ATCTGCCCCAAGCTAAAGGTAAGAGATTGGTTAATGATG
Found at i:21256 original size:100 final size:99
Alignment explanation
Indices: 21118--21413 Score: 291
Period size: 100 Copynumber: 3.0 Consensus size: 99
21108 CGGGTTTGCT
* *** * *
21118 ATTGCGACTTAAACCTTTCCCCTTCAAATCTTCGTGGTATTGGATTCGCTGTTGCGGCTTAAATC
1 ATTGCGACTTAAACCTTTCCCTTTTGTAT-TTCGTGGTATTGGATTCGCCGTTGCGGCTTAGATC
*
21183 TTTCCCTTCTTGTCTTCTGAGGTTC-ACGGTCCGCC
65 TTTCCCTTCTTGTCTTCTGAGGTACTA-GGTCCGCC
* ** *
21218 GTTGCGACTTAAACCTTTCCCTTTTGTATATTTATGGTACTGGA-TCTGCCGTTGCGG-TCTAGA
1 ATTGCGACTTAAACCTTTCCCTTTTGTAT-TTCGTGGTATTGGATTC-GCCGTTGCGGCT-TAGA
*
21281 TCTTTCCCTT-TATGTC-TCTGAGGTACTAGGTCCGTC
63 TCTTTCCCTTCT-TGTCTTCTGAGGTACTAGGTCCGCC
* * * * *
21317 ATTGCGACTTAAACATTTCCCTTGTGT-TTTCGTGGTATTAGATCCGCCGTTGCGACTTAGATCT
1 ATTGCGACTTAAACCTTTCCCTTTTGTATTTCGTGGTATTGGATTCGCCGTTGCGGCTTAGATCT
* * * * *
21381 TTCCCTCCATGTCTTC-GCGGCACTAGATCCGCC
66 TTCCCTTCTTGTCTTCTGAGGTACTAGGTCCGCC
21414 GTTGTGGCTT
Statistics
Matches: 160, Mismatches: 28, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
97 49 0.31
98 5 0.03
99 44 0.28
100 62 0.39
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.38
Consensus pattern (99 bp):
ATTGCGACTTAAACCTTTCCCTTTTGTATTTCGTGGTATTGGATTCGCCGTTGCGGCTTAGATCT
TTCCCTTCTTGTCTTCTGAGGTACTAGGTCCGCC
Found at i:21337 original size:99 final size:98
Alignment explanation
Indices: 21168--21396 Score: 250
Period size: 99 Copynumber: 2.3 Consensus size: 98
21158 TGGATTCGCT
* * * * *
21168 GTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTTCACGGTCCGCCGTTGCGACTTAAACC
1 GTTGCGACTTAGATCTTTCCCTTCTTGTCTTCTGAGGTACACGGTCCGCCATTGCGACTTAAACA
* * * *
21233 TTTCCCTTTTGTATATTTATGGTACTGGATCTGCC
66 TTTCCCTTGTGT-T-TTCATGGTACTAGATCCGCC
* *
21268 GTTGCG-GTCTAGATCTTTCCCTT-TATGTC-TCTGAGGTACTA-GGTCCGTCATTGCGACTTAA
1 GTTGCGACT-TAGATCTTTCCCTTCT-TGTCTTCTGAGGTAC-ACGGTCCGCCATTGCGACTTAA
* *
21329 ACATTTCCCTTGTGTTTTCGTGGTATTAGATCCGCC
63 ACATTTCCCTTGTGTTTTCATGGTACTAGATCCGCC
* *
21365 GTTGCGACTTAGATCTTTCCCTCCATGTCTTC
1 GTTGCGACTTAGATCTTTCCCTTCTTGTCTTC
21397 GCGGCACTAG
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
97 38 0.35
98 4 0.04
99 42 0.39
100 24 0.22
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (98 bp):
GTTGCGACTTAGATCTTTCCCTTCTTGTCTTCTGAGGTACACGGTCCGCCATTGCGACTTAAACA
TTTCCCTTGTGTTTTCATGGTACTAGATCCGCC
Found at i:21406 original size:97 final size:99
Alignment explanation
Indices: 21148--21413 Score: 274
Period size: 97 Copynumber: 2.7 Consensus size: 99
21138 CCTTCAAATC
* * * *
21148 TTCGTGGTATTGGATTCGCTGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTTCAC--G
1 TTCGTGGTATTGGATCCGCCGTTGC-GCTTAGATCTTTCCCTTCATGTCTTCTGAGG--CACTAG
* * *
21211 GTCCGCCGTTGCGACTTAAACCTTTCCCTTTTGTATA
63 GTCCGCCATTGCGACTTAAACATTTCCCTTGTGTATA
** * * * * *
21248 TTTATGGTACTGGATCTGCCGTTGCGGTCTAGATCTTTCCCTTTATGTC-TCTGAGGTACTAGGT
