Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014598.1 Kokia drynarioides strain JFW-HI SEQ_129637, 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: 17977
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:178 original size:48 final size:48
Alignment explanation
Indices: 117--211 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
107 TTGTGGATTT
* * *
117 GGTTTATGAATTGGTGGAGGTTGTGGTTTTGGTTCAGAGGGCAAGTTA
1 GGTTTAGGAATTGGTGGAGGTTGCGGCTTTGGTTCAGAGGGCAAGTTA
* * *
165 GGTTTAGGCATTGGTGGTGGTTGCGGCTTTGGTTCAGAGGGCGAGTT
1 GGTTTAGGAATTGGTGGAGGTTGCGGCTTTGGTTCAGAGGGCAAGTT
212 TAGTGGTGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.15, C:0.07, G:0.42, T:0.36
Consensus pattern (48 bp):
GGTTTAGGAATTGGTGGAGGTTGCGGCTTTGGTTCAGAGGGCAAGTTA
Found at i:291 original size:84 final size:84
Alignment explanation
Indices: 130--288 Score: 250
Period size: 84 Copynumber: 1.9 Consensus size: 84
120 TTATGAATTG
* * *
130 GTGGAGGTTGTGGTTTTGGTTCAGAGGGCAAGTTAGGTTTAGGCATTGGTGGTGGTTGCGGCTTT
1 GTGGAGGTTGTGGTCTTGGTTCAGAGGGCAAGTTAGGTTTAGGCACTGGTAGTGGTTGCGGCTTT
195 GGTTCAGAGGGCGAGTTTA
66 GGTTCAGAGGGCGAGTTTA
* *
214 GTGGTGGTTGTGGTCTTGGTTCAGAGGGC-AGATTAGGTTTAGGCACTGGTAGTGGTTGCGGTTT
1 GTGGAGGTTGTGGTCTTGGTTCAGAGGGCAAG-TTAGGTTTAGGCACTGGTAGTGGTTGCGGCTT
278 TGGTTCA-AGGG
65 TGGTTCAGAGGG
289 GCGGATTTGG
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
83 6 0.09
84 63 0.91
ACGTcount: A:0.14, C:0.09, G:0.43, T:0.35
Consensus pattern (84 bp):
GTGGAGGTTGTGGTCTTGGTTCAGAGGGCAAGTTAGGTTTAGGCACTGGTAGTGGTTGCGGCTTT
GGTTCAGAGGGCGAGTTTA
Found at i:750 original size:45 final size:46
Alignment explanation
Indices: 655--754 Score: 166
Period size: 46 Copynumber: 2.2 Consensus size: 46
645 TATCTCATGA
* *
655 TTTGATTTTTGAAATTTGAATTTATTAGTTGTTTTTAAGATACTAAT
1 TTTG-TTTTAGAAATTTGAATTTATTAGTTGTTTTTAAGATAATAAT
702 TTTGTTTTAGAAATTTGAATTTATTAGTT-TTTTTAAGATAATAAT
1 TTTGTTTTAGAAATTTGAATTTATTAGTTGTTTTTAAGATAATAAT
747 TTTGTTTT
1 TTTGTTTT
755 TATTTAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
45 23 0.45
46 24 0.47
47 4 0.08
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.58
Consensus pattern (46 bp):
TTTGTTTTAGAAATTTGAATTTATTAGTTGTTTTTAAGATAATAAT
Found at i:1967 original size:28 final size:27
Alignment explanation
Indices: 1927--2026 Score: 112
Period size: 29 Copynumber: 3.5 Consensus size: 27
1917 TGGGGTTTTT
*
1927 AAATGGAATTTTTAGACATTCGGGGGTA
1 AAATGGAATTTTTGGA-ATTCGGGGGTA
* *
1955 AAATGGTAA-TTTTGGAAAAATCGGGGTTA
1 AAATGG-AATTTTTGG--AATTCGGGGGTA
1984 AAATGGAATTTTTGGAAGTTCGGGGGTA
1 AAATGGAATTTTTGGAA-TTCGGGGGTA
2012 AAATGGTAATTTTTG
1 AAATGG-AATTTTTG
2027 TAAAAATTGA
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
27 2 0.03
28 27 0.44
29 31 0.51
30 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (27 bp):
AAATGGAATTTTTGGAATTCGGGGGTA
