Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010286.1 Kokia drynarioides strain JFW-HI SEQ_125135, 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: 18726
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Warning! 62 characters in sequence are not A, C, G, or T
Found at i:1649 original size:19 final size:19
Alignment explanation
Indices: 1625--1667 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1615 AAACATAAGT
1625 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
1644 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
1663 TAAAT
1 TAAAT
1668 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:3784 original size:37 final size:37
Alignment explanation
Indices: 3707--3787 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
3697 CTATAATTGA
* * * *
3707 GGTAAGATTGCATGGCTTCACTTTGCCCCACGGCCGG
1 GGTAAGATTGCATGGCTTCACTCTACCCCACGACCAG
* * *
3744 GGTAAGATTGCATGGCTTCACTCTACCTCATGATCAG
1 GGTAAGATTGCATGGCTTCACTCTACCCCACGACCAG
3781 GGTAAGA
1 GGTAAGA
3788 GATTGGACAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.26
Consensus pattern (37 bp):
GGTAAGATTGCATGGCTTCACTCTACCCCACGACCAG
Found at i:4024 original size:46 final size:45
Alignment explanation
Indices: 3940--4305 Score: 310
Period size: 46 Copynumber: 8.0 Consensus size: 45
3930 TGAGAGGGTA
* * *
3940 GCTTTAATCTACCCCTCTTGATTA-AGGGTAAAAGATTGGATGGTG
1 GCTTCAATCTGCCCCTCTTAATTAGA-GGTAAAAGATTGGATGGTG
*
3985 GCTTCAATCTGCCCCTCTTTAATGAGAGGTAAAAGATTGGATGGTG
1 GCTTCAATCTGCCCCTC-TTAATTAGAGGTAAAAGATTGGATGGTG
* ** *
4031 GTTTCAATCTGGTCCTCTTAACTTAGAGGTAAAAGAGTT-TATGGTG
1 GCTTCAATCTGCCCCTCTTAA-TTAGAGGTAAAAGA-TTGGATGGTG
* * * * * * *
4077 GTTTTAATTTGCCCCTCTTAACTTA-AGGGTAAAAGACTGTATAGTA
1 GCTTCAATCTGCCCCTCTTAA-TTAGA-GGTAAAAGATTGGATGGTG
* * *
4123 ACTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAAT-GTG
1 GCTTCAATCTGCCCCTCTTAATTAGAGGTAAAAGATTGG-ATGGTG
* * * * * **
4168 ACTTCAATATACCCCTCTTAACTAGGGGTAAAAGATTGGATGACG
1 GCTTCAATCTGCCCCTCTTAATTAGAGGTAAAAGATTGGATGGTG
* * * *
4213 GCTTCAATTTGCCCCCTCTTGACTTAG-GGGAAAAGGATTGAATGGTG
1 GCTTCAATCTG-CCCCTCTT-AATTAGAGGTAAAA-GATTGGATGGTG
* *
4260 GCTTCAATCTGCCCCTCTTGACTTTAGGGGTAAAAGATTGGATGGT
1 GCTTCAATCTGCCCCTCTT-A-ATTAGAGGTAAAAGATTGGATGGT
4306 AGTTTTGCTT
Statistics
Matches: 263, Mismatches: 44, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