1 TTCGTGGTATTGGATCCGCCGTTGCGCT-TAGATCTTTCCCTTCATGTCTTCTGAGGCACTAGGT
*
21312 CCGTCATTGCGACTTAAACATTTCCCTTGTGT-T-
65 CCGCCATTGCGACTTAAACATTTCCCTTGTGTATA
* * * *
21345 TTCGTGGTATTAGATCCGCCGTTGCGACTTAGATCTTTCCCTCCATGTCTTC-GCGGCACTAGAT
1 TTCGTGGTATTGGATCCGCCGTTGCG-CTTAGATCTTTCCCTTCATGTCTTCTGAGGCACTAGGT
21409 CCGCC
65 CCGCC
21414 GTTGTGGCTT
Statistics
Matches: 134, Mismatches: 27, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
97 54 0.40
98 4 0.03
99 40 0.30
100 36 0.27
ACGTcount: A:0.14, C:0.26, G:0.21, T:0.38
Consensus pattern (99 bp):
TTCGTGGTATTGGATCCGCCGTTGCGCTTAGATCTTTCCCTTCATGTCTTCTGAGGCACTAGGTC
CGCCATTGCGACTTAAACATTTCCCTTGTGTATA
Found at i:21544 original size:100 final size:100
Alignment explanation
Indices: 21392--21741 Score: 432
Period size: 100 Copynumber: 3.5 Consensus size: 100
21382 TCCCTCCATG
* * ** * * *
21392 TCTTCGCGGCACTAGATCCGCCGTTGTGG-CTTAGATATTTCCCGTCATGTCTTTGAGGTACAAG
1 TCTTTGCGGTACTAGATCCGCCGTTACGGTCTTAAATCTTTCCCGTCATGTCTTTGAGGTATAAG
* * *
21456 GTTCACCGTTGCGAATTAAACCCTTCCCTTTCGTA
66 GTTCACCGTTACGACTTAAACCCTTCCCTTTTGTA
* * * *
21491 TCTTTGAGGTACTAGATCCGCCATTATGGTCTTAAATCTTTCCCGTCACGTCTTTGAGGTATAAG
1 TCTTTGCGGTACTAGATCCGCCGTTACGGTCTTAAATCTTTCCCGTCATGTCTTTGAGGTATAAG
* *
21556 GTTCGCCGTTACGACTTAAACCCTTCCGTTTTGTA
66 GTTCACCGTTACGACTTAAACCCTTCCCTTTTGTA
* ** * * * *
21591 TCTTTGCGATACTAGATATGCTGTTGCGGTCTGAAATCTTTCCCGTCATGTCTCTGAGGTATAAG
1 TCTTTGCGGTACTAGATCCGCCGTTACGGTCTTAAATCTTTCCCGTCATGTCTTTGAGGTATAAG
* *
21656 GTTCACCGATAAGACTTAAACCCTTCCCTTTTGTA
66 GTTCACCGTTACGACTTAAACCCTTCCCTTTTGTA
* * * *
21691 TCTTTGCGGTACTGGATTCGTCGTTACGGTCTTAGATCTTTCCCGTCATGT
1 TCTTTGCGGTACTAGATCCGCCGTTACGGTCTTAAATCTTTCCCGTCATGT
21742 TTCATGGTGC
Statistics
Matches: 212, Mismatches: 38, Indels: 1
0.84 0.15 0.00
Matches are distributed among these distances:
99 24 0.11
100 188 0.89
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (100 bp):
TCTTTGCGGTACTAGATCCGCCGTTACGGTCTTAAATCTTTCCCGTCATGTCTTTGAGGTATAAG
GTTCACCGTTACGACTTAAACCCTTCCCTTTTGTA
Found at i:21595 original size:50 final size:50
Alignment explanation
Indices: 21441--21596 Score: 129
Period size: 50 Copynumber: 3.1 Consensus size: 50
21431 TCCCGTCATG
* * * * *
21441 TCTTTGAGGTACAAGGTTCACCGTTGCGAATTAAACCCTTCCCTTTCGTA
1 TCTTTGAGGTATAAGGTTCGCCGTTACGACTTAAACCCTTCCGTTTCGTA
* * * * * * * **
21491 TCTTTGAGGTACT-AGATCCGCCATTATGGTCTTAAATCTTTCCCGTCACG--
1 TCTTTGAGGTA-TAAGGTTCGCCGTTA-CGACTTAAACCCTT-CCGTTTCGTA
*
21541 TCTTTGAGGTATAAGGTTCGCCGTTACGACTTAAACCCTTCCGTTTTGTA
1 TCTTTGAGGTATAAGGTTCGCCGTTACGACTTAAACCCTTCCGTTTCGTA
21591 TCTTTG
1 TCTTTG
21597 CGATACTAGA
Statistics
Matches: 76, Mismatches: 24, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
48 5 0.07
49 11 0.14
50 46 0.61
51 9 0.12
52 5 0.07