Found at i:1978 original size:29 final size:30
Alignment explanation
Indices: 1946--2150 Score: 135
Period size: 29 Copynumber: 7.0 Consensus size: 30
1936 TTTTAGACAT
1946 TCGGGGGTAAAATGGTAA-TTTTGGAAAAA
1 TCGGGGGTAAAATGGTAATTTTTGGAAAAA
* **
1975 TCGGGGTTAAAATGG-AATTTTTGG-AAGT
1 TCGGGGGTAAAATGGTAATTTTTGGAAAAA
*
2003 TCGGGGGTAAAATGGTAATTTTTGTAAAAA
1 TCGGGGGTAAAATGGTAATTTTTGGAAAAA
* * * **
2033 T-TGAGGTCAAAAATGG-AATTTTTTG-AAGT
1 TCGGGGGT--AAAATGGTAATTTTTGGAAAAA
** *
2062 TCAAGGGTAAAATGGTATTTTTTTGGAAAAA
1 TCGGGGGTAAAATGGTA-ATTTTTGGAAAAA
* * **
2093 TC-AGAGTCCAAAATGG-AATTTTTGG-AAGT
1 TCGGGGGT--AAAATGGTAATTTTTGGAAAAA
*
2122 TCGAGGGT--AATGGTAATTTTTGGAAAAA
1 TCGGGGGTAAAATGGTAATTTTTGGAAAAA
2150 T
1 T
2151 TAGGGTCAAA
Statistics
Matches: 135, Mismatches: 27, Indels: 29
0.71 0.14 0.15
Matches are distributed among these distances:
26 5 0.04
27 9 0.07
28 28 0.21
29 40 0.30
30 34 0.25
31 12 0.09
32 7 0.05
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (30 bp):
TCGGGGGTAAAATGGTAATTTTTGGAAAAA
Found at i:2070 original size:59 final size:59
Alignment explanation
Indices: 1927--2204 Score: 297
Period size: 57 Copynumber: 4.8 Consensus size: 59
1917 TGGGGTTTTT
* * * * *
1927 AAATGGAATTTTTAGACA-TTCGGGGGTAAAATGGTAA-TTTTGGAAAAATCGGGGT-TA
1 AAATGGAATTTTTGGA-AGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATTGAGGTCAA
* *
1984 AAATGGAATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGTAAAAATTGAGGTCAA
1 AAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATTGAGGTCAA
* * * * *
2043 AAATGGAATTTTTTGAAGTTCAAGGGTAAAATGGTATTTTTTTGGAAAAA-TCAGAGTCCA
1 AAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTA-ATTTTTGGAAAAATTGAG-GTCAA
2103 AAATGGAATTTTTGGAAGTTCGAGGGT--AATGGTAATTTTTGGAAAAATT-AGGGTCAA
1 AAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATTGA-GGTCAA
* *
2160 AAAT-GAAATTTTGGAAAGCTT-GAGGGCT-AAATTGTAATTTTTGGA
1 AAATGGAATTTTTGG-AAG-TTCGAGGG-TAAAATGGTAATTTTTGGA
2205 CTGTGTAGGG
Statistics
Matches: 192, Mismatches: 18, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
56 10 0.05
57 63 0.33
58 27 0.14
59 52 0.27
60 40 0.21
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.34
Consensus pattern (59 bp):
AAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATTGAGGTCAA
Found at i:2201 original size:117 final size:117
Alignment explanation
Indices: 1950--2175 Score: 318
Period size: 117 Copynumber: 1.9 Consensus size: 117
1940 AGACATTCGG
* * * *
1950 GGGTAAAATGGTAA--TTTTGGAAAAATCGGGGTTAAAATGGAATTTTTGGAAGTTCGGGGGTAA
1 GGGTAAAATGGTAATTTTTTGGAAAAATCAGAGTCAAAATGGAATTTTTGGAAGTTCGAGGGT-A
* * *
2013 AATGGTAATTTTTGTAAAAATTGAGGTCAAAAATGGAATTTTTTGAAGTTCAA
65 AATGGTAATTTTTGGAAAAATTGAGGTCAAAAATGGAAATTTTGGAAGTTCAA
*
2066 GGGTAAAATGGTATTTTTTTGGAAAAATCAGAGTCCAAAATGGAATTTTTGGAAGTTCGAGGGT-
1 GGGTAAAATGGTAATTTTTTGGAAAAATCAGAGT-CAAAATGGAATTTTTGGAAGTTCGAGGGTA