44 2 0.01
45 81 0.31
46 134 0.51
47 40 0.15
48 6 0.02
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (45 bp):
GCTTCAATCTGCCCCTCTTAATTAGAGGTAAAAGATTGGATGGTG
Found at i:4188 original size:137 final size:137
Alignment explanation
Indices: 3940--4305 Score: 402
Period size: 137 Copynumber: 2.7 Consensus size: 137
3930 TGAGAGGGTA
* * *
3940 GCTTTAATCTACCCCTCTTGA-TTAAGGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCTCTT
1 GCTTTAATTTGCCCCTCTTGACTTAAGGGTAAAAGATTGAATGGTGGCTTCAATCTGCCCCTC-T
* * * ** * ***
4004 TAATGAGAGGTAAAAGATTGG-ATGGTGGTTTCAATCTGGTCCTCTTAACTTAGAGGTAAAAGAG
65 TGATTAGGGGTAAAAGATTGGAATGGTGACTTCAATATACCCCTCTTAAC-TAGAGGTAAAAGA-
* **
4068 TT-TATGGTG
128 TTGGATGACG
* * * * * **
4077 GTTTTAATTTGCCCCTCTTAACTTAAGGGTAAAAGACTGTATAGTAACTTCAATCTGCCCCTCTT
1 GCTTTAATTTGCCCCTCTTGACTTAAGGGTAAAAGATTGAATGGTGGCTTCAATCTGCCCCTCTT
*
4142 GATTAGGGGTAAAAGATTGGAAT-GTGACTTCAATATACCCCTCTTAACTAGGGGTAAAAGATTG
66 GATTAGGGGTAAAAGATTGGAATGGTGACTTCAATATACCCCTCTTAACTAGAGGTAAAAGATTG
4206 GATGACG
131 GATGACG
* *
4213 GCTTCAATTTGCCCCCTCTTGACTT-AGGGGAAAAGGATTGAATGGTGGCTTCAATCTGCCCCTC
1 GCTTTAATTTG-CCCCTCTTGACTTAAGGGTAAAA-GATTGAATGGTGGCTTCAATCTGCCCCTC
4277 TTGACTTTAGGGGTAAAAGATTGG-ATGGT
64 TTGA--TTAGGGGTAAAAGATTGGAATGGT
4306 AGTTTTGCTT
Statistics
Matches: 190, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
135 2 0.01
136 33 0.17
137 95 0.50
138 40 0.21
139 20 0.11
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (137 bp):
GCTTTAATTTGCCCCTCTTGACTTAAGGGTAAAAGATTGAATGGTGGCTTCAATCTGCCCCTCTT
GATTAGGGGTAAAAGATTGGAATGGTGACTTCAATATACCCCTCTTAACTAGAGGTAAAAGATTG
GATGACG
Found at i:4260 original size:183 final size:184
Alignment explanation
Indices: 3945--4296 Score: 437
Period size: 183 Copynumber: 1.9 Consensus size: 184
3935 GGGTAGCTTT
* * *
3945 AATCTACCCCTCTTGATTAAGGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCTCTTTAATGA
1 AATCTACCCCTCTTGATTAAGGGTAAAAGATTGGATGGTGACTTCAATATACCCCTCTTTAATGA
** * ** * *
4010 GAGGTAAAAGATTGGATGGTGGTTTCAATCTGGTCCTCTTAACTTAGAGGTAAAAGAGTTTATGG
66 GAGGTAAAAGATTGGATGACGGCTTCAATCTGCCCCTCTTAACTTAGAGGGAAAAGAGTTAATGG
* * *
4075 TGGTTTTAATTTGCCCCTCTTAAC-TTAAGGGTAAAAGACTGTATAGTAACTTC
131 TGGCTTCAATCTGCCCCTCTTAACTTTAAGGGTAAAAGACTGTATAGTAACTTC
* *
4128 AATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAAT-GTGACTTCAATATACCCCTC-TTAACT
