Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_96 ID=scaffold_96-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: 14503
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Found at i:347 original size:28 final size:28
Alignment explanation
Indices: 316--405 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 28
306 GCATATACGC
*
316 ATAT-ATAAATAAGTATAATAATTATAAT
1 ATATAATAAATAA-TATAATAATAATAAT
*
344 ATATAATATATAATATAATAATAATAA-
1 ATATAATAAATAATATAATAATAATAAT
* * *
371 A-CTAAT-AATAATACAGTAATAATAAT
1 ATATAATAAATAATATAATAATAATAAT
397 ATA-AATAAA
1 ATATAATAAA
406 CAGTATTAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
25 16 0.31
26 8 0.16
27 3 0.06
28 17 0.33
29 7 0.14
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (28 bp):
ATATAATAAATAATATAATAATAATAAT
Found at i:355 original size:14 final size:13
Alignment explanation
Indices: 323--404 Score: 71
Period size: 14 Copynumber: 6.2 Consensus size: 13
313 CGCATATATA
323 AATAAGTATAATAAT
1 AATAA-TAT-ATAAT
*
338 TATAATATATAAT
1 AATAATATATAAT
351 ATATAATATAATAAT
1 A-ATAATAT-ATAAT
*
366 AATAA-A-CTAAT
1 AATAATATATAAT
*
377 AATAATACAGTAAT
1 AATAATATA-TAAT
391 AATAATATA-AAT
1 AATAATATATAAT
403 AA
1 AA
405 ACAGTATTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
11 9 0.16
12 6 0.11
13 6 0.11
14 26 0.46
15 10 0.18
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (13 bp):
AATAATATATAAT
Found at i:361 original size:25 final size:25
Alignment explanation
Indices: 323--395 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
313 CGCATATATA
* *
323 AATAAGTATAATAATTATAATATATAAT
1 AATAA-TATAATAATAATAA-A-CTAAT
351 ATATAATATAATAATAATAAACTAAT
1 A-ATAATATAATAATAATAAACTAAT
* *
377 AATAATACAGTAATAATAA
1 AATAATATAATAATAATAA
396 TATAAATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 16 0.40
26 5 0.12
27 1 0.03
28 14 0.35
29 4 0.10
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (25 bp):
AATAATATAATAATAATAAACTAAT
Found at i:366 original size:3 final size:3
Alignment explanation
Indices: 330--397 Score: 68
Period size: 3 Copynumber: 22.0 Consensus size: 3
320 ATAAATAAGT
* *
330 ATA ATA ATT ATA ATA TATA ATA TATA AT- ATA ATA ATA ATA A-A CTA
1 ATA ATA ATA ATA ATA -ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
375 ATA ATA ATA CAGTA ATA ATA ATA
1 ATA ATA ATA -A-TA ATA ATA ATA
398 TAAATAAACA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
2 3 0.05
3 42 0.76
4 8 0.15
5 2 0.04
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:422 original size:22 final size:21
Alignment explanation
Indices: 375--426 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
365 TAATAAACTA
* *
375 ATAATAATACAGTAATAATAAT
1 ATAATAA-ACAGTAATAACAAC
*
397 ATAAATAAACAGTATTAACAAC
1 AT-AATAAACAGTAATAACAAC
419 ATAATAAA
1 ATAATAAA
427 AAACTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 6 0.23
22 15 0.58
23 5 0.19
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.27
Consensus pattern (21 bp):
ATAATAAACAGTAATAACAAC
Found at i:1888 original size:127 final size:126
Alignment explanation
Indices: 1662--1890 Score: 298
Period size: 127 Copynumber: 1.8 Consensus size: 126
1652 AGTCTAATGT
* * * * * * *
1662 GATCTGTTCTCTGCAATCTCAAAGAGATGAGATCTGATTTTAATCCGCTCCACTGCAACTTCAGG
1 GATCTGCTCTCTGCAACCTCAAAGAGATAAGATCTAATGTTAATCCGCTCCACTACAACTTCAGA
* * *
1727 GAGATAGGATTATTGGCTTCAGTCTGCTCCACTGCAACTTCAGGGAGTTAAGACTTGATGC
66 GAGATAGGATTATTGACTTCAATCTGCTCAACTGCAACTTCAGGGAGTTAAGACTTGATGC
*
1788 GATCTGCTCTCTGCAACCTCAGAA-AGATAAGATCTTAATGTTAATCCGCTTCACTACAACTTCA
1 GATCTGCTCTCTGCAACCTCA-AAGAGATAAGATC-TAATGTTAATCCGCTCCACTACAACTTCA
* * * *
1852 GAGAGATAGGATTATTTACTTCAATTTGTTTAACTGCAA
64 GAGAGATAGGATTATTGACTTCAATCTGCTCAACTGCAA
1891 TGTCGGGGAA
Statistics
Matches: 86, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
126 28 0.33
127 58 0.67
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (126 bp):
GATCTGCTCTCTGCAACCTCAAAGAGATAAGATCTAATGTTAATCCGCTCCACTACAACTTCAGA