2130 AATGGTAATTTTTGGAAAAATT-AGGGTCAAAAAT-GAAATTTTGGAA
65 AATGGTAATTTTTGGAAAAATTGA-GGTCAAAAATGGAAATTTTGGAA
2176 AGCTTGAGGG
Statistics
Matches: 98, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
116 24 0.24
117 31 0.32
118 16 0.16
119 27 0.28
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (117 bp):
GGGTAAAATGGTAATTTTTTGGAAAAATCAGAGTCAAAATGGAATTTTTGGAAGTTCGAGGGTAA
ATGGTAATTTTTGGAAAAATTGAGGTCAAAAATGGAAATTTTGGAAGTTCAA
Found at i:2204 original size:30 final size:29
Alignment explanation
Indices: 2109--2204 Score: 76
Period size: 29 Copynumber: 3.3 Consensus size: 29
2099 TCCAAAATGG
*
2109 AATTTTTGG-AAGTTCGAGGG-T-AATGGT
1 AATTTTTGGAAAGTT-GAGGGCTAAATTGT
* * *
2136 AATTTTTGGAAAAATT-AGGGTCAAAAATG-
1 AATTTTTGG-AAAGTTGAGGG-CTAAATTGT
*
2165 AAATTTTGGAAAGCTTGAGGGCTAAATTGT
1 AATTTTTGGAAAG-TTGAGGGCTAAATTGT
2195 AATTTTTGGA
1 AATTTTTGGA
2205 CTGTGTAGGG
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
27 13 0.25
28 3 0.06
29 20 0.38
30 16 0.31
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.35
Consensus pattern (29 bp):
AATTTTTGGAAAGTTGAGGGCTAAATTGT
Found at i:3979 original size:17 final size:17
Alignment explanation
Indices: 3966--4060 Score: 91
Period size: 17 Copynumber: 5.5 Consensus size: 17
3956 TTAAAATTTT
3966 ATTTCAAAATAAATTTAA
1 ATTT-AAAATAAATTTAA
3984 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
* ** **
4001 ACTCCAAATAAGCTTAA
1 ATTTAAAATAAATTTAA
*
4018 ATTTACAATAAATTTAA
1 ATTTAAAATAAATTTAA
* ** *
4035 ACTTAAAATGGATTAAA
1 ATTTAAAATAAATTTAA
4052 ATTTAAAAT
1 ATTTAAAAT
4061 CTAAAATTGA
Statistics
Matches: 60, Mismatches: 17, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
17 56 0.93
18 4 0.07
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:4010 original size:34 final size:34
Alignment explanation
Indices: 3969--4060 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 34
3959 AAATTTTATT
3969 TCAAAATAAATTTAAATTTAAAATAAATTTAAAC
1 TCAAAATAAATTTAAATTTAAAATAAATTTAAAC
* ** *
4003 TCCAAATAAGCTTAAATTTACAATAAATTTAAAC
1 TCAAAATAAATTTAAATTTAAAATAAATTTAAAC
* ** *
4037 TTAAAATGGATTAAAATTTAAAAT
1 TCAAAATAAATTTAAATTTAAAAT
4061 CTAAAATTGA
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (34 bp):
TCAAAATAAATTTAAATTTAAAATAAATTTAAAC
Found at i:6641 original size:32 final size:32
Alignment explanation
Indices: 6605--6665 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
6595 AAATATCTCA
*
6605 ATTTGATTTTATTCCAGTCAAATTGATTTTCG
1 ATTTGATTTGATTCCAGTCAAATTGATTTTCG
* * *
6637 ATTTGATTTGATTCTATTTAAATTGATTT
1 ATTTGATTTGATTCCAGTCAAATTGATTT
6666 ATAGGCTCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.54
Consensus pattern (32 bp):
ATTTGATTTGATTCCAGTCAAATTGATTTTCG
Found at i:7010 original size:25 final size:26
Alignment explanation
Indices: 6982--7032 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
