Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014666.1 Kokia drynarioides strain JFW-HI SEQ_129705, 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: 146800
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4078 original size:28 final size:27
Alignment explanation
Indices: 4038--4164 Score: 110
Period size: 28 Copynumber: 4.6 Consensus size: 27
4028 TGAAGCGAAA
* * *
4038 GGCTAGGATAGAGCAATGTTCTGATTTT
1 GGCTCGGATAGAGCAATATTCT-ATTCT
*
4066 GGCTCGGATAGAGCGATATTCTGATTCT
1 GGCTCGGATAGAGCAATATTCT-ATTCT
* * **
4094 AGCTTGGATAGAGTGATATTCTATATCT
1 GGCTCGGATAGAGCAATATTCTAT-TCT
* *
4122 GGCTCGGGTAGAGCATTATTCTATTTCT
1 GGCTCGGATAGAGCAATATTCTA-TTCT
* *
4150 GGTTCGGGTAGAGCA
1 GGCTCGGATAGAGCA
4165 TTACTTTGAA
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
27 2 0.02
28 80 0.96
29 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (27 bp):
GGCTCGGATAGAGCAATATTCTATTCT
Found at i:4162 original size:56 final size:56
Alignment explanation
Indices: 4102--4311 Score: 178
Period size: 56 Copynumber: 3.8 Consensus size: 56
4092 CTAGCTTGGA
*
4102 TAGAGTGATATTCTATATCTGGCTCGGGTAGAGCATTATTCTATTTCTGGTTCGGG
1 TAGAGCGATATTCTATATCTGGCTCGGGTAGAGCATTATTCTATTTCTGGTTCGGG
* * * * * *
4158 TAGAGC-ATTACTT-TGA-ATTTGGATCGAGTAGAGAATTATTCTATTTCT-ATCTCCGG
1 TAGAGCGA-TA-TTCT-ATATCTGGCTCGGGTAGAGCATTATTCTATTTCTGGT-TCGGG
* * * * *
4214 TAGAGCGTTACTCTAAATCTAGCTTGGGTAGAGCATTATTCTATTTCTGGCTT-GGG
1 TAGAGCGATATTCTATATCTGGCTCGGGTAGAGCATTATTCTATTTCTGG-TTCGGG
* * * * **
4270 TAGAGCGTTATTCTATTTTTGGCTTGGAAAGAGCATTATTCT
1 TAGAGCGATATTCTATATCTGGCTCGGGTAGAGCATTATTCT
4312 GTATCTAGGC
Statistics
Matches: 121, Mismatches: 24, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
55 4 0.03
56 112 0.93
57 4 0.03
58 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (56 bp):
TAGAGCGATATTCTATATCTGGCTCGGGTAGAGCATTATTCTATTTCTGGTTCGGG
Found at i:4165 original size:28 final size:28
Alignment explanation
Indices: 4110--4311 Score: 155
Period size: 28 Copynumber: 7.2 Consensus size: 28
4100 GATAGAGTGA
* *
4110 TATTCTATATCTGGCTCGGGTAGAGCAT
1 TATTCTATTTCTGGTTCGGGTAGAGCAT
4138 TATTCTATTTCTGGTTCGGGTAGAGCAT
1 TATTCTATTTCTGGTTCGGGTAGAGCAT
* * * *
4166 TACTT-TGAATT-TGGATCGAGTAGAGAAT
1 TA-TTCT-ATTTCTGGTTCGGGTAGAGCAT
* * *
4194 TATTCTATTTCT-ATCTCCGGTAGAGCGT
1 TATTCTATTTCTGGT-TCGGGTAGAGCAT
* ** *
4222 TACTCTAAATCTAGCTT-GGGTAGAGCAT
1 TATTCTATTTCT-GGTTCGGGTAGAGCAT
*
4250 TATTCTATTTCTGGCTT-GGGTAGAGCGT
1 TATTCTATTTCTGG-TTCGGGTAGAGCAT
* **
4278 TATTCTATTTTTGGCTT-GGAAAGAGCAT
1 TATTCTATTTCTGG-TTCGGGTAGAGCAT
4306 TATTCT
1 TATTCT
4312 GTATCTAGGC
Statistics
Matches: 138, Mismatches: 28, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
27 6 0.04
28 125 0.91
29 6 0.04
30 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (28 bp):
TATTCTATTTCTGGTTCGGGTAGAGCAT
Found at i:6183 original size:25 final size:25
Alignment explanation
Indices: 6149--6199 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
6139 TCTTTAAGGC
6149 CGATTGAGGCCTAAAGGTTAGCTAA
1 CGATTGAGGCCTAAAGGTTAGCTAA
6174 CGATTGAGGCCTAAAGGTTAGCTAA
1 CGATTGAGGCCTAAAGGTTAGCTAA
6199 C
1 C
6200 ATACTTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (25 bp):
CGATTGAGGCCTAAAGGTTAGCTAA
Found at i:10598 original size:21 final size:21
Alignment explanation
