Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009466.1 Kokia drynarioides strain JFW-HI SEQ_124173, 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: 12197
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:1792 original size:108 final size:110
Alignment explanation
Indices: 1664--1872 Score: 296
Period size: 108 Copynumber: 1.9 Consensus size: 110
1654 AGAAATAAAG
* * *
1664 AACATTTATTGATTTAAAATAGGATACTCGATTATTTAGGTTCAAAGAAAAAATTATACCCAATA
1 AACATTTATTAATTTAAAATAAGATACTCGATTATTTAGGTTCAAAGAAAAAATCATACCCAATA
* * *
1729 -CA-TTTGAGCACAATTTTTCGAATTCCTTAAATTAAAAAAATCA
66 GCAGTTTGAGCACAATTTCTCAAATTCCCTAAATTAAAAAAATCA
* * *
1772 AACATTTATTAATTTTAAATAAGATACTTGATTATTTAGGTTCAACGAAAAAATCATACCCAATA
1 AACATTTATTAATTTAAAATAAGATACTCGATTATTTAGGTTCAAAGAAAAAATCATACCCAATA
*
1837 TGTATGTTTGAGCACAATTTCTCAAATTCCCTAAAT
66 -GCA-GTTTGAGCACAATTTCTCAAATTCCCTAAAT
1873 GAAAGAACAT
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
108 59 0.68
110 1 0.01
112 27 0.31
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (110 bp):
AACATTTATTAATTTAAAATAAGATACTCGATTATTTAGGTTCAAAGAAAAAATCATACCCAATA
GCAGTTTGAGCACAATTTCTCAAATTCCCTAAATTAAAAAAATCA
Found at i:2178 original size:29 final size:30
Alignment explanation
Indices: 2123--2180 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
2113 AAGACAGAAT
* * *
2123 AAAAGAGTAGTTTTAAAAGAAACAAAAATA
1 AAAAGAGTAATTTCAAAAGAAAAAAAAATA
* *
2153 AAAAGGGTAATTTCAAAAAAAAAAAAAA
1 AAAAGAGTAATTTCAAAAGAAAAAAAAA
2181 NNNNNNNNGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.67, C:0.03, G:0.12, T:0.17
Consensus pattern (30 bp):
AAAAGAGTAATTTCAAAAGAAAAAAAAATA
Found at i:4086 original size:46 final size:45
Alignment explanation
Indices: 4019--4165 Score: 157
Period size: 46 Copynumber: 3.4 Consensus size: 45
4009 GTGAGATGGC
*
4019 AGCTTCAATCTT-CCCCTCTTGAATTAGGGGTAAAAGATTGGATAGT
1 AGCTTCAAT-TTGCCTCTCTTGAATTAGGGGTAAAAGATTGGAT-GT
*
4065 AGCTTCAATTTGCCTCTCTTGACTTAGGGGTAAAAGATTGGATGGT
1 AGCTTCAATTTGCCTCTCTTGAATTAGGGGTAAAAGATTGGAT-GT
* *
4111 -GTCTTCAATATGCC-CTC-T-AGTTA-GGGTAAAAGATTGGATG-
1 AG-CTTCAATTTGCCTCTCTTGAATTAGGGGTAAAAGATTGGATGT
*
4151 A-CTTCAATCTGCCTC
1 AGCTTCAATTTGCCTC
4166 ATGGTTGGGG
Statistics
Matches: 91, Mismatches: 6, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
39 11 0.12
40 1 0.01
41 1 0.01
42 16 0.18
43 4 0.04
44 1 0.01
45 6 0.07
46 51 0.56
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (45 bp):
AGCTTCAATTTGCCTCTCTTGAATTAGGGGTAAAAGATTGGATGT
Found at i:4190 original size:81 final size:79
Alignment explanation
Indices: 4046--4424 Score: 296
Period size: 81 Copynumber: 4.6 Consensus size: 79
4036 CTTGAATTAG
* * * *
4046 GGGTAAAAGATTGGATAGTAGCTTCAATTTGCCTCTCTTGACTTAGGGGTAAAAGATTGGATGGT