6972 TCAATCCTCT
*
6982 TTATTTGATT-TTTGGTTTTCAGATC
1 TTATTTAATTATTTGGTTTTCAGATC
*
7007 TTATTTAATTAATTTGTTTTTCAGAT
1 TTATTTAATT-ATTTGGTTTTCAGAT
7033 ATGATGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.41
27 13 0.59
ACGTcount: A:0.22, C:0.06, G:0.12, T:0.61
Consensus pattern (26 bp):
TTATTTAATTATTTGGTTTTCAGATC
Found at i:7108 original size:51 final size:51
Alignment explanation
Indices: 7039--7142 Score: 136
Period size: 51 Copynumber: 2.0 Consensus size: 51
7029 AGATATGATG
* * *
7039 TTTTAAATAAATATAAATATTTATTTAATTTGTTTTGTTTAAATCTGGTAT
1 TTTTAAATAAATATAAATAGTTATTTAATTTATTTTGTTGAAATCTGGTAT
* * * * *
7090 TTTTACATAAATATAAATAGTTGTTTATTTTATTTTGTTGAGATCTTGTAT
1 TTTTAAATAAATATAAATAGTTATTTAATTTATTTTGTTGAAATCTGGTAT
7141 TT
1 TT
7143 AATATAAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.56
Consensus pattern (51 bp):
TTTTAAATAAATATAAATAGTTATTTAATTTATTTTGTTGAAATCTGGTAT
Found at i:9186 original size:30 final size:29
Alignment explanation
Indices: 9130--9328 Score: 204
Period size: 30 Copynumber: 6.7 Consensus size: 29
9120 GGGTCAAAAT
9130 ATTTTGAAAAAGTTTAGGGGTCAAAATAT-
1 ATTTTG-AAAAGTTTAGGGGTCAAAATATA
* * *
9159 ATTTTGAAAATGTTTGAGGGGTTAAAATGTG
1 ATTTTGAAAA-GTTT-AGGGGTCAAAATATA
* * *
9190 ATTTTGGAAAAGTTTATGGGTCAAAACATG
1 ATTTT-GAAAAGTTTAGGGGTCAAAATATA
9220 ATTTTAGAAAAGTTTAGGGGTCAAAATATA
1 ATTTT-GAAAAGTTTAGGGGTCAAAATATA
* *
9250 ATTTTTGAAAAGTTTAAGGGTCAAAATGTAA
1 A-TTTTGAAAAGTTTAGGGGTCAAAATAT-A
* * *
9281 ATTTGGAAAAGTTTAGGGGTTAAAATGTA
1 ATTTTGAAAAGTTTAGGGGTCAAAATATA
*
9310 ATTTTTGAAAAATTT-GGGG
1 A-TTTTGAAAAGTTTAGGGG
9329 ACCTCTTGAG
Statistics
Matches: 146, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
28 4 0.03
29 16 0.11
30 106 0.73
31 15 0.10
32 5 0.03
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.36
Consensus pattern (29 bp):
ATTTTGAAAAGTTTAGGGGTCAAAATATA
Found at i:9201 original size:60 final size:58
Alignment explanation
Indices: 9130--9328 Score: 229
Period size: 60 Copynumber: 3.3 Consensus size: 58
9120 GGGTCAAAAT
* *
9130 ATTTTGAAAAAGTTTAGGGGTCAAAATATATTTTGAAAATGTTTGAGGGGTTAAAATGTG
1 ATTTTGGAAAAGTTTAGGGGTCAAAATATATTTTGAAAA-GTTT-AGGGGTTAAAATGTA
* * * *
9190 ATTTTGGAAAAGTTTATGGGTCAAAACATGATTTTAGAAAAGTTTAGGGGTCAAAATATA
1 ATTTTGGAAAAGTTTAGGGGTCAAAATAT-ATTTT-GAAAAGTTTAGGGGTTAAAATGTA
* * * *
9250 ATTTTTGAAAAGTTTAAGGGTCAAAATGTAAATTTGGAAAAGTTTAGGGGTTAAAATGTA
1 ATTTTGGAAAAGTTTAGGGGTCAAAA--TATATTTTGAAAAGTTTAGGGGTTAAAATGTA
* *
9310 ATTTTTGAAAAATTT-GGGG
1 ATTTTGGAAAAGTTTAGGGG
9329 ACCTCTTGAG
Statistics
Matches: 120, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
59 3 0.03
60 98 0.82
61 13 0.11
62 6 0.05
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.36
Consensus pattern (58 bp):
ATTTTGGAAAAGTTTAGGGGTCAAAATATATTTTGAAAAGTTTAGGGGTTAAAATGTA
Found at i:9246 original size:90 final size:90
