Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_386 ID=scaffold_386-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: 7618
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Found at i:1271 original size:17 final size:17
Alignment explanation
Indices: 1245--1280 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1235 GTGTGCTTTG
*
1245 TTTTGGCTGCATGACAT
1 TTTTGACTGCATGACAT
*
1262 TTTTGACTGCATGGCAT
1 TTTTGACTGCATGACAT
1279 TT
1 TT
1281 CATCATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (17 bp):
TTTTGACTGCATGACAT
Found at i:1743 original size:19 final size:19
Alignment explanation
Indices: 1719--1765 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1709 AATGTCTCTT
*
1719 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
1738 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
1757 TATGCATTA
1 TTTGCATTA
1766 AACACCGCTA
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:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:4626 original size:15 final size:15
Alignment explanation
Indices: 4595--4644 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
4585 GAGTCGTAAA
*
4595 AAAAATG-ATGAGATG
1 AAAAATGAATAAG-TG
4610 AAAAATGAATAAGTG
1 AAAAATGAATAAGTG
*
4625 -AAAATGAA-AACTG
1 AAAAATGAATAAGTG
4638 AAAAATG
1 AAAAATG
4645 GAAAAGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 4 0.13
14 14 0.45
15 9 0.29
16 4 0.13
ACGTcount: A:0.60, C:0.02, G:0.20, T:0.18
Consensus pattern (15 bp):
AAAAATGAATAAGTG
Found at i:4642 original size:14 final size:14
Alignment explanation
Indices: 4608--4649 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
4598 AATGATGAGA
*
4608 TGAAAAATGAATAAG
1 TGAAAAATGAA-AAC
4623 TG-AAAATGAAAAC
1 TGAAAAATGAAAAC
4636 TGAAAAATGGAAAA
1 TGAAAAAT-GAAAA
4650 GTAAAATAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 4 0.17
14 13 0.54
15 7 0.29
ACGTcount: A:0.62, C:0.02, G:0.19, T:0.17
Consensus pattern (14 bp):
TGAAAAATGAAAAC
Found at i:5978 original size:44 final size:44
Alignment explanation
Indices: 5915--6717 Score: 706
Period size: 44 Copynumber: 18.1 Consensus size: 44
5905 GGCAGGTTGA
*
5915 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCG
1 AAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCG
* *
5959 AAGAAAGCAGATCTTGTCTTCCCATACAGGTGGC--GAAGTAGATCG
1 AAGAAAGCAGATCTTGTCTT--CATATA-TTGGCGTGAAGTAGATCG
** *
6004 AAGAAAGTGGATCTTATCTTCATATATTGGCGTGAAGTAGATCG
1 AAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCG
* ** * * *
6048 AAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
1 AAGAAAGCAGATCTTGTCTTCATATATTGG-CGTGAAGTAGATCG
* * *
6093 ATGAAAGCAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCG
1 AAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCG
* * * * * *
6137 AAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCG
1 AAGAAAGCAGATCTTGTCTTCATATATTGG-CGTGAAGTAGATCG
*
6182 AAG-AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCG
1 AAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCG
* * * *
6225 AAGATAAG-AGATCTTGTCTTTATGTATTGGTGTGAAGTAGATCA
1 AAGA-AAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCG
* **
6269 AAGATAGCAGATCTTGTCTTTCCATACTGGTGGC--GAAGTAGATCG
1 AAGAAAGCAGATCTTGTC-TT-CATA-TATTGGCGTGAAGTAGATCG
* * * * *
6314 ATGAAAGCAGATATTGTCTTCATGTATTGGCATAAAGTAGATCG
1 AAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCG
* * ** *
6358 AAGATAGCAGATCTTGTCTTTC-TATATTGGTAGCAAAGTGGATCG
1 AAGAAAGCAGATCTTGTC-TTCATATATTGG-CGTGAAGTAGATCG
* ** * * *
6403 AAG-ATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
1 AAGAAAGCAGATCTTGTCTTCATATATTGG-CGTGAAGTAGATCG
* * * *
6447 AAGAAAGCAGATATTGTCTTCATGTATTGTCGTGAAGTAAATCG
1 AAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCG
* * * * * *
6491 AAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCG
1 AAGAAAGCAGATCTTGTCTTCATATATTGG-CGTGAAGTAGATCG
* ** * * *
6536 AAG-ATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
1 AAGAAAGCAGATCTTGTCTTCATATATTGG-CGTGAAGTAGATCG
* * *
6580 AAGAAAGAATATCTTGTCTTCATGTATTGGCGTGAAGTAGATCG
1 AAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCG
* * * * * *
6624 AAGATAGCAGATCTTATCTTCCTGTATTGGTAGTGAAGTAGATCA
1 AAGAAAGCAGATCTTGTCTTCATATATTGG-CGTGAAGTAGATCG
* * ** * * *
6669 AAGATAGTAGATCTTGTCTTCCCATATCGGTGGCGAAGTAGATCG
1 AAGAAAGCAGATCTTGTCTTCATATATTGG-CGTGAAGTAGATCG
6714 AAGA
1 AAGA
6718 TACAAGTCTT
Statistics
Matches: 612, Mismatches: 125, Indels: 43
0.78 0.16 0.06
Matches are distributed among these distances:
42 9 0.01
43 27 0.04
44 335 0.55
45 227 0.37
46 6 0.01
47 8 0.01
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (44 bp):
AAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCG
Found at i:6024 original size:89 final size:89
Alignment explanation
Indices: 5915--6717 Score: 816
Period size: 89 Copynumber: 9.0 Consensus size: 89
5905 GGCAGGTTGA