1 GGGTAAAAGATTGGAT-G-A-CTTCAATCTG-C-CTCATG-GTT-GGGGTAAGAGATTGGATGGT
*
4111 GTCTTCAATATGCCCTCTAGTT
59 GTCTTTAATATGCCC-CTAGTT
4133 AGGGTAAAAGATTGGATGACTTCAATCTGCCTCATGGTTGGGGTAAGAGATTGGATGGTGTCTTT
1 -GGGTAAAAGATTGGATGACTTCAATCTGCCTCATGGTTGGGGTAAGAGATTGGATGGTGTCTTT
* * *
4198 AATTTGCCCCATAATCG
65 AATATGCCCC-TAGT-T
* * * * *
4215 GGGTAAAAGATTGGAAGGCTTCAATCTGCCTCATGGTCGGGGTAAGAGATTTGATGATGTCTTTA
1 GGGTAAAAGATTGGATGACTTCAATCTGCCTCATGGTTGGGGTAAGAGATTGGATGGTGTCTTTA
*
4280 ATCTGCCCC-ATGATT
66 ATATGCCCCTA-G-TT
* * * * * * * * *
4295 GAGGTAAGAGATTGGATTACTTCAACCTACCCCATGGTTAGGGTAAGAGATTGAAATGATATCTT
1 G-GGTAAAAGATTGGATGACTTCAATCTGCCTCATGGTTGGGGTAAGAGATTG-GATGGTGTCTT
* * *
4360 TAATCTGCCTC-ATGATCG
64 TAATATGCCCCTA-G-T-T
* * * *
4378 GGGTAAAAGATTGGATGACTTTAATTTGTCC-CATGGTCGAGGTAAGA
1 GGGTAAAAGATTGGATGACTTCAATCTG-CCTCATGGTTGGGGTAAGA
4425 TGAGATGATG
Statistics
Matches: 244, Mismatches: 39, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
79 1 0.00
80 2 0.01
81 145 0.59
82 60 0.25
83 8 0.03
84 1 0.00
85 9 0.04
86 1 0.00
87 1 0.00
88 16 0.07
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (79 bp):
GGGTAAAAGATTGGATGACTTCAATCTGCCTCATGGTTGGGGTAAGAGATTGGATGGTGTCTTTA
ATATGCCCCTAGTT
Found at i:4226 original size:42 final size:42
Alignment explanation
Indices: 4045--4394 Score: 227
Period size: 39 Copynumber: 8.4 Consensus size: 42
4035 TCTTGAATTA
* * * *
4045 GGGGTAAAAGATTGGATAGTAG-CTTCAATTTGCCTCTCTTGACTT
1 GGGGTAAAAGATTGGATGGT-GTCTTCAATCTGCC-C-CATG-GTT
* *
4090 AGGGGTAAAAGATTGGATGGTGTCTTCAATATGCCCTC-TAGTT
1 -GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCC-CATGGTT
* * *
4133 AGGGTAAAAGATTGGA---TGACTTCAATCTGCCTCATGGTT
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCATGGTT
* * * ** *
4172 GGGGTAAGAGATTGGATGGTGTCTTTAATTTGCCCCATAATC
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCATGGTT
* * *
4214 GGGGTAAAAGATTGGA-AG-G-CTTCAATCTGCCTCATGGTC
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCATGGTT
* * * * *
4253 GGGGTAAGAGATTTGATGATGTCTTTAATCTGCCCCATGATT
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCATGGTT
* * * * *
4295 GAGGTAAGAGATTGGAT--T-ACTTCAACCTACCCCATGGTT
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCATGGTT
* * * * * * * * *
4334 AGGGTAAGAGATTGAAATGATATCTTTAATCTGCCTCATGATC
1 GGGGTAAAAGATTG-GATGGTGTCTTCAATCTGCCCCATGGTT
4377 GGGGTAAAAGATTGGATG
1 GGGGTAAAAGATTGGATG
4395 ACTTTAATTT
Statistics
Matches: 239, Mismatches: 53, Indels: 28
0.75 0.17 0.09
Matches are distributed among these distances:
38 1 0.00
39 88 0.37
40 4 0.02
41 2 0.01
42 81 0.34
43 28 0.12
44 1 0.00
45 4 0.02
46 30 0.13
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (42 bp):
GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCATGGTT
Found at i:4411 original size:82 final size:80
Alignment explanation
Indices: 4134--4438 Score: 351
Period size: 81 Copynumber: 3.7 Consensus size: 80
4124 CCTCTAGTTA
*
4134 GGGTAAAAGATTGGATGACTTCAATCTGCCTCATGGTTGGGGTAAGAGATTGGATGGTGTCTTTA
1 GGGTAAAAGATTGGATGACTTCAATCTGCCTCATGGTTGGGGTAAGAGATT-GATGATGTCTTTA
* *
4199 ATTTGCCCCATAATCG
65 ATCTGCCCCATGATCG
* * *
4215 GGGTAAAAGATTGGAAGGCTTCAATCTGCCTCATGGTCGGGGTAAGAGATTTGATGATGTCTTTA
1 GGGTAAAAGATTGGATGACTTCAATCTGCCTCATGGTTGGGGTAAGAGA-TTGATGATGTCTTTA
*
4280 ATCTGCCCCATGATTG
65 ATCTGCCCCATGATCG
* * * * * * * *
4296 AGGTAAGAGATTGGATTACTTCAACCTACCCCATGGTTAGGGTAAGAGATTGAAATGATATCTTT
1 GGGTAAAAGATTGGATGACTTCAATCTGCCTCATGGTTGGGGTAAGAGATTG--ATGATGTCTTT
*
4361 AATCTGCCTCATGATCG
64 AATCTGCCCCATGATCG
* * * * *
4378 GGGTAAAAGATTGGATGACTTTAATTTGTCC-CATGGTCGAGGTAAGATGAGATGATGATGT
1 GGGTAAAAGATTGGATGACTTCAATCTG-CCTCATGGTTGGGGTAAGA-GA-TTGATGATGT
4439 AACTTCACTC
Statistics
Matches: 186, Mismatches: 32, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
80 3 0.02
81 110 0.59
82 67 0.36
83 4 0.02
84 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (80 bp):
GGGTAAAAGATTGGATGACTTCAATCTGCCTCATGGTTGGGGTAAGAGATTGATGATGTCTTTAA
TCTGCCCCATGATCG
Found at i:4422 original size:39 final size:38
Alignment explanation
Indices: 4134--4424 Score: 195
Period size: 39 Copynumber: 7.2 Consensus size: 38
4124 CCTCTAGTTA
* * *
4134 GGGTAAAAGATTGGATGACTTCAATCTGCCTCATGGTTG
1 GGGTAAGAGATTGGATGACTTTAATCTGCC-CATGGTCG
* * **
4173 GGGTAAGAGATTGGATGGTGTCTTTAATTTGCCCCATAATCG
1 GGGTAAGAGATTGGA---TGACTTTAATCTG-CCCATGGTCG
* * * *
4215 GGGTAAAAGATTGGAAGGCTTCAATCTGCCTCATGGTCG
1 GGGTAAGAGATTGGATGACTTTAATCTGCC-CATGGTCG
* * *
4254 GGGTAAGAGATTTGATGATGTCTTTAATCTGCCCCATGATTG
1 GGGTAAGAGA-TTG--GATGACTTTAATCTG-CCCATGGTCG
* * * * * **
4296 AGGTAAGAGATTGGATTACTTCAACCTACCCCATGGTTA
1 GGGTAAGAGATTGGATGACTTTAATCT-GCCCATGGTCG
* *
4335 GGGTAAGAGATTGAAATGATATCTTTAATCTGCCTCATGATCG
1 GGGTAAGAGATTG-GATG--A-CTTTAATCTGCC-CATGGTCG
* *
4378 GGGTAAAAGATTGGATGACTTTAATTTGTCCCATGGTCG
1 GGGTAAGAGATTGGATGACTTTAATCTG-CCCATGGTCG
*
4417 AGGTAAGA
1 GGGTAAGA
4425 TGAGATGATG
Statistics
Matches: 193, Mismatches: 43, Indels: 32
0.72 0.16 0.12
Matches are distributed among these distances:
38 2 0.01
39 90 0.47
40 8 0.04
41 3 0.02
42 62 0.32
43 28 0.15
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (38 bp):
GGGTAAGAGATTGGATGACTTTAATCTGCCCATGGTCG
Found at i:4834 original size:49 final size:49
Alignment explanation
Indices: 4788--5377 Score: 425
Period size: 49 Copynumber: 12.3 Consensus size: 49
4778 TTTCATCTTC
* * *
4788 AGGGTATAAGATTCGCTATTGCGGCTTTAATATTTCCCTTCACATCTCT
1 AGGGTATAAGATTCGCTGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * * * * *
4837 AGGGTATAAGGTTCACCGTTGTGGCTTCAACCTTTCCCTTCACATCTTT
1 AGGGTATAAGATTCGCTGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * * * *
4886 AGGGCATGAGATTCGCCGTTGCAGCTTCAATCTTTCCCTTTACATCTCT
1 AGGGTATAAGATTCGCTGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * * *
4935 AGGGCATGAGATTCGTTGTTGCGACTTCAATCTTTCCCTTCACATCTCT
1 AGGGTATAAGATTCGCTGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * * ** * * * *
4984 AGGGTATAAGGTTCGTTGTTACAACTTTAACCTTTCCCTTCACGTCTTT
1 AGGGTATAAGATTCGCTGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
** * ** * * * *
5033 AGGGTATAAGATT-TTTCGTTACGATTTTAATCTTTTCCTCCACATCTTT
1 AGGGTATAAGATTCGCT-GTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* *
5082 AGGG--T--CA-T---TG-T--GGCTTCAATCTTTCCC-TCTATATCTCT
1 AGGGTATAAGATTCGCTGTTGCGGCTTCAATCTTTCCCTTC-ACATCTCT
* * * * *
5120 AAGGTATAAGATTCATCT-TAGCAGCTTCAATTTTTCCCTTCACATCTCT
1 AGGGTATAAGATTC-GCTGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * * * * * **
5169 AGGGTATAAGGTTCGTTTTTGCGGTTTCAACCTTTCCCTCCATGTCTCT
1 AGGGTATAAGATTCGCTGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * * * * * *
5218 AGGGTATAAGGTTAGCCGTTGTGGCTTCAACCTTTTCCTTCACGTCTCT
1 AGGGTATAAGATTCGCTGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
** * * * * **
5267 AGGGTATAAGGCTCGCCGTTACGACTTCAACCTTTCCCCCCACATCTCT
1 AGGGTATAAGATTCGCTGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
** *
5316 AGGGTATAAGATTCGCCATTGCGACTTCAATCTTTCCCTTCACATCTCT
1 AGGGTATAAGATTCGCTGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
*
5365 AGGGTACAAGATT
1 AGGGTATAAGATT
5378 TGCCACTGTG
Statistics
Matches: 433, Mismatches: 92, Indels: 32
0.78 0.17 0.06
Matches are distributed among these distances:
37 1 0.00
38 21 0.05
40 2 0.00
41 1 0.00
42 2 0.00
43 1 0.00
44 1 0.00
45 1 0.00
47 2 0.00
48 3 0.01
49 396 0.91
50 2 0.00
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.37
Consensus pattern (49 bp):
AGGGTATAAGATTCGCTGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
Found at i:4932 original size:98 final size:97
Alignment explanation
Indices: 4745--5450 Score: 436
Period size: 98 Copynumber: 7.3 Consensus size: 97
4735 TTTACAGCTC
* * * * ** *
4745 TAAGATTCGCCTTTGCGACTTCAAT-TTGCTTCTTTTCATCT-TCAGGGTATAAGATTCGCTATT
1 TAAGATTCACCGTTGCGACTTCAATCTTTC-CCTTCACATCTCT-AGGGTATAAGATTCGCTGTT
* ** *
4808 GCGGCTTTAATATTTCCCTTCACATCTCTAGGGTA
64 GC-GCTTCAACCTTTCCCTCCACATCTCTAGGGTA
* * * * * * * *
4843 TAAGGTTCACCGTTGTGGCTTCAACCTTTCCCTTCACATCTTTAGGGCATGAGATTCGCCGTTGC
1 TAAGATTCACCGTTGCGACTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGATTCGCTGTTGC
* ** *
4908 AGCTTCAATCTTTCCCTTTACATCTCTAGGGCA
66 -GCTTCAACCTTTCCCTCCACATCTCTAGGGTA
* *** * * *
4941 TGAGATTCGTTGTTGCGACTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGGTTCGTTGTTAC
1 TAAGATTCACCGTTGCGACTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGATTCGCTGTTGC
* * * * *
5006 AACTTTAACCTTTCCCTTCACGTCTTTAGGGTA
66 -GCTTCAACCTTTCCCTCCACATCTCTAGGGTA
*** * * * * * * *
5039 TAAGATTTTTCGTTACGATTTTAATCTTTTCCTCCACATCTTTAGGG--T--CA-T---TG-TG-
1 TAAGATTCACCGTTGCGACTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGATTCGCTGTTGC
* * * *
5094 GCTTCAATCTTTCCCTCTATATCTCTAAGGTA
66 GCTTCAACCTTTCCCTCCACATCTCTAGGGTA
* * * * *
5126 TAAGATTCATC-TTAGC-AGCTTCAATTTTTCCCTTCACATCTCTAGGGTATAAGGTTCGTTTTT
1 TAAGATTCACCGTT-GCGA-CTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGATTCGCTGTT
* **
5189 GCGGTTTCAACCTTTCCCTCCATGTCTCTAGGGTA
64 GC-GCTTCAACCTTTCCCTCCACATCTCTAGGGTA
* * * * * * ** * *
5224 TAAGGTT-AGCCGTTGTGGCTTCAACCTTTTCCTTCACGTCTCTAGGGTATAAGGCTCGCCGTTA
1 TAAGATTCA-CCGTTGCGACTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGATTCGCTGTTG
*
5288 CGACTTCAACCTTTCCCCCCACATCTCTAGGGTA
65 CG-CTTCAACCTTTCCCTCCACATCTCTAGGGTA
* * * *
5322 TAAGATTCGCCATTGCGACTTCAATCTTTCCCTTCACATCTCTAGGGTACAAGATTTGCCACTG-
1 TAAGATTCACCGTTGCGACTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGA-TT--CGCTGT
* ** * * * *
5386 TGAGCTTCAATATTTCTCTCTATATCTCTAAGGTA
63 TGCGCTTCAACCTTTCCCTCCACATCTCTAGGGTA
** * *
5421 TAAGATTCGTCATTGTGACTTCAATCTTTC
1 TAAGATTCACCGTTGCGACTTCAATCTTTC
5451 TCATCACGTT
Statistics
Matches: 464, Mismatches: 121, Indels: 45
0.74 0.19 0.07
Matches are distributed among these distances:
86 3 0.01
87 56 0.12
89 2 0.00
90 2 0.00
92 1 0.00
93 1 0.00
95 1 0.00
96 3 0.01
97 2 0.00
98 329 0.71
99 59 0.13
100 2 0.00
101 3 0.01
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.38
Consensus pattern (97 bp):
TAAGATTCACCGTTGCGACTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGATTCGCTGTTGC
GCTTCAACCTTTCCCTCCACATCTCTAGGGTA
Found at i:5209 original size:136 final size:135
Alignment explanation
Indices: 4959--5210 Score: 285
Period size: 136 Copynumber: 1.9 Consensus size: 135
4949 GTTGTTGCGA
* * * * *
4959 CTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGGTTCGTTGTTACAACTTTAACCTTTCCCTT
1 CTTCAATCTTTCCCTTCACATCTCTAAGGTATAAGATTCGATCTTACAACTTCAACCTTTCCCTT
* * * * *
5024 CACGTCTTTAGGGTATAAGATTTTTCGTTACGATTTTAATCTTTTCCTCCACATCTTTAGGGTCA
66 CACATCTCTAGGGTATAAGATTTTTC-TTACGATTTCAACCTTTCCCTCCACATCTTTAGGGTCA
5089 TTGTGG
130 TTGTGG
* * **
5095 CTTCAATCTTTCCC-TCTATATCTCTAAGGTATAAGATTC-ATCTTAGCAGCTTCAATTTTTCCC
1 CTTCAATCTTTCCCTTC-ACATCTCTAAGGTATAAGATTCGATCTTA-CAACTTCAACCTTTCCC
* * *
5158 TTCACATCTCTAGGGTATAAGGTTCGTTT-TTGCGGTTTCAACCTTTCCCTCCA
64 TTCACATCTCTAGGGTATAAGATT--TTTCTTACGATTTCAACCTTTCCCTCCA
5211 TGTCTCTAGG
Statistics