Indices: 10566--10605 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
10556 AAAGTTAGAG
10566 TCCTCAATTGACCTTTCAAGT
1 TCCTCAATTGACCTTTCAAGT
10587 TCCT-AATATGACCTTTCAA
1 TCCTCAAT-TGACCTTTCAA
10606 AATTGGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.38
Consensus pattern (21 bp):
TCCTCAATTGACCTTTCAAGT
Found at i:11428 original size:51 final size:50
Alignment explanation
Indices: 11361--11484 Score: 178
Period size: 50 Copynumber: 2.5 Consensus size: 50
11351 TATGAAAATT
* * *
11361 AATTAC-TAATGCATGACTTTATTTAAGATGCAAACTTTAACTATCATGGG
1 AATTACATAATGCATGACATTATTTAAGATGCAAA-TTTAACTAACATGAG
* *
11411 AATTACATAATGCATGACATAATTTATGATGCAAATTTAACTAACATGAG
1 AATTACATAATGCATGACATTATTTAAGATGCAAATTTAACTAACATGAG
*
11461 AGTTACATAATGCATGACATTATT
1 AATTACATAATGCATGACATTATT
11485 AAATGTAGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 41 0.62
51 25 0.38
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (50 bp):
AATTACATAATGCATGACATTATTTAAGATGCAAATTTAACTAACATGAG
Found at i:15530 original size:3 final size:3
Alignment explanation
Indices: 15522--15561 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
15512 TGAAATATAG
15522 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
15562 TAAATGAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:39716 original size:18 final size:18
Alignment explanation
Indices: 39681--39718 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
39671 ATACATTTCA
*
39681 TTTAGTTGTCATTGCATT
1 TTTAGTTGTCATTACATT
39699 TTTAGTTGTC-TCTACATT
1 TTTAGTTGTCAT-TACATT
39717 TT
1 TT
39719 ATTTGTTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.16, C:0.13, G:0.13, T:0.58
Consensus pattern (18 bp):
TTTAGTTGTCATTACATT
Found at i:43933 original size:18 final size:18
Alignment explanation
Indices: 43912--43959 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
43902 ACATAATCAG
43912 ATGCAACCACAAGCTAGA
1 ATGCAACCACAAGCTAGA
43930 ATGCAACCACAAGCTAGA
1 ATGCAACCACAAGCTAGA
43948 ATGCAACCACAA
1 ATGCAACCACAA
43960 TAGACTGTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.46, C:0.29, G:0.15, T:0.10
Consensus pattern (18 bp):
ATGCAACCACAAGCTAGA
Found at i:54787 original size:20 final size:20
Alignment explanation
Indices: 54762--54805 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
54752 TGTCAACACA
54762 TTTTTACATTTACTT-TTATC
1 TTTTTACATTTACTTATT-TC
*
54782 TTTTTACTTTTACTTATTTC
1 TTTTTACATTTACTTATTTC
54802 TTTT
1 TTTT
54806 AAGTCTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTACATTTACTTATTTC
Found at i:54806 original size:13 final size:15
Alignment explanation
Indices: 54769--54806 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
54759 ACATTTTTAC
54769 ATTTACTTTTATCTT
1 ATTTACTTTTATCTT
54784 -TTTACTTTTA-CTT
1 ATTTACTTTTATCTT
54797 ATTT-CTTTTA
1 ATTTACTTTTA
54807 AGTCTTATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTACTTTTATCTT
Found at i:57111 original size:18 final size:18
Alignment explanation
Indices: 57088--57136 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
57078 ATGCATTTCA
57088 TTGTCATTGCATTGTTTT
1 TTGTCATTGCATTGTTTT
57106 TTGTCATTGCATTGTTTT
1 TTGTCATTGCATTGTTTT
57124 TTGTCATTGCATT
1 TTGTCATTGCATT
57137 TTTCCTGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.59
Consensus pattern (18 bp):
TTGTCATTGCATTGTTTT