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (50 bp):
TCTTTGAGGTATAAGGTTCGCCGTTACGACTTAAACCCTTCCGTTTCGTA
Found at i:22949 original size:6 final size:6
Alignment explanation
Indices: 22940--23010 Score: 83
Period size: 6 Copynumber: 11.5 Consensus size: 6
22930 CGACCTCTCC
*
22940 TTTTCT TTTTCT TTTTCT CTTTT-T TTTTCTT TTTGTTT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT -TTTTCT TTTTC-T TTT-TCT TTTTCT TTTTCT
22990 TTTTCT TTTT-T CTTTTCT TTT
1 TTTTCT TTTTCT -TTTTCT TTT
23011 ATTCATTGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
5 5 0.09
6 38 0.67
7 13 0.23
8 1 0.02
ACGTcount: A:0.00, C:0.14, G:0.01, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:28125 original size:96 final size:96
Alignment explanation
Indices: 27937--28128 Score: 237
Period size: 96 Copynumber: 2.0 Consensus size: 96
27927 AATTTTGGAA
* ** ** *
27937 AAAGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGTAAATTTTCA
1 AAAGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTCA
*
28002 GAATCGAAGATAAGAAAACATTGCCTCGATT
66 GAATCGAAGATAAGAAAACATTACCTCGATT
* * *
28033 AAAGGTATTCGATTATTTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTC-
1 AAAGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTCA
*
28097 GAAACTCGAA-ATAA-AAGAATATTACCTCGATT
66 G-AA-TCGAAGATAAGAA-AACATTACCTCGATT
28129 TTAAAGTTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
95 3 0.04
96 74 0.90
97 5 0.06
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (96 bp):
AAAGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTCA
GAATCGAAGATAAGAAAACATTACCTCGATT
Found at i:28388 original size:27 final size:28
Alignment explanation
Indices: 28349--28408 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
28339 AAATGAGACT
28349 TTTTGAATACTCG-GGGGAAAATGGTAA
1 TTTTGAATACTCGAGGGGAAAATGGTAA
* * *
28376 TTTTGGATTCTCGAGGGTAAAATGGTAA
1 TTTTGAATACTCGAGGGGAAAATGGTAA
28404 TTTTG
1 TTTTG
28409 TGAAAATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.37
Consensus pattern (28 bp):
TTTTGAATACTCGAGGGGAAAATGGTAA
Found at i:28465 original size:28 final size:27
Alignment explanation
Indices: 28366--28470 Score: 70
Period size: 29 Copynumber: 3.7 Consensus size: 27
28356 TACTCGGGGG
* *
28366 AAAATGGTAATTTTGGATTCTCGAGGGT
1 AAAATGGTAATTTTAGAATC-CGAGGGT
* **
28394 AAAATGGTAATTTTGTGAAAATTTG-GGGTTT
1 AAAATGGTAA-TTT-T-AGAATCCGAGGG--T
*
28425 AAAATAG-AATTTTAGACATCCGAGGGT
1 AAAATGGTAATTTTAGA-ATCCGAGGGT
28452 AAAATGGTAATTTTTAGAA
1 AAAATGGTAA-TTTTAGAA
28471 AATCGAGTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
27 9 0.16
28 17 0.29
29 19 0.33
30 4 0.07
31 9 0.16
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (27 bp):
AAAATGGTAATTTTAGAATCCGAGGGT
Found at i:28477 original size:29 final size:29
Alignment explanation
Indices: 28386--28477 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