Matches: 95, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
135 6 0.06
136 86 0.91
138 3 0.03
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.42
Consensus pattern (135 bp):
CTTCAATCTTTCCCTTCACATCTCTAAGGTATAAGATTCGATCTTACAACTTCAACCTTTCCCTT
CACATCTCTAGGGTATAAGATTTTTCTTACGATTTCAACCTTTCCCTCCACATCTTTAGGGTCAT
TGTGG
Found at i:5255 original size:185 final size:185
Alignment explanation
Indices: 4909--5271 Score: 426
Period size: 185 Copynumber: 2.0 Consensus size: 185
4899 CGCCGTTGCA
* * * * *
4909 GCTTCAATCTTTCCCTTTACATCTCTAGGGCATGAGATTCGTTGTTGCGACTTCAATCTTTCCCT
1 GCTTCAATCTTTCCCTCTACATCTCTAAGGCATAAGATTCATTGTAGCGACTTCAATCTTTCCCT
* *
4974 TCACATCTCTAGGGTATAAGGTTCGTTGTTACAACTTTAACCTTTCCCTTCACGTCTTTAGGGTA
66 TCACATCTCTAGGGTATAAGGTTCGTTGTTACAACTTTAACCTTTCCCTCCACGTCTCTAGGGTA
*** * * * *
5039 TAAGATTTTTCGTTACGATTTTAATCTTTTCCTCCACATCTTTAGGGTCATTGTG
131 TAAGATTAGCCGTTACGACTTCAACCTTTTCCTCCACATCTCTAGGGTCATTGTG
* * *
5094 GCTTCAATCTTTCCCTCTATATCTCTAAGGTATAAGATTCATCT-TAGC-AGCTTCAATTTTTCC
1 GCTTCAATCTTTCCCTCTACATCTCTAAGGCATAAGATTCAT-TGTAGCGA-CTTCAATCTTTCC
* * ** *
5157 CTTCACATCTCTAGGGTATAAGGTTCGTTTTTGC-GGTTTCAACCTTTCCCTCCATGTCTCTAGG
64 CTTCACATCTCTAGGGTATAAGGTTCGTTGTTACAACTTT-AACCTTTCCCTCCACGTCTCTAGG
* ** * * *
5221 GTATAAGGTTAGCCGTTGTGGCTTCAACCTTTTCCTTCACGTCTCTAGGGT
128 GTATAAGATTAGCCGTTACGACTTCAACCTTTTCCTCCACATCTCTAGGGT
5272 ATAAGGCTCG
Statistics
Matches: 147, Mismatches: 28, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
184 4 0.03
185 142 0.97
186 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.40
Consensus pattern (185 bp):
GCTTCAATCTTTCCCTCTACATCTCTAAGGCATAAGATTCATTGTAGCGACTTCAATCTTTCCCT
TCACATCTCTAGGGTATAAGGTTCGTTGTTACAACTTTAACCTTTCCCTCCACGTCTCTAGGGTA
TAAGATTAGCCGTTACGACTTCAACCTTTTCCTCCACATCTCTAGGGTCATTGTG
Found at i:5426 original size:50 final size:49
Alignment explanation
Indices: 5087--5457 Score: 239
Period size: 49 Copynumber: 7.6 Consensus size: 49
5077 TCTTTAGGGT
* * * * **
5087 CATTGTGGCTTCAATCTTTC-CCTCTATATCTCTAAGGTATAAGATTCAT
1 CATTGTGACTTCAATCTTTCTCTTC-ACATCTCTAGGGTATAAGATTCGC
* * * * *
5136 C-TTAG-CAGCTTCAATTTTTCCCTTCACATCTCTAGGGTATAAGGTTCGT
1 CATT-GTGA-CTTCAATCTTTCTCTTCACATCTCTAGGGTATAAGATTCGC
** * ** * * * ** * *
5185 TTTTGCGGTTTCAACCTTTCCCTCCATGTCTCTAGGGTATAAGGTTAGC
1 CATTGTGACTTCAATCTTTCTCTTCACATCTCTAGGGTATAAGATTCGC
* * * * **
5234 CGTTGTGGCTTCAACCTTT-TCCTTCACGTCTCTAGGGTATAAGGCTCGC
1 CATTGTGACTTCAATCTTTCT-CTTCACATCTCTAGGGTATAAGATTCGC
* ** * * **
5283 CGTTACGACTTCAACCTTTCCCCCCACATCTCTAGGGTATAAGATTCGC
1 CATTGTGACTTCAATCTTTCTCTTCACATCTCTAGGGTATAAGATTCGC
* * * *
5332 CATTGCGACTTCAATCTTTCCCTTCACATCTCTAGGGTACAAGATTTGC
1 CATTGTGACTTCAATCTTTCTCTTCACATCTCTAGGGTATAAGATTCGC
* * * * *
5381 CACTGTGAGCTTCAATATTTCTC-TCTATATCTCTAAGGTATAAGATTCGT
