Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_99 ID=scaffold_99-JGI_221_v2.0
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: 14160
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Found at i:57 original size:22 final size:22
Alignment explanation
Indices: 29--181 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
19 TGTTGATAGT
*
29 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
51 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
73 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
95 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
117 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
139 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
161 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
182 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:320 original size:2 final size:2
Alignment explanation
Indices: 315--341 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
305 TGAAGTTTAA
315 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
342 AATAAGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1916 original size:40 final size:41
Alignment explanation
Indices: 1872--2396 Score: 316
Period size: 40 Copynumber: 12.9 Consensus size: 41
1862 GGTCCTCAAC
* *
1872 CTGCTCCACTGCAACTTCAGGGAGATAAG-GT-TGGTTTCGT
1 CTGCTCCACTACAACTT-AGGGAGATAAGACTGTGGTTTCGT
** *
1912 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTGT
1 CTGCTCCACTACAACTTAGGGAGATAAGA-CTGTGGTTTCGT
* * * *
1954 CTGCTCCACTACTAC-TAGGGAAATAAGACT-T-GATGCGAT
1 CTGCTCCACTACAACTTAGGGAGATAAGACTGTGGTTTCG-T
**
1993 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGG-TTCTGT
1 CTGCTCCACTACAACTTAGGGAGATAAGA-CTGTGGTTTC-GT
* ** * * *
2035 CTACTCCACTACTGCTTAAGGAGATAAGACT-TGATGT-GAT
1 CTGCTCCACTACAACTTAGGGAGATAAGACTGTGGTTTCG-T
* * * *
2075 CTGCTCCACTACTATTTAGGGAGATAAGACT-T-GATGCGAT
1 CTGCTCCACTACAACTTAGGGAGATAAGACTGTGGTTTCG-T
** * * *
2115 CTGCTCCACTACTGCTTAGGGACATAAGACT-T-GATGCGAT
1 CTGCTCCACTACAACTTAGGGAGATAAGACTGTGGTTTCG-T
** *
2155 CTGCTCCACTACTGCTTAGGGAGATAAGATCTATGG-TTCTGT
1 CTGCTCCACTACAACTTAGGGAGATAAGA-CTGTGGTTTC-GT
** * * *
2197 CTGCTCCACTACTGCCTAGGGAGATAAGACT-T-GATGCGAT
1 CTGCTCCACTACAACTTAGGGAGATAAGACTGTGGTTTCG-T
** * *
2237 CTGCTCCACTACTGCTTAGGGAGATAAGACT-T-GATGCGAT
1 CTGCTCCACTACAACTTAGGGAGATAAGACTGTGGTTTCG-T
* ** *
2277 TTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGG-TTCTAT
1 CTGCTCCACTACAACTTAGGGAGATAAGA-CTGTGGTTTC-GT
* ** * *
2319 CTGCTCCAGTACTGCTTAGGGAGATAAGACT-T-GATGCGAT
1 CTGCTCCACTACAACTTAGGGAGATAAGACTGTGGTTTCG-T
* **
2359 CTACTCCACTACCGCTTAGGGAGATAAGATCTGTGGTT
1 CTGCTCCACTACAACTTAGGGAGATAAGA-CTGTGGTT
2397 CTGATCCATC
Statistics
Matches: 414, Mismatches: 44, Indels: 51
0.81 0.09 0.10
Matches are distributed among these distances:
38 3 0.01
39 31 0.07
40 228 0.55
41 28 0.07
42 117 0.28
43 7 0.02
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (41 bp):
CTGCTCCACTACAACTTAGGGAGATAAGACTGTGGTTTCGT
Found at i:2121 original size:122 final size:123
Alignment explanation
Indices: 1872--2402 Score: 688
Period size: 122 Copynumber: 4.3 Consensus size: 123
1862 GGTCCTCAAC
* ** * *
1872 CTGCTCCACTGCAACTTCAGGGAGATAAGGT-TG-GTTTCG-TCTGCTCCACTACTGCTTAGGGA
1 CTGCTCCACTACTGCTT-AGGGAGATAAGATCTGTGATTCGATCTGCTCCACTACTGCTTAGGGA
*
1934 GATAAGATCTGTGGTTTTGTCTGCTCCACTACTA-CTAGGGAAATAAGACTTGATGCGAT
65 GATAAGATCTGTGG-TTTGTCTGCTCCACTACTACCTAGGGAGATAAGACTTGATGCGAT
* * *