28376 TTTTGGATTC
28386 TCGAGGGTAAAATGGTAATTTTGT-GAAAA
1 TCGAGGGTAAAATGGTAATTTT-TAGAAAA
* * *
28415 TTTG-GGGTTTAAAATAG-AA-TTTTAG-ACA
1 -TCGAGGG--TAAAATGGTAATTTTTAGAAAA
28443 TCCGAGGGTAAAATGGTAATTTTTAGAAAA
1 T-CGAGGGTAAAATGGTAATTTTTAGAAAA
28473 TCGAG
1 TCGAG
28478 TTAAAAAATG
Statistics
Matches: 48, Mismatches: 6, Indels: 17
0.68 0.08 0.24
Matches are distributed among these distances:
27 8 0.17
28 6 0.12
29 20 0.42
30 7 0.15
31 7 0.15
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (29 bp):
TCGAGGGTAAAATGGTAATTTTTAGAAAA
Found at i:28501 original size:58 final size:58
Alignment explanation
Indices: 28386--28583 Score: 163
Period size: 58 Copynumber: 3.4 Consensus size: 58
28376 TTTTGGATTC
* * * *
28386 TCGAGGGTAAAATGGTAATTTTGT-GAAAATTTGGGGTT-TAAAAT-AGAA-TTTTAGACAT
1 TCGAGGGTAAAATGGTAATTTT-TAGAAAA--TCGAGTTAAAAAATGA-AATTTTTGGACAT
*
28444 CCGAGGGTAAAATGGTAATTTTTAGAAAATCGAGTTAAAAAATGAAATTTTTGGACAT
1 TCGAGGGTAAAATGGTAATTTTTAGAAAATCGAGTTAAAAAATGAAATTTTTGGACAT
* * *** * * * * *
28502 TCAAGGGTAAAATGATAATTTTTGAGAGTTTCGAGGTAAAAAATGGAGTTTTTGTAGAT
1 TCGAGGGTAAAATGGTAATTTTT-AGAAAATCGAGTTAAAAAATGAAATTTTTGGACAT
*
28561 TCGGGGGTAAAAAT-GTAATTTTT
1 TCGAGGGT-AAAATGGTAATTTTT
28584 GGAAGTTTTG
Statistics
Matches: 115, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
56 5 0.04
57 8 0.07
58 56 0.49
59 41 0.36
60 5 0.04
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.35
Consensus pattern (58 bp):
TCGAGGGTAAAATGGTAATTTTTAGAAAATCGAGTTAAAAAATGAAATTTTTGGACAT
Found at i:28569 original size:59 final size:58
Alignment explanation
Indices: 28448--28674 Score: 205
Period size: 58 Copynumber: 3.9 Consensus size: 58
28438 AGACATCCGA
*** * * *
28448 GGGT-AAAATGGTAATTTTT-AGAAAATCGAGTTAAAAAATGAAATTTTTGGACATTCAA
1 GGGTAAAAAT-GTAATTTTTGAGAGTTTCGAGGTAAAAAATGGAATTTTTGGA-ATTCAG
* * *
28506 GGGT-AAAATGATAATTTTTGAGAGTTTCGAGGTAAAAAATGGAGTTTTTGTAGATTCGG
1 GGGTAAAAATG-TAATTTTTGAGAGTTTCGAGGTAAAAAATGGAATTTTTGGA-ATTCAG
* * * *
28565 GGGTAAAAATGTAATTTTTG-GAAGTTTTGGGGT-TAAAATGGAATTTTTGGAAGTTTAG
1 GGGTAAAAATGTAATTTTTGAG-AGTTTCGAGGTAAAAAATGGAATTTTTGGAA-TTCAG
* * * *
28623 GGGTAAAAATGTAATTTTGGA-AGTTTAGGGGTCAAAAATGGAATTTTTGGAA
1 GGGTAAAAATGTAATTTTTGAGAGTTTCGAGGTAAAAAATGGAATTTTTGGAA
28675 GTTTGAGGCT
Statistics
Matches: 142, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
57 12 0.08
58 73 0.51
59 51 0.36
60 6 0.04
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGAGAGTTTCGAGGTAAAAAATGGAATTTTTGGAATTCAG
Found at i:28629 original size:58 final size:59
Alignment explanation
Indices: 28479--28729 Score: 230
Period size: 58 Copynumber: 4.3 Consensus size: 59
28469 AAAATCGAGT
* * * *
28479 TAAAAAATGAAATTTTTGGACA-TTCAAGGGT-AAAATGATAATTTTT-GAGAGTTTCGAGG
1 TAAAAAATGGAATTTTTGGA-AGTTCAGGGGTAAAAATG-TAATTTTTGGA-AGTTTAGGGG
* * * *
