Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_282 ID=scaffold_282-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: 8677
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1768 original size:45 final size:45
Alignment explanation
Indices: 1709--1834 Score: 116
Period size: 44 Copynumber: 2.8 Consensus size: 45
1699 GTGGTTTTAG
* * * * *
1709 CCTGCTTCATTGCAACGTCAGGGAGATAAGACTTTGATGTTTTAA
1 CCTGCTCCACTGCAACCTCAGGGAGATAAGACTTTGATGCTTCAA
* ** *
1754 TCTGCTCCACTGCAATTTCATGGAGATAAGAC-TT-ATTGCTTCAA
1 CCTGCTCCACTGCAACCTCAGGGAGATAAGACTTTGA-TGCTTCAA
*
1798 CCTACTCC-CTTGCAACCTCAGGGAGATAAGA-TTTGAT
1 CCTGCTCCAC-TGCAACCTCAGGGAGATAAGACTTTGAT
1835 ATGATAAGAT
Statistics
Matches: 64, Mismatches: 13, Indels: 9
0.74 0.15 0.10
Matches are distributed among these distances:
43 2 0.03
44 35 0.55
45 27 0.42
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (45 bp):
CCTGCTCCACTGCAACCTCAGGGAGATAAGACTTTGATGCTTCAA
Found at i:1948 original size:44 final size:44
Alignment explanation
Indices: 1900--1998 Score: 155
Period size: 44 Copynumber: 2.2 Consensus size: 44
1890 TAATCTACTT
* *
1900 CACTGCAACTTTAGGGAGATAGG-ATTAGTAGCTTCAGCCTGCTC
1 CACTGCAACTTTAGGGAGATAGGAATT-GTAGCTTCAACCTGCCC
*
1944 CACTGCAACTTTAGGGAGATAGGAATTGTATCTTCAACCTGCCC
1 CACTGCAACTTTAGGGAGATAGGAATTGTAGCTTCAACCTGCCC
1988 CACTGCAACTT
1 CACTGCAACTT
1999 CAGAGGGATA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
44 48 0.94
45 3 0.06
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.27
Consensus pattern (44 bp):
CACTGCAACTTTAGGGAGATAGGAATTGTAGCTTCAACCTGCCC
Found at i:2024 original size:44 final size:43
Alignment explanation
Indices: 1932--2064 Score: 144
Period size: 44 Copynumber: 3.0 Consensus size: 43
1922 GATTAGTAGC
* * *
1932 TTCAGCCTGCTCCACTGCAACTTTAG-GGAGAT-AGGAATTGTAT
1 TTCAACCTGCTCCACTGCAACTTCAGAGG-GATAAGG-TTTGTAT
*
1975 CTTCAACCTGCCCCACTGCAACTTCAGAGGGATAAGGTTTGTTAT
1 -TTCAACCTGCTCCACTGCAACTTCAGAGGGATAAGGTTTG-TAT
* * *
2020 TTCAACCTACTCTACTGCAACTTCAGAGAGATAAGGTTTGATAT
1 TTCAACCTGCTCCACTGCAACTTCAGAGGGATAAGGTTTG-TAT
2064 T
1 T
2065 ATCTTCTCTA
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
44 69 0.90
45 8 0.10
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (43 bp):
TTCAACCTGCTCCACTGCAACTTCAGAGGGATAAGGTTTGTAT
Found at i:2630 original size:85 final size:85
Alignment explanation
Indices: 2535--2836 Score: 292
Period size: 85 Copynumber: 3.4 Consensus size: 85
2525 TTTAATCGGT
*
2535 TCTACTGCAACTTCAG-GAAGATAAGA-CTCGTAATTTCAACCTGCCCCACTGCAACTTCAGGGA
1 TCTACTGCAACTTCAGAG-AGATAAGATCT-GTAATTTCAACCTGCCCCACTGCAACTTTAGGGA
2598 GATGAGGTTTGATATGATCTGC
64 GATGAGGTTTGATATGATCTGC
* **
2620 TCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCACTCTGTTCCACTGCAACTTT
1 TCTACTGCAACTTCAGAGAGATAAGATCTGTAA-TT-T--C--AAC-CTGCCCCACTGCAACTTT
* * * * * *
2685 AGGGAAAT-AAGATTCACTTCCTTCAGTCTGC
59 AGGGAGATGAGGTTTGA--T--ATGA-TCTGC
* * *
2716 TCCACTGCAACTTCAGAGAGGTGAA-A-CTTGT-ATCTTCAACCTGCCCCACTGCAACTTTAGGA
1 TCTACTGCAACTTCAGAGAGAT-AAGATC-TGTAAT-TTCAACCTGCCCCACTGCAACTTTAGGG
2778 AGATGAGGTTTGATATGATCTGC
63 AGATGAGGTTTGATATGATCTGC
2801 TCTACTGCAACTTCAGAGAGATAAGATCTGTAATTT
1 TCTACTGCAACTTCAGAGAGATAAGATCTGTAATTT
2837 ATAGCTTCAA
Statistics
Matches: 172, Mismatches: 24, Indels: 42
0.72 0.10 0.18
Matches are distributed among these distances:
84 2 0.01
85 59 0.34
86 10 0.06
87 1 0.01
88 1 0.01
89 23 0.13
90 7 0.04
91 7 0.04
92 23 0.13
93 1 0.01
94 2 0.01
95 5 0.03
96 29 0.17
97 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (85 bp):
TCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTCAACCTGCCCCACTGCAACTTTAGGGAGA
TGAGGTTTGATATGATCTGC
Found at i:2862 original size:92 final size:92
Alignment explanation
Indices: 2580--2864 Score: 311
Period size: 92 Copynumber: 3.1 Consensus size: 92
2570 TCAACCTGCC
* *
2580 CCACTGCAACTTCAGGGAGATGAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAG
1 CCACTGCAACTTTAGGAAGATGAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAG
*
2645 ATCTGTAATTTATAGCTTCACTCTGTT
66 ATCTGTAATTTATAGCTTCAATCTGTT
