Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_172 ID=scaffold_172-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: 10521
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.31
Warning! 378 characters in sequence are not A, C, G, or T
Found at i:1574 original size:50 final size:50
Alignment explanation
Indices: 1520--1676 Score: 181
Period size: 50 Copynumber: 3.1 Consensus size: 50
1510 CCTGAGAGGT
*
1520 AAGATTCGCTGTTGTAGCTTTAATATTTTGAACTGCAATGTCGGGGAAGC
1 AAGATTCGCTGTTGTAGCTTTAATCTTTTGAACTGCAATGTCGGGGAAGC
* * * * * ** ** * * *
1570 AAGATTCACCGATGTGGCTTTAATCTATTCTACTGC-ATCACTTGGGAGGT
1 AAGATTCGCTGTTGTAGCTTTAATCTTTTGAACTGCAATGTC-GGGGAAGC
1620 AAGATTCGCTGTTGTAGCTTTAATCTTTTGAACTGCAATGTCGGGGAAGC
1 AAGATTCGCTGTTGTAGCTTTAATCTTTTGAACTGCAATGTCGGGGAAGC
1670 AAGATTC
1 AAGATTC
1677 ACCGATGTGG
Statistics
Matches: 80, Mismatches: 25, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
49 3 0.04
50 74 0.93
51 3 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (50 bp):
AAGATTCGCTGTTGTAGCTTTAATCTTTTGAACTGCAATGTCGGGGAAGC
Found at i:1643 original size:100 final size:100
Alignment explanation
Indices: 1470--1724 Score: 411
Period size: 100 Copynumber: 2.5 Consensus size: 100
1460 TTTGGAAAGT
* * * ** *
1470 AAGATTCGCCGTTGTGGCTTTAATATGTTCTGTTGCATCACCTGAGAGGTAAGATTCGCTGTTGT
1 AAGATTCACCGATGTGGCTTTAATCTGTTCTACTGCATCACCTGGGAGGTAAGATTCGCTGTTGT
1535 AGCTTTAATATTTTGAACTGCAATGTCGGGGAAGC
66 AGCTTTAATATTTTGAACTGCAATGTCGGGGAAGC
* *
1570 AAGATTCACCGATGTGGCTTTAATCTATTCTACTGCATCACTTGGGAGGTAAGATTCGCTGTTGT
1 AAGATTCACCGATGTGGCTTTAATCTGTTCTACTGCATCACCTGGGAGGTAAGATTCGCTGTTGT
*
1635 AGCTTTAATCTTTTGAACTGCAATGTCGGGGAAGC
66 AGCTTTAATATTTTGAACTGCAATGTCGGGGAAGC
* *
1670 AAGATTCACCGATGTGGTTTTAATCTGTTCCACTGCATCACCTGGGAGGTAAGAT
1 AAGATTCACCGATGTGGCTTTAATCTGTTCTACTGCATCACCTGGGAGGTAAGAT
1725 CTGTAATTCT
Statistics
Matches: 142, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 142 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (100 bp):
AAGATTCACCGATGTGGCTTTAATCTGTTCTACTGCATCACCTGGGAGGTAAGATTCGCTGTTGT
AGCTTTAATATTTTGAACTGCAATGTCGGGGAAGC
Found at i:1692 original size:50 final size:50
Alignment explanation
Indices: 1536--1695 Score: 178
Period size: 50 Copynumber: 3.2 Consensus size: 50
1526 CGCTGTTGTA
*
1536 GCTTTAATATTTTGAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTG
1 GCTTTAATCTTTTGAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTG
* ** ** * * * * * * *
1586 GCTTTAATCTATTCTACTGC-ATCACTTGGGAGGTAAGATTCGCTGTTGTA
1 GCTTTAATCTTTTGAACTGCAATGTC-GGGGAAGCAAGATTCACCGATGTG
1636 GCTTTAATCTTTTGAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTG
1 GCTTTAATCTTTTGAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTG
*
1686 GTTTTAATCT
1 GCTTTAATCT