1993 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTG-TCTACTCCACTACTGCTTAAGGA
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGATTC-GATCTGCTCCACTACTGCTTAGGGA
* * **
2057 GATAAGA-CT-TGATGTGATCTGCTCCACTACTATTTAGGGAGATAAGACTTGATGCGAT
65 GATAAGATCTGTGGTTTG-TCTGCTCCACTACTACCTAGGGAGATAAGACTTGATGCGAT
* *
2115 CTGCTCCACTACTGCTTAGGGACATAAGA-CT-TGATGCGATCTGCTCCACTACTGCTTAGGGAG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGATTCGATCTGCTCCACTACTGCTTAGGGAG
* *
2178 ATAAGATCTATGGTTCTGTCTGCTCCACTACTGCCTAGGGAGATAAGACTTGATGCGAT
66 ATAAGATCTGTGGTT-TGTCTGCTCCACTACTACCTAGGGAGATAAGACTTGATGCGAT
* *
2237 CTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGATGCGATTTGCTCCACTACTGCTTAGGGAG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGATTCGATCTGCTCCACTACTGCTTAGGGAG
* * * *
2300 ATAAGATCTGTGGTTCTATCTGCTCCAGTACTGCTTAGGGAGATAAGACTTGATGCGAT
66 ATAAGATCTGTGGTT-TGTCTGCTCCACTACTACCTAGGGAGATAAGACTTGATGCGAT
* * *
2359 CTACTCCACTACCGCTTAGGGAGATAAGATCTGTGGTTCTGATC
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGATTC-GATC
2403 CATCCCACTG
Statistics
Matches: 366, Mismatches: 32, Indels: 20
0.88 0.08 0.05
Matches are distributed among these distances:
119 1 0.00
120 47 0.13
121 37 0.10
122 241 0.66
123 33 0.09
124 4 0.01
125 3 0.01
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (123 bp):
CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGATTCGATCTGCTCCACTACTGCTTAGGGAG
ATAAGATCTGTGGTTTGTCTGCTCCACTACTACCTAGGGAGATAAGACTTGATGCGAT
Found at i:2163 original size:162 final size:161
Alignment explanation
Indices: 1911--2387 Score: 674
Period size: 162 Copynumber: 2.9 Consensus size: 161
1901 GTTGGTTTCG
* ** *
1911 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTG-TCTGCTCCACTACTAC-TAGGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-T-GATGCGATCTGCTCCACTACTGCTTAGGG
1974 AAATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTAC
63 AAATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-TGGTTCTGTCTAC
* *
2039 TCCACTACTGCTTAAGGAGATAAGACTTGATGTGA
127 TCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
** *
2074 TCTGCTCCACTACTATTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGACA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAAA
*
2139 TAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATGGTTCTGTCTGCTCC
66 TAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-TGGTTCTGTCTACTCC
*
2204 ACTACTGCCTAGGGAGATAAGACTTGATGCGA
130 ACTACTGCTTAGGGAGATAAGACTTGATGCGA
* *
2236 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATTTGCTCCACTACTGCTTAGGGAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAAA
* * * * * *
2301 TAAGATCTGTGGTTCTATCTGCTCCAGTACTGCTTAGGGAGATAAGA-CTTGATGC-GATCTACT
66 TAAGA-CT-TGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTGGTTCTG-TCTACT
*
2364 CCACTACCGCTTAGGGAGATAAGA
128 CCACTACTGCTTAGGGAGATAAGA
2388 TCTGTGGTTC
Statistics
Matches: 284, Mismatches: 25, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
160 3 0.01
161 17 0.06
162 198 0.70
163 32 0.11
164 34 0.12
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.30
Consensus pattern (161 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAAA
TAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTGGTTCTGTCTACTCCA
CTACTGCTTAGGGAGATAAGACTTGATGCGA
Found at i:3054 original size:108 final size:108
Alignment explanation
Indices: 2853--3055 Score: 284
Period size: 108 Copynumber: 1.9 Consensus size: 108