28538 TAAAAAATGGAGTTTTT-GTAGATTCGGGGGTAAAAATGTAATTTTTGGAAGTTTTGGGG
1 TAAAAAATGGAATTTTTGGAAG-TTCAGGGGTAAAAATGTAATTTTTGGAAGTTTAGGGG
* *
28597 T-TAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGTAA-TTTTGGAAGTTTAGGGG
1 TAAAAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGTAATTTTTGGAAGTTTAGGGG
* * * * ** *
28654 TCAAAAATGGAATTTTTGGAAGTT-TGAGGCTAAAAATATTGTTTTTTTGAAGTTTAGGGG
1 TAAAAAATGGAATTTTTGGAAGTTCAG-GGGTAAAAAT-GTAATTTTTGGAAGTTTAGGGG
*
28714 T-TAAAATGGAATTTTT
1 TAAAAAATGGAATTTTT
28730 AACCAATTTA
Statistics
Matches: 162, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
57 19 0.12
58 61 0.38
59 57 0.35
60 25 0.15
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (59 bp):
TAAAAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGTAATTTTTGGAAGTTTAGGGG
Found at i:28720 original size:30 final size:29
Alignment explanation
Indices: 28579--28719 Score: 119
Period size: 30 Copynumber: 4.8 Consensus size: 29
28569 AAAAATGTAA
* * *
28579 TTTTTGGAAGTTTTGGGGTT-AAAATGGAA
1 TTTTTGGAAGTTTAGGGGTTAAAAATTG-T
28608 TTTTTGGAAGTTTAGGGG-TAAAAA-TGT
1 TTTTTGGAAGTTTAGGGGTTAAAAATTGT
* * * *
28635 AATTTTGGAAGTTTAGGGGTCAAAAATGGAA
1 -TTTTTGGAAGTTTAGGGGTTAAAAATTG-T
* *
28666 TTTTTGGAAGTTT-GAGGCTAAAAATATTGT
1 TTTTTGGAAGTTTAG-GGGTTAAAA-ATTGT
*
28696 TTTTTTGAAGTTTAGGGGTTAAAA
1 TTTTTGGAAGTTTAGGGGTTAAAA
28720 TGGAATTTTT
Statistics
Matches: 89, Mismatches: 15, Indels: 15
0.75 0.13 0.13
Matches are distributed among these distances:
28 19 0.21
29 27 0.30
30 39 0.44
31 4 0.04
ACGTcount: A:0.31, C:0.01, G:0.28, T:0.40
Consensus pattern (29 bp):
TTTTTGGAAGTTTAGGGGTTAAAAATTGT
Found at i:28729 original size:30 final size:29
Alignment explanation
Indices: 28481--28729 Score: 197
Period size: 29 Copynumber: 8.5 Consensus size: 29
28471 AATCGAGTTA
* * *
28481 AAAAATGAAATTTTTGGACA-TTCAAGGGT
1 AAAAATGGAATTTTTGGA-AGTTTAGGGGT
* * *
28510 -AAAATGATAATTTTT-GAGAGTTTCGAGGT
1 AAAAATG-GAATTTTTGGA-AGTTTAGGGGT
* * **
28539 AAAAAATGGAGTTTTT-GTAGATTCGGGGGT
1 -AAAAATGGAATTTTTGGAAG-TTTAGGGGT
* *
28569 AAAAATGTAATTTTTGGAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAAGTTTAGGGGT
*
28598 TAAAATGGAATTTTTGGAAGTTTAGGGGT
1 AAAAATGGAATTTTTGGAAGTTTAGGGGT
*
28627 AAAAATGTAA-TTTTGGAAGTTTAGGGGT
1 AAAAATGGAATTTTTGGAAGTTTAGGGGT
*
28655 CAAAAATGGAATTTTTGGAAGTTT-GAGGCT
1 -AAAAATGGAATTTTTGGAAGTTTAG-GGGT
* * *
28685 AAAAATATTG-TTTTTTTGAAGTTTAGGGGT
1 -AAAA-ATGGAATTTTTGGAAGTTTAGGGGT
*
28715 TAAAATGGAATTTTT
1 AAAAATGGAATTTTT
28730 AACCAATTTA
Statistics
Matches: 176, Mismatches: 32, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
28 30 0.17
29 86 0.49
30 50 0.28
31 10 0.06
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTAGGGGT
Found at i:30555 original size:6 final size:6
Alignment explanation
Indices: 30544--30613 Score: 72
Period size: 6 Copynumber: 12.0 Consensus size: 6