Found at i:57755 original size:15 final size:15
Alignment explanation
Indices: 57737--57767 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
57727 AAAATCACAA
57737 AAAGAAAAAAAAAAG
1 AAAGAAAAAAAAAAG
*
57752 AAAGAAAAAGAAAAG
1 AAAGAAAAAAAAAAG
57767 A
1 A
57768 GAAAAGGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAAAAG
Found at i:57766 original size:11 final size:11
Alignment explanation
Indices: 57735--57781 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
57725 AAAAAATCAC
*
57735 AAAAAGAAAAA
1 AAAAAGAAAAG
57746 AAAAAG-AAAG
1 AAAAAGAAAAG
57756 AAAAAGAAAAG
1 AAAAAGAAAAG
*
57767 AGAAAAGGAAAG
1 A-AAAAGAAAAG
57779 AAA
1 AAA
57782 TACATTTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 9 0.28
11 13 0.41
12 10 0.31
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:79075 original size:17 final size:17
Alignment explanation
Indices: 79053--79092 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
79043 TTAGTTTTCA
*
79053 TACATTTTTATTGT-GTT
1 TACATTTTAATTGTCG-T
79070 TACATTTTAATTGTCGT
1 TACATTTTAATTGTCGT
79087 TACATT
1 TACATT
79093 CATTTTAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.57
Consensus pattern (17 bp):
TACATTTTAATTGTCGT
Found at i:89350 original size:13 final size:13
Alignment explanation
Indices: 89332--89381 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
89322 AAACTATTTC
*
89332 ATTAATAAATTGG
1 ATTAATTAATTGG
89345 ATTAATTAATTGG
1 ATTAATTAATTGG
89358 -TTAATTAATTGG
1 ATTAATTAATTGG
*
89370 GTTAATTTAATT
1 ATTAA-TTAATT
89382 AATTTAACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 12 0.35
13 16 0.47
14 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (13 bp):
ATTAATTAATTGG
Found at i:89367 original size:25 final size:26
Alignment explanation
Indices: 89333--89381 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
89323 AACTATTTCA
89333 TTAATAAATTGGATTAA-TTAATTGG
1 TTAATAAATTGGATTAATTTAATTGG
* *
89358 TTAATTAATTGGGTTAATTTAATT
1 TTAATAAATTGGATTAATTTAATT
89382 AATTTAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (26 bp):
TTAATAAATTGGATTAATTTAATTGG
Found at i:92989 original size:21 final size:21
Alignment explanation
Indices: 92947--92995 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
92937 TGAGACAATA
*
92947 CTACCAAAACAAGTATGACTT
1 CTACCGAAACAAGTATGACTT
*
92968 CTACCGAAACATGTCATG-CTT
1 CTACCGAAACAAGT-ATGACTT
*
92989 CCACCGA
1 CTACCGA
92996 TACTAAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.35, C:0.31, G:0.12, T:0.22
Consensus pattern (21 bp):
CTACCGAAACAAGTATGACTT
Found at i:93331 original size:20 final size:20
Alignment explanation
Indices: 93308--93356 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
93298 TTCATCATAT
93308 AACACAAAATGCAATCAATC
1 AACACAAAATGCAATCAATC
93328 AACACAAAATGCAATCAATC
1 AACACAAAATGCAATCAATC
93348 AACACAAAA
1 AACACAAAA
93357 CAAACAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.59, C:0.24, G:0.04, T:0.12
Consensus pattern (20 bp):
AACACAAAATGCAATCAATC
Found at i:94765 original size:20 final size:19
Alignment explanation
Indices: 94711--94766 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
94701 AAATGTTTAT
*
94711 CTTTAACATTAAATTAA-A
1 CTTTAATATTAAATTAATA
94729 -TTTAATATTAAGA-TAATCA
1 CTTTAATATTAA-ATTAAT-A
94748 CTTTAATATTAAATTAATA
1 CTTTAATATTAAATTAATA