2843 GCTTGACAAA
2853 GATTATCAAAATGGACAAAATAAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAATCAATCAA
1 GATTATCAAAATGGACAAAATAAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAATCAATCAA
* **
2918 GATAGCAAATTTTGCTGAGATATGAAATGAATAAGATAAAAAT
66 GATAGCAAATTTTACTGAGATACAAAATGAATAAGATAAAAAT
* * * * ** *
2961 GATTATCACAATGGATAAGATGGAAA-TTTGTTGAGAGCAAAGCTCTAAATGAACAAATTAATCA
1 GATTATCAAAATGGACAAAAT-AAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAATCAATCA
3025 AGATAGCAAATTTTACT-AGAATACAAAATGA
65 AGATAGCAAATTTTACTGAG-ATACAAAATGA
3056 GAATAAACTA
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 2 0.02
108 78 0.94
109 3 0.04
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (108 bp):
GATTATCAAAATGGACAAAATAAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAATCAATCAA
GATAGCAAATTTTACTGAGATACAAAATGAATAAGATAAAAAT
Found at i:4689 original size:27 final size:27
Alignment explanation
Indices: 4651--4704 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
4641 TTTCCTCTTC
4651 CTCGTCAACGTTACAACAGTGGGCTGG
1 CTCGTCAACGTTACAACAGTGGGCTGG
4678 CTCGTCAACGTTACAACAGTGGGCTGG
1 CTCGTCAACGTTACAACAGTGGGCTGG
4705 AGCATCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (27 bp):
CTCGTCAACGTTACAACAGTGGGCTGG
Found at i:13527 original size:108 final size:105
Alignment explanation
Indices: 13268--13572 Score: 360
Period size: 108 Copynumber: 2.9 Consensus size: 105
13258 GAAAGTTAAG
* * * *
13268 AAGATATTTGGCTATTTGGTCAAACGAGAAATTGAGACCCAGCACGTTAGGGCCCG-TTCTCTCA
1 AAGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC-CTCG
* * * * *
13332 AATTTCCAAACGCAAATATTGCCTCACTTTGAAATTTTAAA
65 ATTTTCCAAACGCAAATATTGCCTTATTTTAAAATTTAAAA
* * * *
13373 AGGATATTTGGCTATTTGGTCAAACGAGAAGTCAAAACCCAACACGTTAGGGCACGTTTCCTCGA
1 AAGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGA
*
13438 TTTTCCAAACGCGAAATATTACCTTATTTTAAAAGTTTAAAA
66 TTTTCCAAACGC-AAATATTGCCTTATTTTAAAA-TTTAAAA
* ** * * * *
13480 AAGATATTTGGCTATTTTGGTCGAATAAAAAATCGAAACCCAGCACGTTAGGGTATGTTTTCTCG
1 AAGATATTTGGCTA-TTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCG
*
13545 ATTTTCCAAACGCAAAAAATTGCCTTAT
65 ATTTTCCAAACGC-AAATATTGCCTTAT
13573 GTAGAAAATT
Statistics
Matches: 168, Mismatches: 28, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
105 64 0.38
106 20 0.12
107 19 0.11
108 65 0.39
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (105 bp):
AAGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGA
TTTTCCAAACGCAAATATTGCCTTATTTTAAAATTTAAAA
Found at i:13899 original size:20 final size:19
Alignment explanation
Indices: 13876--13929 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 19
13866 AAAAAATGTG
13876 TATATATGTATATCATAAAA
1 TATATATGTATAT-ATAAAA
*
13896 TATATATCAATATTATATAAAA
1 TATATAT--GTA-TATATAAAA
*
13918 AATATATGTATA
1 TATATATGTATA
13930 CATGTACATA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 2 0.07
20 9 0.32
22 14 0.50
23 3 0.11
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (19 bp):
TATATATGTATATATAAAA
Found at i:14138 original size:17 final size:18
Alignment explanation
Indices: 14116--14155 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
14106 ACATGTATAA
14116 GTATGTGTATTA-AAAAT
1 GTATGTGTATTATAAAAT
14133 GTATGTGTATTATAAAAT
1 GTATGTGTATTATAAAAT
14151 GTATG
1 GTATG
14156 CATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.42
Consensus pattern (18 bp):
GTATGTGTATTATAAAAT
Done.