1 AATCTACCCCTCTTGATTAAGGGTAAAAGATTGG-ATGGTGACTTCAATATACCCCTCTTTAA-T
* * *
4191 -AGGGGTAAAAGATTGGATGACGGCTTCAATTTGCCCCCTCTTGACTTAG-GGGAAAAG-GATTG
64 GAGAGGTAAAAGATTGGATGACGGCTTCAATCTG-CCCCTCTTAACTTAGAGGGAAAAGAG-TT-
* *
4253 AATGGTGGCTTCAATCTGCCCCTCTTGACTTTAGGGGTAAAAGA
126 AATGGTGGCTTCAATCTGCCCCTCTTAACTTTAAGGGTAAAAGA
4297 TTGGATGGTA
Statistics
Matches: 143, Mismatches: 20, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
181 1 0.01
182 41 0.29
183 86 0.60
184 15 0.10
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (184 bp):
AATCTACCCCTCTTGATTAAGGGTAAAAGATTGGATGGTGACTTCAATATACCCCTCTTTAATGA
GAGGTAAAAGATTGGATGACGGCTTCAATCTGCCCCTCTTAACTTAGAGGGAAAAGAGTTAATGG
TGGCTTCAATCTGCCCCTCTTAACTTTAAGGGTAAAAGACTGTATAGTAACTTC
Found at i:4846 original size:99 final size:99
Alignment explanation
Indices: 4702--5222 Score: 254
Period size: 99 Copynumber: 5.3 Consensus size: 99
4692 ACTATTACAG
* * * * ** **
4702 CCTCAATCC-TTCCCATCATATTTTCTAAGGTACCAGGTTCGCCGTTACGGTCTAAACCTTTCCC
1 CCTCAA-CCTTTCCCTTCATATCTTC-ATGGTACCAGATTTACCGTTACGACCTAAACCTTTCCC
* **
4766 TTCACATCGTCTAAGGTACTGGGTTCGCCATTGC-A
64 ATCACATCGTCTAAGGTACCAGGTTCGCCATTGCGA
* * * * * * *
4801 GCCTCAATCTTTCTCTTTATATCTTTATGGTACCAGATTTACCGTTGCGACCTCAATCTTTCCCA
1 -CCTCAACCTTTCCCTTCATATCTTCATGGTACCAGATTTACCGTTACGACCTAAACCTTTCCCA
* * * *
4866 TCACTTCTTTTAAGGTACCAGGTTCGCCGTTGCGA
65 TCACATCGTCTAAGGTACCAGGTTCGCCATTGCGA
* * ** * *
4901 CCTCCACCTTTCCCTTCATATCTTCATGGTA-CTGAATTCGCCATTATCG-CCTCAATCC-TTCC
1 CCTCAACCTTTCCCTTCATATCTTCATGGTACCAG-ATTTACCGTTA-CGACCT-AAACCTTTCC
* * ** * * * * *
4963 CATTATATTTTCTAAGGTACCGGGTTCACCGTTGTGG
63 CATCACATCGTCTAAGGTACCAGGTTCGCCATTGCGA
* * * * * ** * *
5000 CCTCCACCTTT-CCTTATATATCTTCATGGTATCGGATTCACCGTTGTGGCCTTAATCC-TTCCC
1 CCTCAACCTTTCCCTT-CATATCTTCATGGTACCAGATTTACCGTTACGACC-TAAACCTTTCCC
* * * * * * *
5063 ATTACATCTTATAAGGTACCGGGTTCGCCGTTGTGG
64 ATCACATCGTCTAAGGTACCAGGTTCGCCATTGCGA
* * * ** * * *
5099 CCTTAACCTTTCCTTTTATATCTTCATGGTACC-GAATTTTTCTTTGC-AGCCTCAATCC-TTCC
1 CCTCAACCTTTCCCTTCATATCTTCATGGTACCAG-ATTTACCGTTACGA-CCT-AAACCTTTCC
* * * *
5161 CATCACATCTTTTAAGGTACCGGGTTCGCCGTTGC-A
63 CATCACATCGTCTAAGGTACCAGGTTCGCCATTGCGA
* *
5197 GCCTGAACCTTTCCCTTCACATCTTC
1 -CCTCAACCTTTCCCTTCATATCTTC
5223 TAAGGTACGG
Statistics
Matches: 335, Mismatches: 72, Indels: 29
0.77 0.17 0.07
Matches are distributed among these distances:
98 9 0.03
99 298 0.89
100 28 0.08
ACGTcount: A:0.18, C:0.30, G:0.15, T:0.36
Consensus pattern (99 bp):
CCTCAACCTTTCCCTTCATATCTTCATGGTACCAGATTTACCGTTACGACCTAAACCTTTCCCAT
CACATCGTCTAAGGTACCAGGTTCGCCATTGCGA
Found at i:4855 original size:49 final size:49
Alignment explanation
Indices: 4573--5321 Score: 201
Period size: 50 Copynumber: 15.1 Consensus size: 49
4563 TTCTCTCCAC
* ** * * * *
4573 ATCTTTATGGTACAAGATTTGCCGTTGTGGCTTCAATCTTTCCCTATCAC
1 ATCTTTATGGTACCAGATTCACCGTTGCGACCTCAATCTTTCCCT-TCAT
* * * * * * * * * *
4623 GTCTCTAAGGTACAACATTCACCGTTGTGGCTTCAACCTTTCCCTCCAT
1 ATCTTTATGGTACCAGATTCACCGTTGCGACCTCAATCTTTCCCTTCAT
* * * ** * * *
4672 ATCTTTATCGTATCAGATTTACTATTAC-AGCCTCAATCCTTCCCATCAT
1 ATCTTTATGGTACCAGATTCACCGTTGCGA-CCTCAATCTTTCCCTTCAT
* * * * * ** * * *
4721 ATTTTCTAAGGTACCAGGTTCGCCGTTACGGTCTAAACCTTTCCCTTCAC
1 ATCTT-TATGGTACCAGATTCACCGTTGCGACCTCAATCTTTCCCTTCAT
* * ** * * * * *
4771 ATCGTCTAAGGTACTGGGTTCGCCATTGC-AGCCTCAATCTTTCTCTTTAT
1 ATC-TTTATGGTACCAGATTCACCGTTGCGA-CCTCAATCTTTCCCTTCAT
* *
4821 ATCTTTATGGTACCAGATTTACCGTTGCGACCTCAATCTTTCCCATCACT
1 ATCTTTATGGTACCAGATTCACCGTTGCGACCTCAATCTTTCCCTTCA-T
* * * * *
4871 -TCTTTTAAGGTACCAGGTTCGCCGTTGCGACCTCCACCTTTCCCTTCAT
1 ATC-TTTATGGTACCAGATTCACCGTTGCGACCTCAATCTTTCCCTTCAT
* * * * * *
4920 ATCTTCATGGTA-CTGAATTCGCCATTATCG-CCTCAATCCTTCCCATT-AT
1 ATCTTTATGGTACCAG-ATTCACCGTT-GCGACCTCAATCTTTCCC-TTCAT
* * * * * * * * *
4969 ATTTTCTAAGGTACCGGGTTCACCGTTGTGGCCTCCACCTTT-CCTTATAT
1 ATCTT-TATGGTACCAGATTCACCGTTGCGACCTCAATCTTTCCCTT-CAT
* * * * * * * *
5019 ATCTTCATGGTATCGGATTCACCGTTGTGGCCTTAATCCTTCCCATT-AC
1 ATCTTTATGGTACCAGATTCACCGTTGCGACCTCAATCTTTCCC-TTCAT
* * * * * * * * * *
5068 ATCTTATAAGGTACCGGGTTCGCCGTTGTGGCCTTAACCTTTCCTTTTAT
1 ATCTT-TATGGTACCAGATTCACCGTTGCGACCTCAATCTTTCCCTTCAT
* *** * * * *
5118 ATCTTCATGGTACC-GAATTTTTCTTTGC-AGCCTCAATCCTTCCCATCAC
1 ATCTTTATGGTACCAG-ATTCACCGTTGCGA-CCTCAATCTTTCCCTTCAT
* * * * * * *
5167 ATCTTTTAAGGTACCGGGTTCGCCGTTGC-AGCCTGAACCTTTCCCTTCAC
1 ATC-TTTATGGTACCAGATTCACCGTTGCGA-CCTCAATCTTTCCCTTCAT
* ** * * *
5217 ATCTTCTAAGGTACGGGGTTC-CTCGTTGTGACCTCAACCTTTCCCTTCAT
1 ATCTT-TATGGTACCAGATTCAC-CGTTGCGACCTCAATCTTTCCCTTCAT
* ** ** * * *
5267 ATCTTCATGGTATTAGATTCGTCGTTGC-AGCCTCAGTCTTTCCCATCAC
1 ATCTTTATGGTACCAGATTCACCGTTGCGA-CCTCAATCTTTCCCTTCAT
5316 ATCTTT
1 ATCTTT
5322 TAAGGTATCG