94767 AAATACTCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
17 13 0.41
18 1 0.03
19 3 0.09
20 15 0.47
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (19 bp):
CTTTAATATTAAATTAATA
Found at i:94797 original size:17 final size:17
Alignment explanation
Indices: 94775--94808 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
94765 TAAAATACTC
94775 TTAAAA-TAAGTATTAAA
1 TTAAAATTAA-TATTAAA
94792 TTAAAATTAATATTAAA
1 TTAAAATTAATATTAAA
94809 CTATTACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TTAAAATTAATATTAAA
Found at i:96007 original size:17 final size:17
Alignment explanation
Indices: 95985--96024 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
95975 TGTATTGCTC
*
95985 GCAATGTAAACGTTCTT
1 GCAATGAAAACGTTCTT
96002 GCAATGAAAACGTTCTT
1 GCAATGAAAACGTTCTT
*
96019 ACAATG
1 GCAATG
96025 CCACTTATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (17 bp):
GCAATGAAAACGTTCTT
Found at i:110257 original size:41 final size:41
Alignment explanation
Indices: 110147--110280 Score: 117
Period size: 41 Copynumber: 3.2 Consensus size: 41
110137 TAAACATATA
* * * *
110147 CTCATGCTCATTTAGAGTCATGAGTCTTACTTGAACACATT
1 CTCATGCTCCTTTTGAGTCATGAGTCTTCCTTTAACACATT
* * ** **
110188 CTCATTCTCAC-CTTGACACATGAGTCTTCCTTTAACATTTT
1 CTCATGCTC-CTTTTGAGTCATGAGTCTTCCTTTAACACATT
* * *
110229 CTCATGCTCCTTTTGAGTCACGAGTCTTCCTTTTATATAAATT
1 CTCATGCTCCTTTTGAGTCATGAGTCTTCC-TTTA-ACACATT
110272 CTCATGCTC
1 CTCATGCTC
110281 AACCCAATAC
Statistics
Matches: 71, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
40 1 0.01
41 53 0.75
42 4 0.06
43 13 0.18
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.40
Consensus pattern (41 bp):
CTCATGCTCCTTTTGAGTCATGAGTCTTCCTTTAACACATT
Found at i:111258 original size:16 final size:17
Alignment explanation
Indices: 111228--111260 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
111218 TCCGTCTAGC
111228 ACTACTTTAGCCCCTTT
1 ACTACTTTAGCCCCTTT
*
111245 ACTA-TTTAGTCCCTTT
1 ACTACTTTAGCCCCTTT
111261 TTCTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.18, C:0.30, G:0.06, T:0.45
Consensus pattern (17 bp):
ACTACTTTAGCCCCTTT
Found at i:114076 original size:22 final size:23
Alignment explanation
Indices: 114048--114090 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
114038 AGAAAAAAAG
114048 AAAAGAAAAATGAGT-AGAAACA
1 AAAAGAAAAATGAGTAAGAAACA
**
114070 AAAAGAATCATGAGTAAGAAA
1 AAAAGAAAAATGAGTAAGAAA
114091 ACATGTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.65, C:0.05, G:0.19, T:0.12
Consensus pattern (23 bp):
AAAAGAAAAATGAGTAAGAAACA
Found at i:137177 original size:159 final size:159
Alignment explanation
Indices: 136888--137210 Score: 592
Period size: 159 Copynumber: 2.0 Consensus size: 159
136878 AACCTAAAGT
*
136888 ATTTAGTGGGTGGATTATTATGGAATGTATTGATTAAATGAGATTAATTAAGGTTGAGTAAATGG
1 ATTTAGTGGGTGGATTATTATGGAATGTATTGATTAAATGAGATTAATTAAGGTCGAGTAAATGG
* *
136953 TTTATTATGTTAATCATGAAAGTCTTAAAATTTACAAATTTTTCATTAAGTATATATATGAATTA
66 TTTATTAAGTTAATCATGAAAGTCTTAAAATTTACAAATTTGTCATTAAGTATATATATGAATTA
137018 AATGAAAGAAAATGAGAAAAATTCACCTA
131 AATGAAAGAAAATGAGAAAAATTCACCTA
137047 ATTTAGTGGGTGGATTATTATGGAATGTATTGATTAAATGAGATTAATTAAGGTCGAGTAAATGG
1 ATTTAGTGGGTGGATTATTATGGAATGTATTGATTAAATGAGATTAATTAAGGTCGAGTAAATGG