Alignment explanation
Indices: 9137--9305 Score: 252
Period size: 90 Copynumber: 1.9 Consensus size: 90
9127 AATATTTTGA
* * * *
9137 AAAAGTTTAGGGGTCAAAATAT-A-TTTTGAAAATGTTTGAGGGGTTAAAATGTGATTTTGGAAA
1 AAAAGTTTAGGGGTCAAAATATAATTTTTGAAAA-GTTT-AAGGGTCAAAATGTAAATTTGGAAA
*
9200 AGTTTATGGGTCAAAACATGATTTTAG
64 AGTTTAGGGGTCAAAACATGATTTTAG
9227 AAAAGTTTAGGGGTCAAAATATAATTTTTGAAAAGTTTAAGGGTCAAAATGTAAATTTGGAAAAG
1 AAAAGTTTAGGGGTCAAAATATAATTTTTGAAAAGTTTAAGGGTCAAAATGTAAATTTGGAAAAG
*
9292 TTTAGGGGTTAAAA
66 TTTAGGGGTCAAAA
9306 TGTAATTTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
90 57 0.80
91 5 0.07
92 9 0.13
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.34
Consensus pattern (90 bp):
AAAAGTTTAGGGGTCAAAATATAATTTTTGAAAAGTTTAAGGGTCAAAATGTAAATTTGGAAAAG
TTTAGGGGTCAAAACATGATTTTAG
Found at i:9314 original size:90 final size:90
Alignment explanation
Indices: 9137--9328 Score: 246
Period size: 90 Copynumber: 2.1 Consensus size: 90
9127 AATATTTTGA
* * * *
9137 AAAAGTTTAGGGGTCAAAATATATTTTGAAAATGTTTGAGGGGTTAAAATGTGATTTTGGAAAAG
1 AAAAGTTTAGGGGTCAAAATATATTTTGAAAATGTTTGAAGGGTCAAAATGTAAATTTGGAAAAG
* *
9202 TTTATGGGTCAAAACATGATTTTAG
66 TTTAGGGGTCAAAACATAATTTTAG
9227 AAAAGTTTAGGGGTCAAAATATAATTTTTGAAAA-GTTT-AAGGGTCAAAATGTAAATTTGGAAA
1 AAAAGTTTAGGGGTCAAAATAT-A-TTTTGAAAATGTTTGAAGGGTCAAAATGTAAATTTGGAAA
* ** *
9290 AGTTTAGGGGTTAAAATGTAATTTTTG
64 AGTTTAGGGGTCAAAACATAATTTTAG
*
9317 AAAAATTT-GGGG
1 AAAAGTTTAGGGG
9329 ACCTCTTGAG
Statistics
Matches: 89, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
89 4 0.04
90 71 0.80
91 5 0.06
92 9 0.10
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.35
Consensus pattern (90 bp):
AAAAGTTTAGGGGTCAAAATATATTTTGAAAATGTTTGAAGGGTCAAAATGTAAATTTGGAAAAG
TTTAGGGGTCAAAACATAATTTTAG
Found at i:11536 original size:49 final size:49
Alignment explanation
Indices: 11483--11983 Score: 365
Period size: 49 Copynumber: 10.2 Consensus size: 49
11473 GCCGTTATAG
* *
11483 CTTAAATATTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCGTTGCGA
1 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGA
* * * * * * *
11532 CTTAAACCTTTCCCTTTAT-ATCCTTGTGGTACTAGATTCGCCGTTGCGA
1 CTTAAATCTTTCCCTTCATGCTTC-TGAGGTACAAGGTTCGCCGTTGCGA
* * **
11581 CTTAAATCTTTCCCTTCATGCTTCTAAGATACAAGGTTCATCGTTGCGA
1 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGA
* * * * * * * *
11630 ATTAAA-CTTTTCCTTCCATG-TCCTCGTGGTACTAGATTCGTCGTTGCGG
1 CTTAAATCTTTCCCTT-CATGCTTCT-GAGGTACAAGGTTCGCCGTTGCGA
** * * *
11679 CTTAAATCTTTCCCTTCATATTTTTGAGGTACAAGGTTCGTCATTGCGA
1 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGA
* * * * *
11728 CTTAAACCTTTCCCTTCAAAT-CTTC-GTGGTAC-TGGATTCGGCGTTGCGG
1 CTTAAATCTTTCCCTTC--ATGCTTCTGAGGTACAAGG-TTCGCCGTTGCGA
* * * * *
11777 TTTAAATCTTTCCCTTCATGTTTCTGAGATACAAGGTTTGCCGTTACGA