GAGATAGGATTATTGACTTCAATCTGCTCAACTGCAACTTCAGGGAGTTAAGACTTGATGC
Found at i:1964 original size:50 final size:50
Alignment explanation
Indices: 1896--2078 Score: 152
Period size: 50 Copynumber: 3.7 Consensus size: 50
1886 TGCAATGTCG
** * * *
1896 GGGAAACAAGATTTGCCGTCGCAACTTCAATCTATTCCACTACACCGCCA
1 GGGAAACAAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGCCA
* * * ** * ** * *
1946 GGGAAATAAGATCCGCCGTTGTGGCTTCAATCCT-TTTAATTGCAATGTCG
1 GGGAAACAAGATCCGCCGTCGTAGCTTCAAT-CTATTCCACTGCACCGCCA
* * *
1996 GGGAAACCAGATTCGCCGTCGTAGCTTTAATCTATTCCACTGCACCGCCA
1 GGGAAACAAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGCCA
* * * *
2046 GGGAAATAAGATCCGCCATTGTGGCTTCAATCT
1 GGGAAACAAGATCCGCCGTCGTAGCTTCAATCT
2079 TTTTAATTGC
Statistics
Matches: 96, Mismatches: 35, Indels: 4
0.71 0.26 0.03
Matches are distributed among these distances:
49 2 0.02
50 92 0.96
51 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (50 bp):
GGGAAACAAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGCCA
Found at i:2043 original size:100 final size:100
Alignment explanation
Indices: 1880--2091 Score: 343
Period size: 100 Copynumber: 2.1 Consensus size: 100
1870 CTTCAATTTG
* *
1880 TTTAACTGCAATGTCGGGGAAACAAGATTTGCCGTCGCAACTTCAATCTATTCCACTACACCGCC
1 TTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGCAACTTCAATCTATTCCACTACACCGCC
*
1945 AGGGAAATAAGATCCGCCGTTGTGGCTTCAATCCT
66 AGGGAAATAAGATCCGCCATTGTGGCTTCAATCCT
* * * * *
1980 TTTAATTGCAATGTCGGGGAAACCAGATTCGCCGTCGTAGCTTTAATCTATTCCACTGCACCGCC
1 TTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGCAACTTCAATCTATTCCACTACACCGCC
*
2045 AGGGAAATAAGATCCGCCATTGTGGCTTCAATCTT
66 AGGGAAATAAGATCCGCCATTGTGGCTTCAATCCT
2080 TTTAATTGCAAT
1 TTTAATTGCAAT
2092 TCCAAATAAA
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 103 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (100 bp):
TTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGCAACTTCAATCTATTCCACTACACCGCC
AGGGAAATAAGATCCGCCATTGTGGCTTCAATCCT
Found at i:6210 original size:17 final size:17
Alignment explanation
Indices: 6188--6222 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
6178 TAGTCCAAAG
6188 GGCATCACTTTATAACA
1 GGCATCACTTTATAACA
6205 GGCATCACTTTATAACA
1 GGCATCACTTTATAACA
6222 G
1 G
6223 AACATTCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (17 bp):
GGCATCACTTTATAACA
Found at i:6426 original size:8 final size:8
Alignment explanation
Indices: 6413--6437 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6403 CTGTAATCCA
6413 CACACATT
1 CACACATT
6421 CACACATT
1 CACACATT
6429 CACACATT
1 CACACATT
6437 C
1 C
6438 CCATCTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (8 bp):
CACACATT
Found at i:7038 original size:23 final size:24
Alignment explanation
Indices: 7004--7057 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
6994 TGAACAAAAT
*
7004 ATGATTATG-AAATCAATAAAAGA
1 ATGATTATGAAAAACAATAAAAGA
*
7027 ATGATGTA-GAAAAAGAATAAAAGA
1 ATGAT-TATGAAAAACAATAAAAGA
*
7051 ATAATTA
1 ATGATTA
7058 CTCAAAAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.59, C:0.02, G:0.15, T:0.24
Consensus pattern (24 bp):
ATGATTATGAAAAACAATAAAAGA
Found at i:7087 original size:26 final size:25
Alignment explanation
Indices: 7036--7091 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
7026 AATGATGTAG
*
7036 AAAAAGAATAAAAGAATAATTACTC
1 AAAAAGAATAAAAGAATAATGACTC
* * *
7061 AAAAGAGAATGAAAGAATACTGGCTC
1 AAAA-AGAATAAAAGAATAATGACTC
7087 AAAAA
1 AAAAA
7092 TGCATACGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.61, C:0.09, G:0.14, T:0.16
Consensus pattern (25 bp):
AAAAAGAATAAAAGAATAATGACTC
Found at i:14160 original size:13 final size:15
Alignment explanation
Indices: 14139--14170 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
14129 TGACAAAATC
*
14139 AAAATATATTTTAAA
1 AAAATATATGTTAAA
14154 AAAATATATGTTAAA
1 AAAATATATGTTAAA
14169 AA
1 AA
14171 TGTTAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAAATATATGTTAAA
Done.