137112 TTTATTAAGTTAATCATGAAAGTCTTAAAATTTACAAATTTGTCATTAAGTATATATATGAATTA
66 TTTATTAAGTTAATCATGAAAGTCTTAAAATTTACAAATTTGTCATTAAGTATATATATGAATTA
* **
137177 AATGACAGAAAATGAGAAAAATTCGGCTA
131 AATGAAAGAAAATGAGAAAAATTCACCTA
137206 ATTTA
1 ATTTA
137211 TCATCTTCTT
Statistics
Matches: 158, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
159 158 1.00
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.37
Consensus pattern (159 bp):
ATTTAGTGGGTGGATTATTATGGAATGTATTGATTAAATGAGATTAATTAAGGTCGAGTAAATGG
TTTATTAAGTTAATCATGAAAGTCTTAAAATTTACAAATTTGTCATTAAGTATATATATGAATTA
AATGAAAGAAAATGAGAAAAATTCACCTA
Found at i:137802 original size:16 final size:17
Alignment explanation
Indices: 137781--137813 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
137771 ACCGATCGTG
137781 AAAAAA-GAAAATTAGC
1 AAAAAAGGAAAATTAGC
137797 AAAAAAGGAAAATTAGC
1 AAAAAAGGAAAATTAGC
137814 GGAATAGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.67, C:0.06, G:0.15, T:0.12
Consensus pattern (17 bp):
AAAAAAGGAAAATTAGC
Found at i:138052 original size:26 final size:26
Alignment explanation
Indices: 138023--138105 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
138013 ACGTGTCATC
138023 ATGAGTATATGAATCCTTTACGGATT
1 ATGAGTATATGAATCCTTTACGGATT
* * * *
138049 ATGAGGTCTGATGACTACATTT-C--ATC
1 ATGA-GTAT-ATGAAT-CCTTTACGGATT
* *
138075 GTGAGTATATGAATCCTTTATGGATT
1 ATGAGTATATGAATCCTTTACGGATT
138101 ATGAG
1 ATGAG
138106 GTCCGATTAC
Statistics
Matches: 40, Mismatches: 11, Indels: 12
0.63 0.17 0.19
Matches are distributed among these distances:
23 4 0.10
24 5 0.12
25 3 0.08
26 15 0.38
27 3 0.08
28 6 0.15
29 4 0.10
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (26 bp):
ATGAGTATATGAATCCTTTACGGATT
Found at i:138080 original size:52 final size:52
Alignment explanation
Indices: 138000--138186 Score: 302
Period size: 52 Copynumber: 3.6 Consensus size: 52
137990 TAAATGAAAA
*
138000 AGGTCCGATGACTACGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
138052 AGGTCTGATGACTACATTTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
138104 AGGTCCGATTACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
138156 AGGTCTGATGACTACGTGTCATTGTGAGTAT
1 AGGTCCGATGACTACGTGTCATCGTGAGTAT
138187 GTGATTCTTT
Statistics
Matches: 122, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 122 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:139408 original size:13 final size:12
Alignment explanation
Indices: 139366--139406 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
139356 ATGTTATTTT
139366 AAAAAAAATTC-
1 AAAAAAAATTCA
*
139377 AAAAAAAA-TGA
1 AAAAAAAATTCA
139388 AAAAAATAATTCA
1 AAAAAA-AATTCA
139401 AAAAAA
1 AAAAAA
139407 TAGTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 1 0.04
11 14 0.56
12 2 0.08
13 8 0.32
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:139594 original size:42 final size:42
Alignment explanation
Indices: 139536--139641 Score: 162
Period size: 42 Copynumber: 2.6 Consensus size: 42
139526 CACACTGGTG
* *
139536 TGTGTGAGACTA--TGCCCCACACTCTCTGGGCACACAGGCA
1 TGTGTAAGACTATGTGCCCCACACTCCCTGGGCACACAGGCA
* *
139576 TGTGTAAGACTTTGTGCCCCACACTCCCTGGGCACACGGGCA
1 TGTGTAAGACTATGTGCCCCACACTCCCTGGGCACACAGGCA
139618 TGTGTAAGACTATGTGCCCCACAC
1 TGTGTAAGACTATGTGCCCCACAC
139642 GACCTTGCAT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 10 0.17