1696 GTTCCACTGC
Statistics
Matches: 82, Mismatches: 26, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
49 3 0.04
50 76 0.93
51 3 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (50 bp):
GCTTTAATCTTTTGAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTG
Found at i:1724 original size:50 final size:50
Alignment explanation
Indices: 1468--1724 Score: 158
Period size: 50 Copynumber: 5.1 Consensus size: 50
1458 CTTTTGGAAA
* * * * *** *
1468 GTAAGATTCGCCGTTGTGGCTTTAATATGTTCTGTTGCATCACCTGAGAG
1 GTAAGATTCACCGATGTGGCTTTAATCTATTCAACTGCATCACCTGGGAG
* * * * * * * ** * *
1518 GTAAGATTCGCTGTTGTAGCTTTAATATTTTGAACTGCAAT-GTCGGGGAA
1 GTAAGATTCACCGATGTGGCTTTAATCTATTCAACTGC-ATCACCTGGGAG
* * *
1568 GCAAGATTCACCGATGTGGCTTTAATCTATTCTACTGCATCACTTGGGAG
1 GTAAGATTCACCGATGTGGCTTTAATCTATTCAACTGCATCACCTGGGAG
* * * * * * ** * *
1618 GTAAGATTCGCTGTTGTAGCTTTAATCTTTTGAACTGCAAT-GTCGGGGAA
1 GTAAGATTCACCGATGTGGCTTTAATCTATTCAACTGC-ATCACCTGGGAG
* * * *
1668 GCAAGATTCACCGATGTGGTTTTAATCTGTTCCACTGCATCACCTGGGAG
1 GTAAGATTCACCGATGTGGCTTTAATCTATTCAACTGCATCACCTGGGAG
1718 GTAAGAT
1 GTAAGAT
1725 CTGTAATTCT
Statistics
Matches: 150, Mismatches: 53, Indels: 8
0.71 0.25 0.04
Matches are distributed among these distances:
49 4 0.03
50 142 0.95
51 4 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (50 bp):
GTAAGATTCACCGATGTGGCTTTAATCTATTCAACTGCATCACCTGGGAG
Found at i:1850 original size:44 final size:44
Alignment explanation
Indices: 1788--2028 Score: 176
Period size: 44 Copynumber: 5.5 Consensus size: 44
1778 GATCTACTGT
* *
1788 ACTGTAA-CTTCAGAGAGATAAGATCCTTTACTTTAATCCGCTCC
1 ACTGTAATC-TCAGGGAGATAAGATCCTTTACTTCAATCCGCTCC
* * * * *
1832 GCTGTAATATCAGGGAGATAGGAT--TACTAGCTTCAATCTGCTCC
1 ACTGTAATCTCAGGGAGATAAGATCCT-TTA-CTTCAATCCGCTCC
* * * ** *
1876 ACTGTAATCTCAGGGAGATAAGA-CC-TGA-TGCGATCTACTCT
1 ACTGTAATCTCAGGGAGATAAGATCCTTTACTTCAATCCGCTCC
* * * *
1917 ACTGTAA-CTTAAGAGAGATAAGATCCTTTATTTTAATCCGCTCC
1 ACTGTAATC-TCAGGGAGATAAGATCCTTTACTTCAATCCGCTCC
* *
1961 ACTGTAATCTCAGGGAGATAGGAT--TATCAGCTTCAATCCGCTCC
1 ACTGTAATCTCAGGGAGATAAGATCCT-TTA-CTTCAATCCGCTCC
* *
2005 GCTTTAATCTCAGGGAGATAAGAT
1 ACTGTAATCTCAGGGAGATAAGAT
2029 TTGTCACCTT
Statistics
Matches: 151, Mismatches: 34, Indels: 24
0.72 0.16 0.11
Matches are distributed among these distances:
40 1 0.01
41 28 0.19
42 4 0.03
43 7 0.05
44 110 0.73
45 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (44 bp):
ACTGTAATCTCAGGGAGATAAGATCCTTTACTTCAATCCGCTCC
Found at i:1974 original size:129 final size:129
Alignment explanation
Indices: 1744--2027 Score: 444
Period size: 129 Copynumber: 2.2 Consensus size: 129
1734 TTCGGTCTAT
* * * * * *
1744 TCCACCGTGATCTCAGGAAGATAAGACCTGATGTGATCTACTGTACTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTAAGAGAGATAA
* *
1809 GATCCTTTACTTTAATCCGCTCCGCTGTAATATCAGGGAGATAGGATTA-CTAGCTTCAATCTGC
66 GATCCTTTACTTTAATCCGCTCCACTGTAATATCAGGGAGATAGGATTATC-AGCTTCAATCCGC
1873 TCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTAAGAGAGATAA
1 TCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTAAGAGAGATAA
* *
1938 GATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTATCAGCTTCAATCCGC
66 GATCCTTTACTTTAATCCGCTCCACTGTAATATCAGGGAGATAGGATTATCAGCTTCAATCCGC
* *
2002 TCCGCTTTAATCTCAGGGAGATAAGA
1 TCCACTGTAATCTCAGGGAGATAAGA
2028 TTTGTCACCT
Statistics
Matches: 142, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
129 141 0.99
130 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (129 bp):
TCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTAAGAGAGATAA
GATCCTTTACTTTAATCCGCTCCACTGTAATATCAGGGAGATAGGATTATCAGCTTCAATCCGC
Found at i:2289 original size:131 final size:130
Alignment explanation
Indices: 2016--2251 Score: 337
Period size: 131 Copynumber: 1.8 Consensus size: 130
2006 CTTTAATCTC
* * * *
2016 AGGGAGATAAGATTTGTCACCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGCAATT
1 AGGGAGATAAGATTCGCCACCTTCGATCCGCTCCACTACTGCTCAGGGAGACAAGATCTGCAATT
* * * *
2081 TCCAACCTATTCCACTGCTGGTCGGGGACATAGGACTTATGGCTTAAATTTGTTTCCCTACTCCT
66 TCCAACCTATTCCACTGCTGGTCAGGGACATAGGACTGATGGCTTAAATCTGTCTCCCTACTCCT
* ** * * *
2146 GGGGAAGATAAGATTCGCCGTCTTTGATCCGCTCCGCTACTGCTCAGGGAGATAAGATCTGCAAT
1 AGGG-AGATAAGATTCGCCACCTTCGATCCGCTCCACTACTGCTCAGGGAGACAAGATCTGCAAT
2211 TTCCAACCTATTCCACTGCTGGTCAGGGACATAGGACTGAT
65 TTCCAACCTATTCCACTGCTGGTCAGGGACATAGGACTGAT
2252 TTCTTCTGTC
Statistics
Matches: 93, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
130 3 0.03
131 90 0.97
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (130 bp):
AGGGAGATAAGATTCGCCACCTTCGATCCGCTCCACTACTGCTCAGGGAGACAAGATCTGCAATT
TCCAACCTATTCCACTGCTGGTCAGGGACATAGGACTGATGGCTTAAATCTGTCTCCCTACTCCT
Found at i:2559 original size:86 final size:87
Alignment explanation
Indices: 2315--2649 Score: 447
Period size: 87 Copynumber: 3.9 Consensus size: 87
2305 TCCACTGTCG
* * * *
2315 ACGCAGGAGGGCAATATCTGCTATCTTTAACCAGCTCCACTACAAACGATGGAGGCAAGGCTTCA
1 ACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAAACGATGGAGGCAAGACTTCG
2380 TTTTCGATCTGCTTCGCTGTTA
66 TTTTCGATCTGCTTCGCTGTTA
* * * *
2402 ACGCAGGAAGGCAAGATCTACTATCTTTAATCAACTCCACTACAACCGATGGAGGCAAGACTTCG
1 ACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAAACGATGGAGGCAAGACTTCG
2467 TTTTCGATCTGCTTCGCTGTTA
66 TTTTCGATCTGCTTCGCTGTTA
* * * ** *
2489 ACGCAGGACGGTAAGATCTGCT-TCTTTAACCAGCTCCAATGTAAACGATGGAGGCAAGACTTTG
1 ACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAAACGATGGAGGCAAGACTTCG
2553 TTTTCGATCTGCTTCGCTGTTA
66 TTTTCGATCTGCTTCGCTGTTA