1 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGA
* * *
11826 CTTAAACCTTTCCCTTCAAAT-CTTC--ATGGTACTAGATTCGCCGTTGC-A
1 CTTAAATCTTTCCCTTC--ATGCTTCTGA-GGTACAAGGTTCGCCGTTGCGA
* * *
11874 GCTTAAATCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCGCCGTTGCAA
1 -CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGA
* * * ** * * * * * *
11924 CTTAAACCTTTCTCTCCATATTTTTGTGGTACTAGATTCGCCATTGCGG
1 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGA
11973 CTTAAATCTTT
1 CTTAAATCTTT
11984 TCCATCTCAT
Statistics
Matches: 348, Mismatches: 84, Indels: 40
0.74 0.18 0.08
Matches are distributed among these distances:
47 4 0.01
48 23 0.07
49 296 0.85
50 21 0.06
51 4 0.01
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (49 bp):
CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGA
Found at i:11569 original size:98 final size:97
Alignment explanation
Indices: 11438--11983 Score: 655
Period size: 98 Copynumber: 5.6 Consensus size: 97
11428 TTGAGGTCAT
* * ** *
11438 AACCTTTCCCTCCATATTTTCGTGGTACTAGATTCGCCGTTATAGCTTAAATATTTCCCTTCATG
1 AACCTTTCCCTTCATATCTT-GTGGTACTAGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATG
*
11503 CTTCTGAGGTACAAGGTTCGTCGTTGCGACTTA
65 TTTCTGAGGTACAAGGTTCGTCGTTGCGACTTA
*
11536 AACCTTTCCCTTTATATCCTTGTGGTACTAGATTCGCCGTTGC-GACTTAAATCTTTCCCTTCAT
1 AACCTTTCCCTTCATAT-CTTGTGGTACTAGATTCGCCGTTGCAG-CTTAAATCTTTCCCTTCAT
* * * * *
11600 GCTTCTAAGATACAAGGTTCATCGTTGCGAATTA
64 GTTTCTGAGGTACAAGGTTCGTCGTTGCGACTTA
* * * * *
11634 AA-CTTTTCCTTCCATGTCCTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCAT
1 AACCTTTCCCTT-CATAT-CTTGTGGTACTAGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCAT
* * *
11698 ATTTTTGAGGTACAAGGTTCGTCATTGCGACTTA
64 GTTTCTGAGGTACAAGGTTCGTCGTTGCGACTTA
* * * * *
11732 AACCTTTCCCTTCAAATCTTCGTGGTACTGGATTCGGCGTTGCGGTTTAAATCTTTCCCTTCATG
1 AACCTTTCCCTTCATATCTT-GTGGTACTAGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATG
* * * *
11797 TTTCTGAGATACAAGGTTTGCCGTTACGACTTA
65 TTTCTGAGGTACAAGGTTCGTCGTTGCGACTTA
* *
11830 AACCTTTCCCTTCAAATCTTCATGGTACTAGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATG
1 AACCTTTCCCTTCATATCTT-GTGGTACTAGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATG
* * *
11895 TTTCTGAGGTATAAGGTTCGCCGTTGCAACTTA
65 TTTCTGAGGTACAAGGTTCGTCGTTGCGACTTA
* * * * *
11928 AACCTTTCTCTCCATATTTTTGTGGTACTAGATTCGCCATTGCGGCTTAAATCTTT
1 AACCTTTCCCTTCATA-TCTTGTGGTACTAGATTCGCCGTTGCAGCTTAAATCTTT
11984 TCCATCTCAT
Statistics
Matches: 387, Mismatches: 54, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
97 11 0.03
98 362 0.94
99 14 0.04
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.38
Consensus pattern (97 bp):
AACCTTTCCCTTCATATCTTGTGGTACTAGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGT
TTCTGAGGTACAAGGTTCGTCGTTGCGACTTA
Found at i:14094 original size:10 final size:11
Alignment explanation