Statistics
Matches: 511, Mismatches: 158, Indels: 61
0.70 0.22 0.08
Matches are distributed among these distances:
48 6 0.01
49 207 0.41
50 291 0.57
51 7 0.01
ACGTcount: A:0.19, C:0.29, G:0.15, T:0.37
Consensus pattern (49 bp):
ATCTTTATGGTACCAGATTCACCGTTGCGACCTCAATCTTTCCCTTCAT
Found at i:4855 original size:149 final size:148
Alignment explanation
Indices: 4655--5362 Score: 551
Period size: 149 Copynumber: 4.8 Consensus size: 148
4645 CGTTGTGGCT
** * * ** *
4655 TCAACCTTTCCCTCCATATCTTTATCGTATCAGATTTACTATTACAGCCTCAATCCTTCCCATCA
1 TCAACCTTTCCCTTTATATCTTTATGGTACCAGATTTACCGTTGCAGCCTCAATCCTTCCCATCA
* * *
4720 TAT-TTTCTAAGGTACCAGGTTCGCCGTTACGGTCTAAACCTTTCCCTTCACATCGTCTAAGGTA
66 TATCTTT-TAAGGTACCAGGTTCGCCGTTGCGGCCTAAACCTTTCCCTTCACATCTTCTAAGGTA
4784 CTGGGTTCGCCATTGCAGCC
130 CTGGGTTCGCCATTGC-GCC
* * *
4804 TCAATCTTTCTCTTTATATCTTTATGGTACCAGATTTACCGTTGC-GACCTCAATCTTTCCCATC
1 TCAACCTTTCCCTTTATATCTTTATGGTACCAGATTTACCGTTGCAG-CCTCAATCCTTCCCATC
* ** * *
4868 ACT-TCTTTTAAGGTACCAGGTTCGCCGTTGCGACCTCCACCTTTCCCTTCATATCTTC-ATGGT
65 A-TATCTTTTAAGGTACCAGGTTCGCCGTTGCGGCCTAAACCTTTCCCTTCACATCTTCTAAGGT
** *
4931 ACTGAATTCGCCATTATCGCC
129 ACTGGGTTCGCCATT-GCGCC
* * * * * * ** * *
4952 TCAATCC-TTCCCATTATATTTTCTAAGGTACCGGGTTCACCGTTGTGGCCTCCA-CCTTTCCTT
1 TCAA-CCTTTCCCTTTATATCTT-TATGGTACCAGATTTACCGTTGCAGCCTCAATCC-TTCC-C
* * * * * * *
5015 AT-ATATC-TTCATGGTATC-GGATTCACCGTTGTGGCCTTAATCC-TTCCCATT-ACATCTTAT
62 ATCATATCTTTTAAGGTACCAGG-TTCGCCGTTGCGGCC-TAAACCTTTCCC-TTCACATCTTCT
* * *
5075 AAGGTACCGGGTTCGCCGTTGTGGCC
124 AAGGTACTGGGTTCGCCATTG-CGCC
* * * ** *
5101 TTAACCTTTCCTTTTATATCTTCATGGTACC-GAATTTTTCTTTGCAGCCTCAATCCTTCCCATC
1 TCAACCTTTCCCTTTATATCTTTATGGTACCAG-ATTTACCGTTGCAGCCTCAATCCTTCCCATC
* * * *
5165 ACATCTTTTAAGGTACCGGGTTCGCCGTTGCAGCCTGAACCTTTCCCTTCACATCTTCTAAGGTA
65 ATATCTTTTAAGGTACCAGGTTCGCCGTTGCGGCCTAAACCTTTCCCTTCACATCTTCTAAGGTA
* * *
5230 CGGGGTTC-CTCGTTGTGACC
130 CTGGGTTCGC-CATTGCG-CC
* * ** *** * *
5250 TCAACCTTTCCCTTCATATCTTCATGGTATTAGATTCGTCGTTGCAGCCTCAGTCTTTCCCATCA
1 TCAACCTTTCCCTTTATATCTTTATGGTACCAGATTTACCGTTGCAGCCTCAATCCTTCCCATCA
* * * * * * *
5315 CATCTTTTAAGGTATCGGGTTCGTCATTGCGGTCTCAACCTTTCCCTT
66 TATCTTTTAAGGTACCAGGTTCGCCGTTGCGGCCTAAACCTTTCCCTT
5363 TATATTTTCA
Statistics
Matches: 439, Mismatches: 94, Indels: 52
0.75 0.16 0.09
Matches are distributed among these distances:
