Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_414 ID=scaffold_414-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: 7795
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.30
Warning! 504 characters in sequence are not A, C, G, or T
Found at i:1242 original size:3 final size:3
Alignment explanation
Indices: 1234--1301 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
1224 GTGCTATTTT
** * *
1234 TTA TTA TTA TATA TTA TTA TTA AAA CTA TTA TAA TTA TTA TTA TTTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* *
1281 GTA TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
1302 AATACTTTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:3864 original size:19 final size:19
Alignment explanation
Indices: 3840--3886 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
3830 ACGTCTCTTT
*
3840 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTGCAT-CA
3859 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
3878 TATGCATTA
1 TTTGCATTA
3887 GATCTTTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:5155 original size:23 final size:23
Alignment explanation
Indices: 5119--5184 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
5109 AGTTCAGACT
*
5119 AAAAAA-AAACAAAA-AAAAATC
1 AAAAAATAAAAAAAAGAAAAATC
** *
5140 AAAAAAATAAAAAAAATCAAAGTC
1 -AAAAAATAAAAAAAAGAAAAATC
*
5164 AAAAATTAAAAAAAAGAAAAA
1 AAAAAATAAAAAAAAGAAAAA
5185 GGAAAGGTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
22 6 0.17
23 24 0.69
24 5 0.14
ACGTcount: A:0.82, C:0.06, G:0.03, T:0.09
Consensus pattern (23 bp):
AAAAAATAAAAAAAAGAAAAATC
Found at i:6041 original size:7 final size:8
Alignment explanation
Indices: 6008--6050 Score: 61
Period size: 8 Copynumber: 5.4 Consensus size: 8
5998 ACTTTGAGTC
6008 AAAA-GAA
1 AAAATGAA
*
6015 AAGATGAAA
1 AAAATG-AA
6024 AAAATGAA
1 AAAATGAA
6032 AAAATGAA
1 AAAATGAA
6040 AAAATGAA
1 AAAATGAA
6048 AAA
1 AAA
6051 GTAAAAATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
7 3 0.09
8 22 0.69
9 7 0.22
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (8 bp):
AAAATGAA
Found at i:6057 original size:16 final size:16
Alignment explanation
Indices: 6008--6057 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
5998 ACTTTGAGTC
*
6008 AAAA-GAAAAGATGAAA
1 AAAATGAAAAAAT-AAA
*
6024 AAAATGAAAAAATGAA
1 AAAATGAAAAAATAAA
*
6040 AAAATGAAAAAGTAAA
1 AAAATGAAAAAATAAA
6056 AA
1 AA
6058 TGGAGAGGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 22 0.76
17 7 0.24
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (16 bp):
AAAATGAAAAAATAAA
Found at i:7356 original size:43 final size:43
Alignment explanation
Indices: 7293--7443 Score: 125
Period size: 43 Copynumber: 3.5 Consensus size: 43
7283 CAGCGAAGTA
*
7293 GGTCGAAGACAAAA-ACCTTGCCTCTCTCGGTTGTGATGTAGCT
1 GGTCGAAGACAAAAGATCTTGCCTCTCTCGGTTGTGATG-AGCT
* * * *
7336 GGTGGAAGA-AAAAGATCTTGCCT-TC-CTGTAT-TGACAGCGAAGCA
1 GGTCGAAGACAAAAGATCTTGCCTCTCTCGGT-TGTG--A-TG-AGCT
* *
7380 GGTCGAAGACACAA-ACCTTGCCTCTCTCGGTTGTGATAGAGCT
1 GGTCGAAGACAAAAGATCTTGCCTCTCTCGGTTGTGAT-GAGCT
*
7423 GGTTGAAGACAAAAGATCTTG
1 GGTCGAAGACAAAAGATCTTG
7444 TCTTCCTGTA
Statistics
Matches: 82, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
41 5 0.06
42 7 0.09
43 32 0.39
44 27 0.33
45 6 0.07
46 5 0.06
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (43 bp):
GGTCGAAGACAAAAGATCTTGCCTCTCTCGGTTGTGATGAGCT
Found at i:7400 original size:44 final size:44
Alignment explanation
Indices: 7265--7402 Score: 124
Period size: 44 Copynumber: 3.2 Consensus size: 44
7255 AGTTGCAGAT
* *
7265 CTTGCCTTCCTGCATTGACAGCGAAGTAGGTCGAAGACAAAAAC
1 CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACAAAAAC
* * * * * *
7309 CTTGCCTCTCTCGGT-TGTG--A-TGTAGCTGGTGGAAGA-AAAAGAT
1 CTTGCCT-TC-CTGTAT-TGACAGCGAAGCAGGTCGAAGACAAAA-AC
*
7352 CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACAAAAAC
7396 CTTGCCT
1 CTTGCCT
7403 CTCTCGGTTG
Statistics
Matches: 70, Mismatches: 15, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