42 49 0.83
ACGTcount: A:0.22, C:0.32, G:0.25, T:0.22
Consensus pattern (42 bp):
TGTGTAAGACTATGTGCCCCACACTCCCTGGGCACACAGGCA
Found at i:139703 original size:41 final size:39
Alignment explanation
Indices: 139630--139726 Score: 131
Period size: 39 Copynumber: 2.4 Consensus size: 39
139620 TGTAAGACTA
* * *
139630 TGTGCCCCACACGACCTTGCATACAGGCGTGTGTGAGAT
1 TGTGTCCCACACGACCTTACACACAGGCGTGTGTGAGAT
*
139669 TGTGTCCCACACGACCTTACACACCGGCGTGTGTGAGAT
1 TGTGTCCCACACGACCTTACACACAGGCGTGTGTGAGAT
*
139708 TGTGTGCCCCACATGACCT
1 TGTGT--CCCACACGACCT
139727 CGCACATGGG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 40 0.78
41 11 0.22
ACGTcount: A:0.20, C:0.31, G:0.26, T:0.24
Consensus pattern (39 bp):
TGTGTCCCACACGACCTTACACACAGGCGTGTGTGAGAT
Found at i:140113 original size:6 final size:6
Alignment explanation
Indices: 140102--140158 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 6
140092 TTTCATTTTA
* *
140102 TTTATT TTTATT TTTATT TTTGTGT TTTATGT TTTGTGT TTTA-T TTTA-T
1 TTTATT TTTATT TTTATT TTTAT-T TTTAT-T TTTAT-T TTTATT TTTATT
140151 TTTATT TT
1 TTTATT TT
140159 ATTATGCACT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
5 10 0.22
6 19 0.42
7 16 0.36
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:140122 original size:22 final size:22
Alignment explanation
Indices: 140074--140121 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
140064 AATCAAAGTT
*
140074 ATTTCATTTAGTTTTATATTTC
1 ATTTTATTTAGTTTTATATTTC
* *
140096 ATTTTATTTATTTTTAT-TTTT
1 ATTTTATTTAGTTTTATATTTC
140117 ATTTT
1 ATTTT
140122 TGTGTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (22 bp):
ATTTTATTTAGTTTTATATTTC
Found at i:140136 original size:14 final size:13
Alignment explanation
Indices: 140102--140148 Score: 69
Period size: 14 Copynumber: 3.6 Consensus size: 13
140092 TTTCATTTTA
*
140102 TTTATTTTTAT-T
1 TTTATTTTTGTGT
140114 TTTATTTTTGTGT
1 TTTATTTTTGTGT
140127 TTTATGTTTTGTGT
1 TTTAT-TTTTGTGT
140141 TTTATTTT
1 TTTATTTT
140149 ATTTTATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 10 0.31
13 9 0.28
14 13 0.41
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.79
Consensus pattern (13 bp):
TTTATTTTTGTGT
Found at i:143220 original size:49 final size:49
Alignment explanation
Indices: 143164--143282 Score: 175
Period size: 49 Copynumber: 2.4 Consensus size: 49
143154 TCTACAATTT
* *
143164 TGGTGGCTTGACCACAATATTTTGTATTTGGCAGCTTGACTGCATTATA
1 TGGTGGCTTGACCACAATATTCTGTATCTGGCAGCTTGACTGCATTATA
* *
143213 TGGTGGCTTGACCACAATATTCTGTATCTGGCAGCTTGACTGCTTTATC
1 TGGTGGCTTGACCACAATATTCTGTATCTGGCAGCTTGACTGCATTATA
* * *
143262 TGGTGACTTGCCCACATTATT
1 TGGTGGCTTGACCACAATATT
143283 GGTGTATTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 63 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (49 bp):
TGGTGGCTTGACCACAATATTCTGTATCTGGCAGCTTGACTGCATTATA
Found at i:143442 original size:15 final size:15
Alignment explanation
Indices: 143414--143457 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
143404 CATAATGATG
* *
143414 ATGCAAGCATGGATA
1 ATGCGAGCAAGGATA
* *
143429 GTGCGAGCACGGATA
1 ATGCGAGCAAGGATA
143444 ATGCGAGCAAGGAT
1 ATGCGAGCAAGGAT
143458 GAAGGACAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.34, C:0.16, G:0.34, T:0.16
Consensus pattern (15 bp):
ATGCGAGCAAGGATA
Done.