Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_276 ID=scaffold_276-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: 8754
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Found at i:1062 original size:44 final size:44
Alignment explanation
Indices: 978--1593 Score: 655
Period size: 44 Copynumber: 13.9 Consensus size: 44
968 ATCAGACTTG
* * *
978 TATCTTCGATCTACTTCGCCACCAATATGA-GAAGACAAGATCTGC
1 TATCTTCGATCTACTTC-ACGCCAATA-CATGAAGACAAGATCTGC
* * *
1023 TATCTTTGATCTACTTCAAGCCAATACATGAAGATAAGATCTGC
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* * * * ***
1067 TTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGC
* **
1112 TATCTTCGATTTACTTCACGCCAATACATGAAGACAAGATCTAT
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* *
1156 TTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGG
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
1200 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
*
1244 TATCTTCGATCTACTTCACGCCAATACATGAAGACAATATCTGC
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* *
1288 TATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGAT-T-C
1 TATCTTC-GATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* * * * *** * *
1330 ATTACCTTCGATCTACTTCTCCACCAGTATGGGAAGACGAGATCTTC
1 --TATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGC
* **
1377 TATCTTTGATCTACTTCACGCCAATACGGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* *
1421 TATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTAC
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* * * *
1465 TTTCTTTGATCTACTTCATGCCAATACATGAAGACAAGATCTAC
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* * * * *** * *
1509 TTTCTTCGATCTACTTCGCCACCAGTATGGGAGGACAAGATCTGT
1 TATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGC
* * * * *
1554 TGTCTTTGGTCTGCTTCATGCCAATACATGAAGACAAGAT
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
1594 TTGTTATATT
Statistics
Matches: 475, Mismatches: 86, Indels: 21
0.82 0.15 0.04
Matches are distributed among these distances:
42 1 0.00
43 4 0.01
44 357 0.75
45 111 0.23
46 1 0.00
47 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (44 bp):
TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
Found at i:1225 original size:177 final size:177
Alignment explanation
Indices: 980--1593 Score: 795
Period size: 177 Copynumber: 3.5 Consensus size: 177
970 CAGACTTGTA
*
980 TCTTCGATCTACTTCGCCACCAATAT-GAGAAGACAAGATCTGCTATCTTTGATCTACTTCAAGC
1 TCTTCGATCTACTTCGCCACCAATATAG-GAAGACAAGATCTGCTATCTTTGATCTACTTCACGC
* * * * * ***
1044 CAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATC
65 CAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATC
* *
1109 TGCTATCTTCGATTTACTTCACGCCAATACATGAAGACAAGATCTATTT
129 TGCTATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTATTT
* * * * * *
1158 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGGTATCTTCGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
*
1222 AATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAATATCTG
66 AATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
* *
1287 CTATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGAT-TCATTA
131 CTATCTTC-GATCTACTTCATGCCAATACATGAAGACAAGATCT-ATTT
* * * * * *
1334 CCTTCGATCTACTTCTCCACCAGTATGGGAAGACGAGATCTTCTATCTTTGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
** * *
1399 AATACGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTA
66 AATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
* * *
1464 CTTTCTTTGATCTACTTCATGCCAATACATGAAGACAAGATCTACTT
131 CTATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTATTT
* * * * * * * *
1511 TCTTCGATCTACTTCGCCACCAGTATGGGAGGACAAGATCTGTTGTCTTTGGTCTGCTTCATGCC
1 TCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
1576 AATACATGAAGACAAGAT
66 AATACATGAAGACAAGAT
1594 TTGTTATATT
Statistics
Matches: 377, Mismatches: 53, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
175 3 0.01
176 71 0.19
177 286 0.76
178 17 0.05
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (177 bp):
TCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
AATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
CTATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTATTT
Found at i:3861 original size:20 final size:20
Alignment explanation
Indices: 3836--3876 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3826 GGTTCGGCAG
3836 AAAAAATCCAAAAGAATGAA
1 AAAAAATCCAAAAGAATGAA
**
3856 AAAAAATCGTAAAGAATGAA
1 AAAAAATCCAAAAGAATGAA
3876 A
1 A
3877 GAACATTTGC
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:0.68, C:0.07, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAAAATCCAAAAGAATGAA
Found at i:6251 original size:17 final size:17
Alignment explanation
Indices: 6216--6251 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6206 TTCTATGATG
*
6216 AAATGTCATGCAGTAAA
1 AAATGTCATGCAGCAAA
6233 AAATGTCATGCAGCCAAA
1 AAATGTCATGCAG-CAAA
6251 A
1 A
6252 CAAAACACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (17 bp):
AAATGTCATGCAGCAAA
Found at i:7787 original size:2 final size:2
Alignment explanation
Indices: 7780--7810 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7770 ATAAGGGTAC
7780 AT AT 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 AT AT A
7811 GAAATTAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.