30534 TAATAATTTT
** * *
30544 TTTAAA TTTAAA AATAAA TTTAAA TTTAAA TTCAAA TTTAAA -ATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
30591 TCTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
30614 AAGGGCCCGA
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
5 8 0.16
6 43 0.84
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:30597 original size:17 final size:17
Alignment explanation
Indices: 30546--30613 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
30536 ATAATTTTTT
*
30546 TAAATTTAAAAATAAATT
1 TAAATTT-AAAATAAATC
30564 TAAATTT-AAAT---TC
1 TAAATTTAAAATAAATC
30577 -AAATTTAAAATAAATC
1 TAAATTTAAAATAAATC
*
30593 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATC
30610 TAAA
1 TAAA
30614 AAGGGCCCGA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
12 6 0.14
13 5 0.12
16 6 0.14
17 19 0.44
18 7 0.16
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTTAAAATAAATC
Found at i:33813 original size:22 final size:21
Alignment explanation
Indices: 33777--33834 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
33767 TGTTTAAATT
33777 TTTTTTTACTGTTTTG-GTTG
1 TTTTTTTACTGTTTTGTGTTG
*
33797 CTTTTTTTATTGTTTTTGTGTTG
1 -TTTTTTTACTG-TTTTGTGTTG
* *
33820 TTTTTCTACTTTTTT
1 TTTTTTTACTGTTTT
33835 TTTTATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 14 0.45
22 13 0.42
23 4 0.13
ACGTcount: A:0.05, C:0.07, G:0.14, T:0.74
Consensus pattern (21 bp):
TTTTTTTACTGTTTTGTGTTG
Found at i:33835 original size:23 final size:22
Alignment explanation
Indices: 33788--33836 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
33778 TTTTTTACTG
*
33788 TTTTGGTTGCTTTTTTTATTGT
1 TTTTGGTTGCTTTTTCTATTGT
*
33810 TTTTGTGTTG-TTTTTCTACTTTT
1 TTTTG-GTTGCTTTTTCTA-TTGT
33833 TTTT
1 TTTT
33837 TTATTATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.04, C:0.06, G:0.14, T:0.76
Consensus pattern (22 bp):
TTTTGGTTGCTTTTTCTATTGT
Found at i:33938 original size:12 final size:12
Alignment explanation
Indices: 33793--33943 Score: 51
Period size: 12 Copynumber: 12.6 Consensus size: 12
33783 TACTGTTTTG
33793 GTTGCTTTTT-TT
1 GTTG-TTTTTGTT
*
33805 ATTGTTTTTG-T
1 GTTGTTTTTGTT
*
33816 GTTGTTTTTCTACT
1 GTTGTTTTTGT--T
* * *
33830 TTTTTTTTTATT
1 GTTGTTTTTGTT
* *
33842 ATTGTTTTGGTT
1 GTTGTTTTTGTT
* *
33854 GTTG-ATTTGGT
1 GTTGTTTTTGTT
*
33865 GCTGTTTTT-TCT
1 GTTGTTTTTGT-T
* *
33877 ATTATTTTTGTT
1 GTTGTTTTTGTT
* *
33889 GCTATTTTTGTT
1 GTTGTTTTTGTT
* *
33901 GTTG-TTTCGCT
1 GTTGTTTTTGTT
* **
33912 GTTATTTTTACT
1 GTTGTTTTTGTT
33924 GTTGTTTTTGTT
1 GTTGTTTTTGTT
33936 GTTAGTTT
1 GTT-GTTT
33944 AGTTGTTTGG
Statistics
Matches: 98, Mismatches: 32, Indels: 17
0.67 0.22 0.12
Matches are distributed among these distances:
11 29 0.30
12 55 0.56
13 5 0.05
14 9 0.09
ACGTcount: A:0.07, C:0.06, G:0.18, T:0.69
Consensus pattern (12 bp):
GTTGTTTTTGTT
Done.