Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_928 ID=scaffold_928-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: 2349
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Found at i:484 original size:20 final size:20
Alignment explanation
Indices: 459--499 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
449 AACCACAAAC
459 CCCCAACATCTAACCCCTAA
1 CCCCAACATCTAACCCCTAA
* *
479 CCCCAACCTTTAACCCCTAA
1 CCCCAACATCTAACCCCTAA
499 C
1 C
500 TACTAACCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.51, G:0.00, T:0.17
Consensus pattern (20 bp):
CCCCAACATCTAACCCCTAA
Found at i:614 original size:14 final size:14
Alignment explanation
Indices: 585--649 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 14
575 CAAATCTATA
*
585 AACCCTAAATCCCT
1 AACCCTTAATCCCT
* *
599 AACTCTTAATCTCT
1 AACCCTTAATCCCT
613 AACCCTTAATCCCT
1 AACCCTTAATCCCT
* *
627 AACCCCTAAATCAC-
1 AA-CCCTTAATCCCT
641 AACCCTTAA
1 AACCCTTAA
650 ACCAGAACCC
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
13 6 0.14
14 27 0.64
15 9 0.21
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.26
Consensus pattern (14 bp):
AACCCTTAATCCCT
Found at i:644 original size:28 final size:29
Alignment explanation
Indices: 585--663 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 29
575 CAAATCTATA
* * * *
585 AACCCTAAATCCCTAA-CTCTTAATCTCT
1 AACCCTTAATCCCTAACCCCTAAATCACT
613 AACCCTTAATCCCTAACCCCTAAATCAC-
1 AACCCTTAATCCCTAACCCCTAAATCACT
* **
641 AACCCTTAAACCAGAACCCCTAA
1 AACCCTTAATCCCTAACCCCTAA
664 TCCATAGTCC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 35 0.81
29 8 0.19
ACGTcount: A:0.37, C:0.39, G:0.01, T:0.23
Consensus pattern (29 bp):
AACCCTTAATCCCTAACCCCTAAATCACT
Found at i:802 original size:14 final size:14
Alignment explanation
Indices: 757--794 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
747 ATCCTAAATT
757 AACCATATATCCTA
1 AACCATATATCCTA
*
771 AACCATATACCCTA
1 AACCATATATCCTA
785 AACCATATAT
1 AACCATATAT
795 ATTAAACCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (14 bp):
AACCATATATCCTA
Found at i:1246 original size:41 final size:41
Alignment explanation
Indices: 1057--1246 Score: 299
Period size: 41 Copynumber: 4.6 Consensus size: 41
1047 TTTTGCAGCT
* * *
1057 CTTTTTCAAAAACGTCGCTAAAGCCAAGAGCATTAGCGGCG
1 CTTTTCCAAAAACGCCGCTAAAGCCCAGAGCATTAGCGGCG
* ** *
1098 CTTTACCAAAAACGCCGCTAAAGCAAATAGCATTAGCGGCG
1 CTTTTCCAAAAACGCCGCTAAAGCCCAGAGCATTAGCGGCG
1139 CTTTTCCAAAAACGCCGCTAAAGCCCAGAGCATTAGCGGCG
1 CTTTTCCAAAAACGCCGCTAAAGCCCAGAGCATTAGCGGCG
*
1180 CTTTTCCAAAAACGCCGCTAAAGCCCAGAGCATTAGCGACG
1 CTTTTCCAAAAACGCCGCTAAAGCCCAGAGCATTAGCGGCG
*
1221 CTTTTCAAAAAACGCCGCTAAAGCCC
1 CTTTTCCAAAAACGCCGCTAAAGCCC
1247 CAAATGGTCT
Statistics
Matches: 138, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 138 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.18
Consensus pattern (41 bp):
CTTTTCCAAAAACGCCGCTAAAGCCCAGAGCATTAGCGGCG
Found at i:1351 original size:39 final size:40
Alignment explanation
Indices: 1308--1407 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 40
1298 TCAAAAAACA
* * *
1308 CCGCTAATTCTC-ATTTTTAGCAGAGCTTTCCCTAAAGCG
1 CCGCTAATGCTCGATTTTTAGCAGAGCTTTACATAAAGCG
* * * * *
1347 CCGCTAATGCTCTATCTTTAGCGGCGTTTTACATAAAGCG
1 CCGCTAATGCTCGATTTTTAGCAGAGCTTTACATAAAGCG
1387 CCGCTAATGCTCGATTTTTAG
1 CCGCTAATGCTCGATTTTTAG
1408 TGGCGTTTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
39 11 0.22
40 40 0.78
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (40 bp):
CCGCTAATGCTCGATTTTTAGCAGAGCTTTACATAAAGCG
Found at i:1384 original size:40 final size:40
Alignment explanation
Indices: 1340--1416 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
1330 GAGCTTTCCC
*
1340 TAAAGCGCCGCTAATGCTCTATCTTTAGCGGCGTTTTACA
1 TAAAGCGCCGCTAATGCTCGATCTTTAGCGGCGTTTTACA
* *
1380 TAAAGCGCCGCTAATGCTCGATTTTTAGTGGCGTTTT
1 TAAAGCGCCGCTAATGCTCGATCTTTAGCGGCGTTTT
1417 TTATCCAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (40 bp):
TAAAGCGCCGCTAATGCTCGATCTTTAGCGGCGTTTTACA
Done.