147 5 0.01
148 107 0.24
149 317 0.72
150 10 0.02
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.37
Consensus pattern (148 bp):
TCAACCTTTCCCTTTATATCTTTATGGTACCAGATTTACCGTTGCAGCCTCAATCCTTCCCATCA
TATCTTTTAAGGTACCAGGTTCGCCGTTGCGGCCTAAACCTTTCCCTTCACATCTTCTAAGGTAC
TGGGTTCGCCATTGCGCC
Found at i:4882 original size:248 final size:248
Alignment explanation
Indices: 4539--4995 Score: 578
Period size: 248 Copynumber: 1.8 Consensus size: 248
4529 TAATGTATAA
* * * * * *
4539 GGTTCGTCATTGCGGCTTCAACCTTTCTCTCCACATCTTTATGGTACAAGATTTGCCGTTGTGGC
1 GGTTCGCCATTGCAGCCTCAACCTTTCTCTCCACATCTTTATGGTACAAGATTTACCGTTGCGAC
* * * *
4604 TTCAATCTTTCCCTATCACGTCTCTAAGGTACAACATTCACCGTTGTGGCTTCAACCTTTCCCTC
66 CTCAATCTTTCCCTATCACGTCTCTAAGGTACAACATTCACCGTTGCGACCTCAACCTTTCCCTC
* * *
4669 CATATCTTTATCGTATCAG-ATTTACTATTA-CAGCCTCAATCCTTCCCATCATATTTTCTAAGG
131 CATATCTTCATCGTA-CAGAATTCACCATTATC-GCCTCAATCCTTCCCATCATATTTTCTAAGG
*
4732 TACCAGGTTCGCCGTTACGGTCTAAACCTTTCCCTTCACATCGTCTAAGGTACTG
194 TACCAGGTTCACCGTTACGGTCTAAACCTTTCCCTTCACATCGTCTAAGGTACTG
* ** * *
4787 GGTTCGCCATTGCAGCCTCAATCTTTCTCTTTATATCTTTATGGTACCAGATTTACCGTTGCGAC
1 GGTTCGCCATTGCAGCCTCAACCTTTCTCTCCACATCTTTATGGTACAAGATTTACCGTTGCGAC
* * * ** * *
4852 CTCAATCTTTCCC-ATCACTTCTTTTAAGGTACCAGGTTCGCCGTTGCGACCTCCACCTTTCCCT
66 CTCAATCTTTCCCTATCACGTC-TCTAAGGTACAACATTCACCGTTGCGACCTCAACCTTTCCCT
* * * * *
4916 TCATATCTTCATGGTACTGAATTCGCCATTATCGCCTCAATCCTTCCCATTATATTTTCTAAGGT
130 CCATATCTTCATCGTACAGAATTCACCATTATCGCCTCAATCCTTCCCATCATATTTTCTAAGGT
*
4981 ACCGGGTTCACCGTT
195 ACCAGGTTCACCGTT
4996 GTGGCCTCCA
Statistics
Matches: 174, Mismatches: 32, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
247 9 0.05
248 164 0.94
249 1 0.01
ACGTcount: A:0.20, C:0.30, G:0.14, T:0.36
Consensus pattern (248 bp):
GGTTCGCCATTGCAGCCTCAACCTTTCTCTCCACATCTTTATGGTACAAGATTTACCGTTGCGAC
CTCAATCTTTCCCTATCACGTCTCTAAGGTACAACATTCACCGTTGCGACCTCAACCTTTCCCTC
CATATCTTCATCGTACAGAATTCACCATTATCGCCTCAATCCTTCCCATCATATTTTCTAAGGTA
CCAGGTTCACCGTTACGGTCTAAACCTTTCCCTTCACATCGTCTAAGGTACTG
Found at i:5122 original size:198 final size:199
Alignment explanation
Indices: 4761--5209 Score: 523
Period size: 198 Copynumber: 2.3 Consensus size: 199
4751 GTCTAAACCT
* * * * *
4761 TTCCCTTCACATC-GTCTAAGGTACTGGGTTCGCCATTGCAGCCTCAATCTTTCTCTTTATATCT
1 TTCCCATCACATCTTTCTAAGGTACCGGGTTCGCCGTTGCAGCCTCAACCTTTCTCTTTATATCT