** * * * * * * *
2575 ATACAGGAAGGAAAAATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTG
1 ACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAAACGATGGAGGCAAGACTTCG
*
2640 TTTTTGATCT
66 TTTTCGATCT
2650 TCACTGATCT
Statistics
Matches: 218, Mismatches: 29, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
86 73 0.33
87 145 0.67
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (87 bp):
ACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAAACGATGGAGGCAAGACTTCG
TTTTCGATCTGCTTCGCTGTTA
Found at i:2602 original size:173 final size:174
Alignment explanation
Indices: 2315--2649 Score: 474
Period size: 173 Copynumber: 1.9 Consensus size: 174
2305 TCCACTGTCG
* * * *
2315 ACGCAGGAGGGCAATATCTGCTATCTTTAACCAGCTCCACTACAAACGATGGAGGCAAGGCTTCA
1 ACGCAGGACGGCAAGATCTGCTATCTTTAACCAGCTCCAATACAAACGATGGAGGCAAGACTTCA
* * * *
2380 TTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTACTATCTTTAATCAACTCCACTAC
66 TTTTCGATCTGCTTCGCTGTTAACACAGGAAGGAAAAATCTACTATCTTTAACCAACTCCACTAC
2445 AACCGATGGAGGCAAGACTTCGTTTTCGATCTGCTTCGCTGTTA
131 AACCGATGGAGGCAAGACTTCGTTTTCGATCTGCTTCGCTGTTA
* ** **
2489 ACGCAGGACGGTAAGATCTGCT-TCTTTAACCAGCTCCAATGTAAACGATGGAGGCAAGACTTTG
1 ACGCAGGACGGCAAGATCTGCTATCTTTAACCAGCTCCAATACAAACGATGGAGGCAAGACTTCA
* ** * *
2553 TTTTCGATCTGCTTCGCTGTTAATACAGGAAGGAAAAATCTGTTATCTTTAACCAGCTCCACTGC
66 TTTTCGATCTGCTTCGCTGTTAACACAGGAAGGAAAAATCTACTATCTTTAACCAACTCCACTAC
* * *
2618 AACCGATGGAGGCAAGGCTTTGTTTTTGATCT
131 AACCGATGGAGGCAAGACTTCGTTTTCGATCT
2650 TCACTGATCT
Statistics
Matches: 140, Mismatches: 21, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
173 121 0.86
174 19 0.14
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (174 bp):
ACGCAGGACGGCAAGATCTGCTATCTTTAACCAGCTCCAATACAAACGATGGAGGCAAGACTTCA
TTTTCGATCTGCTTCGCTGTTAACACAGGAAGGAAAAATCTACTATCTTTAACCAACTCCACTAC
AACCGATGGAGGCAAGACTTCGTTTTCGATCTGCTTCGCTGTTA
Found at i:4793 original size:19 final size:21
Alignment explanation
Indices: 4751--4799 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
4741 TTCATTCTGA
4751 TTTTTTCA-TCTTGATTTCTC
1 TTTTTTCATTCTTGATTTCTC
*
4771 TTTTTTCATTCTT-CTTTCT-
1 TTTTTTCATTCTTGATTTCTC
*
4790 TTTTCTCATT
1 TTTTTTCATT
4800 TTCATTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 9 0.35
20 13 0.50
21 4 0.15
ACGTcount: A:0.08, C:0.20, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTTTCATTCTTGATTTCTC
Found at i:4850 original size:19 final size:18
Alignment explanation
Indices: 4816--4855 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
4806 TTGATCTTGG
**
4816 TTTTGATTTTTTTTTTCTT
1 TTTTGATTTTGATTTT-TT
4835 TTTTGATTTTGATTTTTT
1 TTTTGATTTTGATTTTTT
4853 TTT
1 TTT
4856 GAATCTGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.82
Consensus pattern (18 bp):
TTTTGATTTTGATTTTTT
Done.