5915 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTC
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTC
**
5980 CCATACAGGTGGCGAAGTAGATCG
66 CCATATTGGTGGCGAAGTAGATCG
** * * *
6004 AAGAAAGTGGATCTTATCTTCATATATTGGCGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTC
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTC
*
6069 CCATACTGGTGGCGAAGTAGATCG
66 CCATATTGGTGGCGAAGTAGATCG
* * * *
6093 ATGAAAGCAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTC
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTC
* * *
6158 CTATATTGGTAGCGAAGTGGATCG
66 CCATATTGGTGGCGAAGTAGATCG
6182 AAG-AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAAG-AGATCTTGTCTT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGA-AAGCAGATCTTGTCTT
**** * *
6245 TATGTATTGGT-GTGAAGTAGATCA
65 CCCATATTGGTGGCGAAGTAGATCG
* * * * * *
6269 AAGATAGCAGATCTTGTCTTTCCA--TACTGGTGGCGAAGTAGATCGATGAAAGCAGATATTGTC
1 AAGAAAGCAGATCTTGTC-TT-CATGTATTGG-CGTGAAGTAGATCGAAGAAAGCAGATCTTGTC
*** ****
6332 TTCATGTATTGG-CATAAAGTAGATCG
63 TTCCCATATTGGTGGCGAAGTAGATCG
* * * ** * *
6358 AAGATAGCAGATCTTGTCTTTC-TATATTGGTAGCAAAGTGGATCGAAG-ATGCAGATCTTGTCT
1 AAGAAAGCAGATCTTGTC-TTCATGTATTGG-CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCT
*
6421 TCCCATACTGGTGGCGAAGTAGATCG
64 TCCCATATTGGTGGCGAAGTAGATCG
* * * * *
6447 AAGAAAGCAGATATTGTCTTCATGTATTGTCGTGAAGTAAATCGAAGATAGCAGATCCTGTCTTC
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTC
* * *
6512 CTATATTGGTAGCGAAGTGGATCG
66 CCATATTGGTGGCGAAGTAGATCG
* *** * * * * *
6536 AAG-ATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGAATATCTTGTCTT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
*** * *
6600 CATGTATTGG-CGTGAAGTAGATCG
65 CCCATATTGGTGGCGAAGTAGATCG
* * * * * * *
6624 AAGATAGCAGATCTTATCTTCCTGTATTGGTAGTGAAGTAGATCAAAGATAGTAGATCTTGTCTT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
*
6689 CCCATATCGGTGGCGAAGTAGATCG
65 CCCATATTGGTGGCGAAGTAGATCG
6714 AAGA
1 AAGA
6718 TACAAGTCTT
Statistics
Matches: 592, Mismatches: 107, Indels: 29
0.81 0.15 0.04
Matches are distributed among these distances:
87 13 0.02
88 152 0.26
89 409 0.69
90 18 0.03
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (89 bp):
AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTC
CCATATTGGTGGCGAAGTAGATCG
Found at i:6157 original size:133 final size:133
Alignment explanation
Indices: 5915--6717 Score: 903
Period size: 133 Copynumber: 6.0 Consensus size: 133
5905 GGCAGGTTGA
5915 AAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
* * * * ** * ** * *
5979 CCCATACA-GGTGGCGAAGTAGATCGAAGAAAGTGGATCTTATCTTCATATATTGG-CGTGAAGT
66 --CATATATTG-GGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATATTGGTGGCGAAGT
6042 AGATCG
128 AGATCG
* *** * * * *
6048 AAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGATGAAAGCAGATCTTGTCTT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
* * * * * *
6113 CATGTATTAGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGG
66 CATATATT-GGGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAG
6178 ATCG
130 ATCG
6182 AAG-AAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAAG-AGATCTTGTCT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGTCGTGAAGTAGATCGAAGA-AAGCAGATCTTGTCT
* * * * *
6244 TTATGTATTGGTGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTTCCATACTGGTGGCGAAGTA
65 TCATATATTGG-GTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTA
6309 GATCG
129 GATCG
* * * * *
6314 ATGAAAGCAGATATTGTCTTCATGTATTGG-CATAAAGTAGATCGAAGATAGCAGATCTTGTCTT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTGTC-T
* *
6378 TC-TATATT-GGTAGCAAAGTGGATCGAAGAT-GCAGATCTTGTCTTCCCATACTGGTGGCGAAG
65 TCATATATTGGGT-G--AAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATATTGGTGGCGAAG
6440 TAGATCG
127 TAGATCG
* * * *
6447 AAGAAAGCAGATATTGTCTTCATGTATT-GTCGTGAAGTAAATCGAAGATAGCAGATCCTGTCTT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
* * * *
6511 CCTATATTGGTAGCGAAGTGGATCGAAGAT-GCAGATCTTGTCTTCCCATACTGGTGGCGAAGTA
66 CATATATTGG--GTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTA
6575 GATCG
129 GATCG
* * * *
6580 AAGAAAGAATATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAGATCTTATCTT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
* * * * *
6644 CCTGTATTGGTAGTGAAGTAGATCAAAGATAGTAGATCTTGTCTTCCCATATCGGTGGCGAAGTA
66 CATATATTGG--GTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTA
6709 GATCG
129 GATCG
6714 AAGA
1 AAGA
6718 TACAAGTCTT
Statistics
Matches: 583, Mismatches: 68, Indels: 37
0.85 0.10 0.05
Matches are distributed among these distances:
131 3 0.01
132 99 0.17
133 376 0.64
134 103 0.18
135 1 0.00
136 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (133 bp):
AAGAAAGCAGATCTTGTCTTCATGTATTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
CATATATTGGGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGA
TCG
Done.