41 5 0.07
42 7 0.10
43 20 0.29
44 28 0.40
45 6 0.09
46 4 0.06
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.25
Consensus pattern (44 bp):
CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACAAAAAC
Found at i:7407 original size:87 final size:88
Alignment explanation
Indices: 7261--7463 Score: 320
Period size: 87 Copynumber: 2.3 Consensus size: 88
7251 ATGAAGTTGC
* *
7261 AGATCTTGCCTTCCTGCATTGACAGCGAAGTAGGTCGAAGACAAAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACAAAAACCTTGCCTCTCTCGGTTG
7326 TGAT-GTAGCTGGTGGAAGA-AAA
66 TGATAG-AGCTGGTGGAAGACAAA
*
7348 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACAAAAACCTTGCCTCTCTCGGTTG
*
7413 TGATAGAGCTGGTTGAAGACAAA
66 TGATAGAGCTGGTGGAAGACAAA
* *
7436 AGATCTTGTCTTCCTGTAATTGGCAGCG
1 AGATCTTGCCTTCCTGT-ATTGACAGCG
7464 GAGGGGATCG
Statistics
Matches: 107, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
87 78 0.73
88 20 0.19
89 9 0.08
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (88 bp):
AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACAAAAACCTTGCCTCTCTCGGTTG
TGATAGAGCTGGTGGAAGACAAA
Found at i:7505 original size:46 final size:46
Alignment explanation
Indices: 7436--7793 Score: 493
Period size: 46 Copynumber: 7.8 Consensus size: 46
7426 TGAAGACAAA
* *
7436 AGATCTTGTCTTCCTGTAATTGGCAGCGGAGGGGATCGGAGATAGC
1 AGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGC
* **
7482 AGATCTTGCCTTCCTGTATTTGGCAGCGGAGAAGATCGAAGATAGC
1 AGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGC
* * * * *
7528 ATATTTTATCTTCCTGTAATTGGCAGCGGA-GGGATCGAAGATAGT
1 AGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGC
* *
7573 AGATCTTGTCTTCCTGTATTTGGCAGCAGAGAGGATCGAAGATAGC
1 AGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGC
* *
7619 AGATCTTGTCTTCCTGTATTTCGCAGCGGATGGGATCGAAGATAGC
1 AGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGC
* *
7665 AGATCTTGTCCTCCTGTATTTGGCAGCGGAGGGGATCAAAGATAGC
1 AGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGC
* * * *
7711 AGATCTTATCTTCCTGTATTTGGCAGCGAAGGAGATCGAAGGTAGC
1 AGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGC
* * * *
7757 AGATCTTATCTTCATGTATTTGGCAACGGAGGAGATC
1 AGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
7794 AA
Statistics
Matches: 274, Mismatches: 37, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
45 37 0.14
46 237 0.86
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (46 bp):
AGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGC
Found at i:7664 original size:183 final size:184
Alignment explanation
Indices: 7436--7781 Score: 534
Period size: 183 Copynumber: 1.9 Consensus size: 184
7426 TGAAGACAAA
* *
7436 AGATCTTGTCTTCCTGTAATTGGCAGCGGAGGGGATCGGAGATAGCAGATCTTG-CCTTCCTGTA
1 AGATCTTGTCTTCCTGTAATTCGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCC-TCCTGTA
* * * *
7500 TTTGGCAGCGGAGAAGATCGAAGATAGCATATTTTATCTTCCTGTAATTGGCAGCGGAGG-GATC
65 TTTGGCAGCGGAGAAGATCAAAGATAGCAGATCTTATCTTCCTGTAATTGGCAGCGAAGGAGATC
* * *
7564 GAAGATAGTAGATCTTGTCTTCCTGTATTTGGCAGCAGAGAGGATCGAAGATAGC
130 GAAGATAGCAGATCTTATCTTCATGTATTTGGCAGCAGAGAGGATCGAAGATAGC
* *
7619 AGATCTTGTCTTCCTGTATTTCGCAGCGGATGGGATCGAAGATAGCAGATCTTGTCCTCCTGTAT
1 AGATCTTGTCTTCCTGTAATTCGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCCTCCTGTAT
** *
7684 TTGGCAGCGGAGGGGATCAAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGAAGGAGATCG
66 TTGGCAGCGGAGAAGATCAAAGATAGCAGATCTTATCTTCCTGTAATTGGCAGCGAAGGAGATCG
*
7749 AAGGTAGCAGATCTTATCTTCATGTATTTGGCA
131 AAGATAGCAGATCTTATCTTCATGTATTTGGCA
7782 ACGGAGGAGA
Statistics
Matches: 146, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
183 110 0.75
184 36 0.25
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (184 bp):
AGATCTTGTCTTCCTGTAATTCGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCCTCCTGTAT
TTGGCAGCGGAGAAGATCAAAGATAGCAGATCTTATCTTCCTGTAATTGGCAGCGAAGGAGATCG
AAGATAGCAGATCTTATCTTCATGTATTTGGCAGCAGAGAGGATCGAAGATAGC
Done.