* * * * * *
2672 CCACTGCAACTTTAGGGAA-AT-AAGATTCACTTCCTTCAGTCTGCTCCACTGCAACTTCAGAGA
1 CCACTGCAACTTTA-GGAAGATGAGGTTTGA--T--ATGA-TCTGCTCTACTGCAACTTCAGAGA
* * * **
2735 GGTGAA-A-C--T--TGTAT--CTTCAACCTGCC
60 GAT-AAGATCTGTAATTTATAGCTTCAATCTGTT
2761 CCACTGCAACTTTAGGAAGATGAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAG
1 CCACTGCAACTTTAGGAAGATGAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAG
2826 ATCTGTAATTTATAGCTTCAATCTGTT
66 ATCTGTAATTTATAGCTTCAATCTGTT
2853 CCACTGCAACTT
1 CCACTGCAACTT
2865 CAGGGAAATA
Statistics
Matches: 151, Mismatches: 25, Indels: 34
0.72 0.12 0.16
Matches are distributed among these distances:
84 2 0.01
85 26 0.17
86 3 0.02
88 6 0.04
89 24 0.16
90 9 0.06
91 9 0.06
92 36 0.24
93 5 0.03
95 3 0.02
96 26 0.17
97 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (92 bp):
CCACTGCAACTTTAGGAAGATGAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAG
ATCTGTAATTTATAGCTTCAATCTGTT
Found at i:2961 original size:181 final size:181
Alignment explanation
Indices: 2569--2906 Score: 525
Period size: 181 Copynumber: 1.9 Consensus size: 181
2559 GACTCGTAAT
* * *
2569 TTCAACCTGCCCCACTGCAACTTCAGGGAGATGAGGTTTGATATGATCTGCTCTACTGCAACTTC
1 TTCAACCTACCCCACTGCAACTACAGGAAGATGAGGTTTGATATGATCTGCTCTACTGCAACTTC
* *
2634 AGAGAGATAAGATCTGTAATTTATAGCTTCACTCTGTTCCACTGCAACTTTAGGGAAATAAGATT
66 AGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATT
* * * *
2699 CACTTCCTTCAGTCTGCTCCACTGCAACTTCAGAGAGGTGAAACTTGTATC
131 CACTTCCTGCAGCCTGCTCCACTGCAACTTCAGAGAGGCGAAACTGGTATC
* **
2750 TTCAACCTGCCCCACTGCAACTTTAGGAAGATGAGGTTTGATATGATCTGCTCTACTGCAACTTC
1 TTCAACCTACCCCACTGCAACTACAGGAAGATGAGGTTTGATATGATCTGCTCTACTGCAACTTC
2815 AGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATT
66 AGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATT
* * *
2880 CGCTAT-CTGCAGCCTGTTCCGCTGCAA
131 CACT-TCCTGCAGCCTGCTCCACTGCAA
2907 ACTCAGGAAG
Statistics
Matches: 147, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
181 146 0.99
182 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (181 bp):
TTCAACCTACCCCACTGCAACTACAGGAAGATGAGGTTTGATATGATCTGCTCTACTGCAACTTC
AGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATT
CACTTCCTGCAGCCTGCTCCACTGCAACTTCAGAGAGGCGAAACTGGTATC
Found at i:4278 original size:5 final size:5
Alignment explanation
Indices: 4259--4314 Score: 64
Period size: 5 Copynumber: 11.8 Consensus size: 5
4249 GGCCTCTACT
* * *
4259 TTTTC TTTT- TCTTC TTTTC TTTTC TTTTC TTTTT TTTTA TTTTC -TTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
4307 TTTT- TTTT
1 TTTTC TTTT
4315 AACATTCTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
4 11 0.25
5 33 0.75
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTC
Found at i:4291 original size:24 final size:23
Alignment explanation
Indices: 4259--4314 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
4249 GGCCTCTACT
*
4259 TTTTCTTTTTCTTCTTTTCTTTTC
1 TTTTCTTTTTCTTATTTTC-TTTC
*
4283 TTTTCTTTTTTTTTATTTTCTTTC
1 TTTTC-TTTTTCTTATTTTCTTTC
4307 TTTT-TTTT
1 TTTTCTTTT
4315 AACATTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 4 0.14
24 13 0.45
25 12 0.41
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTCTTTTTCTTATTTTCTTTC
Found at i:4306 original size:19 final size:19
Alignment explanation
Indices: 4259--4314 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
4249 GGCCTCTACT
* *
4259 TTTTCTTT-TTCTTCTTTTC
1 TTTTCTTTCTT-TTTTTTTA
4278 TTTTCTTTTCTTTTTTTTTA
1 TTTTC-TTTCTTTTTTTTTA
4298 TTTTCTTTCTTTTTTTT
1 TTTTCTTTCTTTTTTTT
4315 AACATTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.52
20 14 0.42
21 2 0.06
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTCTTTCTTTTTTTTTA
Found at i:4322 original size:19 final size:19
Alignment explanation
Indices: 4284--4324 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
4274 TTTCTTTTCT
* **
4284 TTTCTTTTTTTTTATTTTC
1 TTTCTTTTTTTTAACATTC
4303 TTTCTTTTTTTTAACATTC
1 TTTCTTTTTTTTAACATTC
4322 TTT
1 TTT
4325 GATTGAATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTCTTTTTTTTAACATTC
Done.