Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_231 ID=scaffold_231-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: 9163
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Found at i:1754 original size:44 final size:44
Alignment explanation
Indices: 1628--1758 Score: 158
Period size: 44 Copynumber: 3.0 Consensus size: 44
1618 CTATGGTAGA
* * ** *
1628 TTTAATCCGAC-CTACTGCAACTTCA-GAAGTATAGGATTCATCAT
1 TTTAATCC-ACTCCACTGCAACTTCAGGGAG-ATAGGATTTGTGAT
*
1672 TTTAATCCACTCCACTGCAACTTTAGGGAGATAGGATTTGTGAT
1 TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTTGTGAT
* *
1716 TTTAATCCGCTCCATTGCAACTTCAGGGAGATAGGATTTGTGA
1 TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTTGTGA
1759 CTCTTCATGG
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
43 2 0.03
44 71 0.93
45 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (44 bp):
TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTTGTGAT
Found at i:2134 original size:50 final size:50
Alignment explanation
Indices: 1971--2910 Score: 775
Period size: 50 Copynumber: 18.9 Consensus size: 50
1961 TCTGTTTAAA
* * * * * *
1971 TGCAATTTCA-GGAAGTAAGATTCGCCGTCGTGGCTTCAATCTATTT-ACT
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT-TTTCAAT
* * * * * * * ***
2020 TGCAATGTCGGGGAAATGAGATTCACTGTCGTAGCTTCAATCTGTTCCGC
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAAT
* * * * ** * * *
2070 TGCATTGCCTGGGAAGTAAGATTCGCCATTGTGGCCTCAATCTTTTAAAT
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAAT
* ** * *
2120 TGCAATGTCAGGGAAGTAAGATCCACTGTTGTAGCTTCAATCTGCTCCAC
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAAT
* * *
2170 TGCAACG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAAT
1 TGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAAT
** * * * *
2220 TGCAATGTCAGGGAAGTGTGATCCGCTGTTGTAACTTCAATCTGTTCCAC
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAAT
* *
2270 TGCAACG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTT-AAT
1 TGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTT-TTCAAT
* * * *
2320 TGCAATGTGAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCAC
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAAT
*
2370 TGCAACG-CTA-GGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTATT-AAT
1 TGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTT-TTCAAT
** * * *
2419 TGCAATGTCAGCGGAAGTAAGATCCATTGTTGTAGCTTCAATCTGTTCCAC
1 TGCAATGTCAG-GGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAAT
*
2470 TGCAATG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTT-AAT
1 TGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTT-TTCAAT
* * * * *
2520 TGCAATGTGAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTATTCCAC
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAAT
* *
2570 TGCAACG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTT-AAT
1 TGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTT-TTCAAT
2620 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTT-AAT
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTT-TTCAAT
* * * *
2670 TGCAATGTCAGGGAAGTAAGATCCGCTGCTGTAGCTTCAATCTGTTCCAC
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAAT
*** * * * * * * *
2720 TGCGCCGCCTA--GAAATAAGATTCGCCGTTGTGGCCTCAATCTTTT-GAT
1 TGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAAT
* * * * ***
2768 TGCAATGTCAAGGAAGTGAGATTCG-TCGTTGTAGCTTCAATCTATTCCGC
1 TGCAATGTCAGGGAAGTAAGATCCGCT-GTTGTAGCTTCAATCTTTTCAAT
** * * * * * * *
2818 TGCACCG-CTTGAGAAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTT-GAT
1 TGCAATGTC-AG-GGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAAT
* * *
2868 TGCAATGTCATGGAAGTGAGATCCGCCGTTGTAGCTTCAATCT
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT
2911 GTTCCGCTGC
Statistics
Matches: 704, Mismatches: 156, Indels: 62
0.76 0.17 0.07
Matches are distributed among these distances:
47 1 0.00
48 6 0.01
49 140 0.20
50 479 0.68
51 78 0.11
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (50 bp):
TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAAT
Found at i:2154 original size:100 final size:100
Alignment explanation
Indices: 1983--2712 Score: 1004
Period size: 100 Copynumber: 7.3 Consensus size: 100
1973 CAATTTCAGG
* * * * * * * * * *
1983 AAGTAAGATTCGCCGTCGTGGCTTCAATCTAT-TTACTTGCAATGTCGGGGAAATGAGATTCACT
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCT-TCTTAATTGCAATGTCAGGGAAGTAAGATCCGCT
* * ** *
2047 GTCGTAGCTTCAATCTGTTCCGCTGCATTGCCT-GGG
65 GTTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGA
* ** * * *
2083 AAGTAAGATTCGCCATTGTGGCCTCAATCTT-TTAAATTGCAATGTCAGGGAAGTAAGATCCACT
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTT-AATTGCAATGTCAGGGAAGTAAGATCCGCT
*
2147 GTTGTAGCTTCAATCTGCTCCACTGCAACGCTAGGA
65 GTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGA
* **
2183 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTGTGATCCGCTG
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTG
*
2248 TTGTAACTTCAATCTGTTCCACTGCAACGCTAGGA
66 TTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGA
*
2283 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTGAGGGAAGTAAGATCCGCTG
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTG
2348 TTGTAGCTTCAATCTGTTCCACTGCAACGCTAGG-
66 TTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGA
* **
2382 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTATTAATTGCAATGTCAGCGGAAGTAAGATCCATT
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAG-GGAAGTAAGATCCGCT
*
2447 GTTGTAGCTTCAATCTGTTCCACTGCAATGCTAGGA
65 GTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGA
* *
2483 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTGAGGGAAGTAAGATCTGCTG
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTG
*
2548 TTGTAGCTTCAATCTATTCCACTGCAACGCTAGGA
66 TTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGA
2583 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTG
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTG
** * * *
2648 TTGTAGCTTCAATCT-TCTTAATTGCAATG-TCAGGG
66 TTGTAGCTTCAATCTGT-TCCACTGCAACGCT-AGGA
*
2683 AAGTAAGATCCGCTGCTGTAGCTTCAATCT
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCT
2713 GTTCCACTGC
Statistics
Matches: 574, Mismatches: 49, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
99 53 0.09
100 473 0.82
101 48 0.08
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (100 bp):
AAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTG
TTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGA
Found at i:2866 original size:100 final size:99
Alignment explanation
Indices: 2633--2973 Score: 479
Period size: 100 Copynumber: 3.4 Consensus size: 99
2623 AATGTCAGGG
* * * * * *
2633 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTG
1 AAGTAAGATTCGCCGTTGTGGCCTCAATCTT-TTAATTGCAATGTCAAGGAAGTGAGATCCGC-G
* * * *
2698 CTGTAGCTTCAATCTGTTCCACTGCGCCGCCT-AGA
64 TTGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGA
* *
2733 AA-TAAGATTCGCCGTTGTGGCCTCAATCTTTTGATTGCAATGTCAAGGAAGTGAGATTCGTCGT
1 AAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTCAAGGAAGTGAGATCCG-CGT
*
2797 TGTAGCTTCAATCTATTCCGCTGCACCGCTTGAGA
65 TGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGA
* *
2832 AAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTGATTGCAATGTCATGGAAGTGAGATCCGCCGT
1 AAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTCAAGGAAGTGAGATCCG-CGT
2897 TGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGA
65 TGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGA
*
2932 AAGTAAGATTTGCCGTTGTGGCCTCAATCTTTTAAATTGCAA
1 AAGTAAGATTCGCCGTTGTGGCCTCAATCTTTT-AATTGCAA
2974 ACTATGATTA
Statistics
Matches: 218, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
98 54 0.25
99 30 0.14
100 127 0.58
101 7 0.03
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (99 bp):
AAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTCAAGGAAGTGAGATCCGCGTT
GTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGA
Found at i:4145 original size:43 final size:42
Alignment explanation
Indices: 4056--4157 Score: 109
Period size: 43 Copynumber: 2.4 Consensus size: 42
4046 TGCCCCGATC
* *
4056 TGATCAAAATTTGAGCTGCTCTGATCGCCTCATCCCCCAATT
1 TGATCAAAATTTGAGCTGCTCTGATCACCTAATCCCCCAATT
* **
4098 TGATCCAAAATTTGAG-TCGCTCTGATCACTTAATGTCCC-ATT
1 TGAT-CAAAATTTGAGCT-GCTCTGATCACCTAATCCCCCAATT
4140 ATGATCAAAATTTTGAGC
1 -TGATCAAAA-TTTGAGC
4158 CGCCCTTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
42 13 0.26
43 37 0.74
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (42 bp):
TGATCAAAATTTGAGCTGCTCTGATCACCTAATCCCCCAATT
Found at i:5424 original size:14 final size:14
Alignment explanation
Indices: 5398--5436 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
5388 CTCCTTTTTC
*
5398 TTTTTC-TTCTCTT
1 TTTTTCTTTTTCTT
5411 TTTTTCTTTTTCTT
1 TTTTTCTTTTTCTT
5425 TTTTTCTATTTT
1 TTTTTCT-TTTT
5437 AACTTTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.26
14 13 0.57
15 4 0.17
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTCTTTTTCTT
Found at i:5452 original size:9 final size:9
Alignment explanation
Indices: 5440--5495 Score: 105
Period size: 9 Copynumber: 6.3 Consensus size: 9
5430 CTATTTTAAC
5440 TTTGATTTT
1 TTTGATTTT
5449 TTTGA-TTT
1 TTTGATTTT
5457 TTTGATTTT
1 TTTGATTTT
5466 TTTGATTTT
1 TTTGATTTT
5475 TTTGATTTT
1 TTTGATTTT
5484 TTTGATTTT
1 TTTGATTTT
5493 TTT
1 TTT
5496 TCTTAGTCTG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.17
9 38 0.83
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.79
Consensus pattern (9 bp):
TTTGATTTT
Found at i:5468 original size:18 final size:17
Alignment explanation
Indices: 5440--5494 Score: 101
Period size: 17 Copynumber: 3.2 Consensus size: 17
5430 CTATTTTAAC
5440 TTTGATTTTTTTGATTT
1 TTTGATTTTTTTGATTT
5457 TTTGATTTTTTTGATTTT
1 TTTGATTTTTTTGA-TTT
5475 TTTGATTTTTTTGATTT
1 TTTGATTTTTTTGATTT
5492 TTT
1 TTT
5495 TTCTTAGTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
17 20 0.54
18 17 0.46
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (17 bp):
TTTGATTTTTTTGATTT
Found at i:6248 original size:17 final size:18
Alignment explanation
Indices: 6216--6252 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
6206 TCTGCACAGT
6216 ATGATTATGAATGAAAGA
1 ATGATTATGAATGAAAGA
*
6234 ATGATT-TGGATGAAAGA
1 ATGATTATGAATGAAAGA
6251 AT
1 AT
6253 AAAAGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (18 bp):
ATGATTATGAATGAAAGA
Done.