Indices: 14064--14102 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
14054 TTCATCTTAA
14064 CCTT-TTCTTT
1 CCTTCTTCTTT
14074 CCTT-TTCTTT
1 CCTTCTTCTTT
14084 CCTTCTT-TTT
1 CCTTCTTCTTT
14094 -CTTCTTCTT
1 CCTTCTTCTT
14103 CTTTTTTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 6 0.22
10 19 0.70
11 2 0.07
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (11 bp):
CCTTCTTCTTT
Found at i:15535 original size:96 final size:96
Alignment explanation
Indices: 15361--15545 Score: 286
Period size: 96 Copynumber: 1.9 Consensus size: 96
15351 GAAAAGGATG
** *
15361 TTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAATGCGCAAATTTTCAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
15426 AGATAAGAAAATATTGCCTCGATTAAGGGTA
66 AGATAAGAAAATATTGCCTCGATTAAGGGTA
*
15457 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTC-GAAACTC
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAG-AA-TC
15521 GAA-ATAA-AAGAATATTGCCTCGATT
64 GAAGATAAGAA-AATATTGCCTCGATT
15546 TTAAAGTTTT
Statistics
Matches: 82, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
95 3 0.04
96 74 0.90
97 5 0.06
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
AGATAAGAAAATATTGCCTCGATTAAGGGTA
Found at i:15925 original size:57 final size:58
Alignment explanation
Indices: 15837--15957 Score: 156
Period size: 57 Copynumber: 2.1 Consensus size: 58
15827 AGTTCGAGGT
* * *
15837 TAAAAATGGAATTTTTAGACACCCGAGGGTAAAATGGTAAC-TTTAAAAAAATCGGGA
1 TAAAAACGAAATTTTTAGACACCCGAGGGTAAAATGGCAACTTTTAAAAAAATCGGGA
* * * *
15894 TCAAAACGAAATTTTT-GAACATCCGGGGGTAAAATGGCAACTTTTAGAAAAATCGGGA
1 TAAAAACGAAATTTTTAG-ACACCCGAGGGTAAAATGGCAACTTTTAAAAAAATCGGGA
15952 TAAAAA
1 TAAAAA
15958 ATGGAATTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
56 1 0.02
57 33 0.61
58 20 0.37
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.24
Consensus pattern (58 bp):
TAAAAACGAAATTTTTAGACACCCGAGGGTAAAATGGCAACTTTTAAAAAAATCGGGA
Found at i:15968 original size:58 final size:56
Alignment explanation
Indices: 15837--15985 Score: 172
Period size: 58 Copynumber: 2.6 Consensus size: 56
15827 AGTTCGAGGT
* * *
15837 TAAAAATGGAATTTTTAGACACCCGAGGGTAAAATGGTAACTTTAAAAAAATCGGGA
1 TAAAAATGGAATTTTGA-ACATCCGAGGGTAAAATGGCAACTTTAAAAAAATCGGGA
* * * * *
15894 TCAAAACGAAATTTTTGAACATCCGGGGGTAAAATGGCAACTTTTAGAAAAATCGGGA
1 TAAAAATGGAA-TTTTGAACATCCGAGGGTAAAATGGCAAC-TTTAAAAAAATCGGGA
* *
15952 TAAAAAATGGAATTTTGAACATTCGAAGGTAAAA
1 T-AAAAATGGAATTTTGAACATCCGAGGGTAAAA
15986 GGATAATTTT
Statistics
Matches: 75, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
57 28 0.37
58 40 0.53
59 7 0.09
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.25
Consensus pattern (56 bp):
TAAAAATGGAATTTTGAACATCCGAGGGTAAAATGGCAACTTTAAAAAAATCGGGA
Found at i:16015 original size:30 final size:30
Alignment explanation
Indices: 15973--16181 Score: 134