* * * * *
4825 TTATGGTACCAGATTTACCGTTGCGACCTCAATCTTTCCCATCACTTCTTTTAAGGTACCAGGTT
66 TCATGGTACCAGATTCACCGTTGCGACCTCAATCCTTCCCATCACATCTTATAAGGTACCAGGTT
* *
4890 CGCCGTTGCGACCTCCACCTTTCCCTTCATATCTTCATGGTACTGAATTCGCCATTAT-C-GCCT
131 CGCCGTTGCGACCTCAACCTTTCCCTTCATATCTTCATGGTACCGAATTCGCC-TT-TGCAGCCT
4953 CAATCC
194 CAATCC
* * * ** *
4959 TTCCCATTATAT-TTTCTAAGGTACCGGGTTCACCGTTGTGGCCTCCACCTTTC-CTTATATATC
1 TTCCCATCACATCTTTCTAAGGTACCGGGTTCGCCGTTGCAGCCTCAACCTTTCTCTT-TATATC
* * * * * * *
5022 TTCATGGTATCGGATTCACCGTTGTGGCCTTAATCCTTCCCATTACATCTTATAAGGTACCGGGT
65 TTCATGGTACCAGATTCACCGTTGCGACCTCAATCCTTCCCATCACATCTTATAAGGTACCAGGT
* * * * * ***
5087 TCGCCGTTGTGGCCTTAACCTTTCCTTTTATATCTTCATGGTACCGAATTTTTCTTTGCAGCCTC
130 TCGCCGTTGCGACCTCAACCTTTCCCTTCATATCTTCATGGTACCGAATTCGCCTTTGCAGCCTC
5152 AATCC
195 AATCC
*
5157 TTCCCATCACATCTTT-TAAGGTACCGGGTTCGCCGTTGCAGCCTGAACCTTTC
1 TTCCCATCACATCTTTCTAAGGTACCGGGTTCGCCGTTGCAGCCTCAACCTTTC
5210 CCTTCACATC
Statistics
Matches: 206, Mismatches: 40, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
196 1 0.00
197 6 0.03
198 196 0.95
199 3 0.01
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.37
Consensus pattern (199 bp):
TTCCCATCACATCTTTCTAAGGTACCGGGTTCGCCGTTGCAGCCTCAACCTTTCTCTTTATATCT
TCATGGTACCAGATTCACCGTTGCGACCTCAATCCTTCCCATCACATCTTATAAGGTACCAGGTT
CGCCGTTGCGACCTCAACCTTTCCCTTCATATCTTCATGGTACCGAATTCGCCTTTGCAGCCTCA
ATCC
Found at i:5294 original size:99 final size:99
Alignment explanation
Indices: 5185--5374 Score: 247
Period size: 99 Copynumber: 1.9 Consensus size: 99
5175 AGGTACCGGG
* * * *
5185 TTCGCCGTTGCAGCCTGAACCTTTCCCTTCACATCTTCTAAGGTA-CGGGGTTCCTCGTTGTGAC
1 TTCGCCGTTGCAGCCTCAACCTTTCCCATCACATCTTCTAAGGTATC-GGGTTCCTCATTGCGAC
5249 CTCAACCTTTCCCTTCATATCTTCATGGTATTAGA
65 CTCAACCTTTCCCTTCATATCTTCATGGTATTAGA
* ** * * **
5284 TTCGTCGTTGCAGCCTCAGTCTTTCCCATCACATCTTTTAAGGTATCGGGTTCGTCATTGCGGTC
1 TTCGCCGTTGCAGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCCTCATTGCGACC
* *
5349 TCAACCTTTCCCTTTATATTTTCATG
66 TCAACCTTTCCCTTCATATCTTCATG
5375 TTCCCTTGAT
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
99 76 0.99
100 1 0.01
ACGTcount: A:0.16, C:0.29, G:0.17, T:0.38
Consensus pattern (99 bp):
TTCGCCGTTGCAGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCCTCATTGCGACC
TCAACCTTTCCCTTCATATCTTCATGGTATTAGA