1 CATTGTGA-CTTCAATCTTTCTCTTC-ACATCTCTAGGGTATAAGATTCGC
*
5431 CATTGTGACTTCAATCTTTCTCATCAC
1 CATTGTGACTTCAATCTTTCTCTTCAC
5458 GTTTTCAAGG
Statistics
Matches: 256, Mismatches: 56, Indels: 20
0.77 0.17 0.06
Matches are distributed among these distances:
48 2 0.01
49 209 0.82
50 45 0.18
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (49 bp):
CATTGTGACTTCAATCTTTCTCTTCACATCTCTAGGGTATAAGATTCGC
Found at i:6432 original size:6 final size:6
Alignment explanation
Indices: 6421--6482 Score: 81
Period size: 6 Copynumber: 10.0 Consensus size: 6
6411 TTAACCACTC
*
6421 CTTTTT CTTTTT CTTTTT -TTTTT CTTTCTT CTTTCTCT TTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTT-TT CTTT-T-T CTTTTT CTTTTT
6471 CTTTTT CTTTTT
1 CTTTTT CTTTTT
6483 GGGTGAAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
5 5 0.10
6 33 0.65
7 9 0.18
8 4 0.08
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
CTTTTT
Found at i:7398 original size:7 final size:7
Alignment explanation
Indices: 7381--7424 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
7371 CATCTTGACT
7381 TTTTCTTC
1 TTTT-TTC
7389 TTTTTTC
1 TTTTTTC
7396 TTTTTTC
1 TTTTTTC
*
7403 -TCTTT-
1 TTTTTTC
7408 TTTTTTC
1 TTTTTTC
7415 TTTTTTC
1 TTTTTTC
7422 TTT
1 TTT
7425 AGGTTTCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 8 0.25
7 20 0.62
8 4 0.12
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTC
Found at i:7411 original size:19 final size:19
Alignment explanation
Indices: 7380--7422 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
7370 TCATCTTGAC
7380 TTTT-TCTTCTTTTTTCTT
1 TTTTCTCTTCTTTTTTCTT
*
7398 TTTTCTCTTTTTTTTTCTT
1 TTTTCTCTTCTTTTTTCTT
7417 TTTTCT
1 TTTTCT
7423 TTAGGTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTCTCTTCTTTTTTCTT
Found at i:10597 original size:108 final size:109
Alignment explanation
Indices: 10456--10670 Score: 342
Period size: 108 Copynumber: 2.0 Consensus size: 109
10446 AAAAATAAAG
* *
10456 AACATTTATTGATTTAAAATAGGATACTCGATTATTTAGGTTAAAAGAAAAAATCATACCAAGTA
1 AACATTTATTAATTTAAAATAGGATACTCGATTATTTAAGTTAAAAGAAAAAATCATACCAAGTA
*
10521 TGTTTGAGCACAATTTCTCGAATTCCATAAATAAAAAAACATCA
66 CGTTTGAGCACAATTTCTCGAATTCCATAAATAAAAAAACATCA
* * *
10565 AACATTT-TTAATTTTAAATAGGATACTCGATTATTTAAGTTCAAAGAAAAAATCATACCCAGTA
1 AACATTTATTAATTTAAAATAGGATACTCGATTATTTAAGTTAAAAGAAAAAATCATACCAAGTA
* * *
10629 CGTTTGAGCACAATTTCTTGAATTCCTTAAATAAAAGAACAT
66 CGTTTGAGCACAATTTCTCGAATTCCATAAATAAAAAAACAT
10671 TGCCCCTTTT
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
108 90 0.93
109 7 0.07
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (109 bp):
AACATTTATTAATTTAAAATAGGATACTCGATTATTTAAGTTAAAAGAAAAAATCATACCAAGTA
CGTTTGAGCACAATTTCTCGAATTCCATAAATAAAAAAACATCA
Done.