Period size: 30 Copynumber: 7.1 Consensus size: 30
15963 ATTTTGAACA
*
15973 TTCGAAGG-TAAAAGGATAATTTTTGAAAGT
1 TTCG-AGGTTAAAATGATAATTTTTGAAAGT
*
16003 TTCGAGGTTAAAAATGA-AATTTTTGGACA-T
1 TTCGAGGTT-AAAATGATAATTTTT-GAAAGT
* * ** * *
16033 ATAG-GGGCAAAATGGTAATTTTTGGAAGT
1 TTCGAGGTTAAAATGATAATTTTTGAAAGT
* * *
16062 TTCAAGGTTAAAAATG-GAATTTTTGGAAGT
1 TTCGAGGTT-AAAATGATAATTTTTGAAAGT
* *
16092 TT-GAGGGTAAAAATG-TAATTTTT-AGGAGT
1 TTCGA-GGTTAAAATGATAATTTTTGA-AAGT
* *
16121 TTAG-GGGTAAAAT-ATAATTTTTGAAAGT
1 TTCGAGGTTAAAATGATAATTTTTGAAAGT
16149 TTCGAGGTTAAAAATGA-AATTTTTGAACAGT
1 TTCGAGGTT-AAAATGATAATTTTTGAA-AGT
16180 TT
1 TT
16182 AGGGACCTCC
Statistics
Matches: 138, Mismatches: 25, Indels: 31
0.71 0.13 0.16
Matches are distributed among these distances:
28 29 0.21
29 37 0.27
30 51 0.37
31 21 0.15
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.36
Consensus pattern (30 bp):
TTCGAGGTTAAAATGATAATTTTTGAAAGT
Found at i:16110 original size:59 final size:58
Alignment explanation
Indices: 15989--16173 Score: 182
Period size: 59 Copynumber: 3.2 Consensus size: 58
15979 GGTAAAAGGA
* * * **
15989 TAATTTTTGAAAGTTTCGAGGTTAAAAATGAAATTTTTGGACA-TAT-AGGGGCAAAATGG
1 TAATTTTTGGAAGTTTCAAGGTTAAAAATG-AATTTTTGGA-AGTTTGAGGGTAAAAAT-G
16048 TAATTTTTGGAAGTTTCAAGGTTAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATG
1 TAATTTTTGGAAGTTTCAAGGTTAAAAAT-GAATTTTTGGAAGTTTGAGGGTAAAAATG
* * * *
16107 TAATTTTTAGG-AGTTT-AGGGGTAAAATAT-AATTTTTGAAAGTTTCGAGGTTAAAAATG
1 TAATTTTT-GGAAGTTTCAAGGTTAAAA-ATGAATTTTTGGAAGTTT-GAGGGTAAAAATG
*
16165 AAATTTTTG
1 TAATTTTTG
16174 AACAGTTTAG
Statistics
Matches: 110, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
57 15 0.14
58 28 0.25
59 55 0.50
60 12 0.11
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (58 bp):
TAATTTTTGGAAGTTTCAAGGTTAAAAATGAATTTTTGGAAGTTTGAGGGTAAAAATG
Found at i:17225 original size:23 final size:23
Alignment explanation
Indices: 17166--17344 Score: 118
Period size: 23 Copynumber: 7.8 Consensus size: 23
17156 GTGAGTACCG
* *
17166 AAGTACTAAACAGAGAGCACA-T
1 AAGTGCTAAACAGAGAGCACACA
*
17188 AAGTGCTGGGCAACAGAGAGCACACA
1 AAGTGCT---AAACAGAGAGCACACA
* *
17214 AAGTGCTAAACAGAGAGTAAACA
1 AAGTGCTAAACAGAGAGCACACA
* *
17237 AAGTACT--AC--TGAGCACACA
1 AAGTGCTAAACAGAGAGCACACA
* *
17256 AAGTGCTAATCAAAGAGCACACA
1 AAGTGCTAAACAGAGAGCACACA
* *
17279 CAGTGCTAATAACAGAGAGCACGA-G
1 AAGTGCT-A-AACAGAGAGCAC-ACA
* *
17304 ACGTGCTAAACAGAAAGCACACA
1 AAGTGCTAAACAGAGAGCACACA
* * *
17327 CAGTGCTAATCGGAGAGC
1 AAGTGCTAAACAGAGAGC
17345 GCGCTAGTGT
Statistics
Matches: 119, Mismatches: 26, Indels: 23
0.71 0.15 0.14
Matches are distributed among these distances:
19 13 0.11
21 3 0.03
22 7 0.06
23 58 0.49
24 2 0.02
25 28 0.24
26 8 0.07
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (23 bp):
AAGTGCTAAACAGAGAGCACACA
Done.