Found at i:6235 original size:17 final size:16
Alignment explanation
Indices: 6199--6264 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 16
6189 TCGATACCTC
* *
6199 TTTTTCTTTTTCCTTCT
1 TTTTTCTTTTT-TTTTT
6216 TTTTTCTTTTTATTTTT
1 TTTTTCTTTTT-TTTTT
*
6233 TTTCTCTTCTTTTTTTT
1 TTTTTCTT-TTTTTTTT
*
6250 ATTTTTATTTTTTTT
1 -TTTTTCTTTTTTTT
6265 GGGTGAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
17 32 0.78
18 9 0.22
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTT
Found at i:6243 original size:27 final size:27
Alignment explanation
Indices: 6205--6264 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 27
6195 CCTCTTTTTC
*
6205 TTTTTCCTTC-TTTTTTCTTTTTATTT
1 TTTTTCCTTCTTTTTTTATTTTTATTT
6231 TTTTTCTCTTCTTTTTTTTATTTTTATTT
1 TTTTTC-CTTC-TTTTTTTATTTTTATTT
6260 TTTTT
1 TTTTT
6265 GGGTGAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 6 0.20
27 4 0.13
29 20 0.67
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (27 bp):
TTTTTCCTTCTTTTTTTATTTTTATTT
Found at i:6827 original size:81 final size:81
Alignment explanation
Indices: 6706--6857 Score: 279
Period size: 81 Copynumber: 1.9 Consensus size: 81
6696 AATGATGTTC
*
6706 AATAAGCGTAGAGAGCAAATGATAACTTCTCATGCAAATCTTTGTAGGTCTTGATCTTTTTGATA
1 AATAAGCGTAGAGAGCAAATGATAACTTCTCATGCAAATCTTTGTAGGTCTTGATCTTCTTGATA
6771 TTCTTGATTTATTTTT
66 TTCTTGATTTATTTTT
6787 AATAAGCGTAGAGAGCAAATGATAACTTCTCATGTC-AATCTTTGTAGGTCTTGATCTTCTTGAT
1 AATAAGCGTAGAGAGCAAATGATAACTTCTCATG-CAAATCTTTGTAGGTCTTGATCTTCTTGAT
6851 ATTCTTG
65 ATTCTTG
6858 TTAACTGCTT
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
81 68 0.99
82 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (81 bp):
AATAAGCGTAGAGAGCAAATGATAACTTCTCATGCAAATCTTTGTAGGTCTTGATCTTCTTGATA
TTCTTGATTTATTTTT
Found at i:18469 original size:46 final size:46
Alignment explanation
Indices: 18384--18472 Score: 135
Period size: 47 Copynumber: 1.9 Consensus size: 46
18374 GTAAATCTTA
* * *
18384 AAAGATGTGTTTTTGGGTAAATTTTAAAATATGGCTTTTATTTATC
1 AAAGATGTGTTTTTGGGTAAATTTTAAAAGATAGATTTTATTTATC
18430 AAAGATGTGTTTTTTGGGTAAATTTTAAAAGA-AGATTTTATTT
1 AAAGATGTG-TTTTTGGGTAAATTTTAAAAGATAGATTTTATTT
18473 TTCTTTCTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
46 18 0.46
47 21 0.54
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (46 bp):
AAAGATGTGTTTTTGGGTAAATTTTAAAAGATAGATTTTATTTATC
Done.