Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_107 ID=scaffold_107-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: 16655
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.27
Warning! 3216 characters in sequence are not A, C, G, or T
Found at i:232 original size:16 final size:16
Alignment explanation
Indices: 211--262 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
201 GATTTGTTAT
211 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
227 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
243 TACACATCTAATCCAA
1 TACACCTCTAATCCAA
259 TACA
1 TACA
263 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1480 original size:30 final size:30
Alignment explanation
Indices: 1444--1503 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1434 ATAACTTTTT
*
1444 TTTATTTACCAAAATATTA-TAAAAAAAAAA
1 TTTATTTACCAAAATA-TACCAAAAAAAAAA
1474 TTTATTTACCAAAATATACCAAAAAAAAAA
1 TTTATTTACCAAAATATACCAAAAAAAAAA
1504 AACCTGACAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (30 bp):
TTTATTTACCAAAATATACCAAAAAAAAAA
Found at i:1564 original size:27 final size:27
Alignment explanation
Indices: 1525--1610 Score: 127
Period size: 27 Copynumber: 3.2 Consensus size: 27
1515 GCCTGATCAG
* * *
1525 GCCAATCACATTGGAGGCACCAAAGGT
1 GCCAATGAGATTGGAGGCACCAATGGT
1552 GCCAATGAGATTGGAGGCACCAATGGT
1 GCCAATGAGATTGGAGGCACCAATGGT
* *
1579 GCCAAAGAGATTGGCGGCACCAATGGT
1 GCCAATGAGATTGGAGGCACCAATGGT
1606 GCCAA
1 GCCAA
1611 AGGACTAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.31, C:0.23, G:0.30, T:0.15
Consensus pattern (27 bp):
GCCAATGAGATTGGAGGCACCAATGGT
Found at i:1611 original size:27 final size:27
Alignment explanation
Indices: 1534--1612 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
1524 GGCCAATCAC
* *
1534 ATTGGAGGCACCAAAGGTGCCAATGAG
1 ATTGGAGGCACCAATGGTGCCAAAGAG
1561 ATTGGAGGCACCAATGGTGCCAAAGAG
1 ATTGGAGGCACCAATGGTGCCAAAGAG
*
1588 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGAGGCACCAATGGTGCCAAAG
1613 GACTAAAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.32, C:0.20, G:0.33, T:0.15
Consensus pattern (27 bp):
ATTGGAGGCACCAATGGTGCCAAAGAG
Found at i:2186 original size:18 final size:18
Alignment explanation
Indices: 2163--2226 Score: 83
Period size: 18 Copynumber: 3.5 Consensus size: 18
2153 TAAGATAGAG
2163 TTATTAAATGAGAATAGT
1 TTATTAAATGAGAATAGT
* * *
2181 TTATTAAATTAAAATAGAG
1 TTATTAAATGAGAATAG-T
*
2200 TTATTAAATGAGAATTGT
1 TTATTAAATGAGAATAGT
2218 TTATTAAAT
1 TTATTAAAT
2227 TAAAATAAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 24 0.63
19 14 0.37
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTATTAAATGAGAATAGT
Found at i:2198 original size:37 final size:37
Alignment explanation
Indices: 2150--2245 Score: 165
Period size: 37 Copynumber: 2.6 Consensus size: 37
2140 GTTAAGTGAT
*
2150 AATTAAGATAGAGTTATTAAATGAGAATAGTTTATTA
1 AATTAAAATAGAGTTATTAAATGAGAATAGTTTATTA
*
2187 AATTAAAATAGAGTTATTAAATGAGAATTGTTTATTA
1 AATTAAAATAGAGTTATTAAATGAGAATAGTTTATTA
*
2224 AATTAAAATAAAGTTATTAAAT
1 AATTAAAATAGAGTTATTAAAT
2246 AAACTATTCT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (37 bp):
AATTAAAATAGAGTTATTAAATGAGAATAGTTTATTA
Found at i:2205 original size:19 final size:19
Alignment explanation
Indices: 2150--2245 Score: 97
Period size: 19 Copynumber: 5.2 Consensus size: 19
2140 GTTAAGTGAT
*
2150 AATTAAGATAGAGTTATTA
1 AATTAAAATAGAGTTATTA
* * *
2169 AATGAGAATAG-TTTATTA
1 AATTAAAATAGAGTTATTA
2187 AATTAAAATAGAGTTATTA
1 AATTAAAATAGAGTTATTA
* * * *
2206 AATGAGAATTG-TTTATTA
1 AATTAAAATAGAGTTATTA
*
2224 AATTAAAATAAAGTTATTA
1 AATTAAAATAGAGTTATTA
2243 AAT
1 AAT
2246 AAACTATTCT
Statistics
Matches: 59, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
18 28 0.47
19 31 0.53
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (19 bp):
AATTAAAATAGAGTTATTA
Found at i:2264 original size:37 final size:37
Alignment explanation
Indices: 2150--2265 Score: 121
Period size: 37 Copynumber: 3.1 Consensus size: 37
2140 GTTAAGTGAT
* * *
2150 AATTAAGATAGAGTTATTAAATGAGAA-TAGTTTATTA
1 AATTAAAATAAAGTTATTAAATGAGAACTA-TTTATCA
* * * *
2187 AATTAAAATAGAGTTATTAAATGAGAATTGTTTATTA
1 AATTAAAATAAAGTTATTAAATGAGAACTATTTATCA
2224 AATTAAAATAAAGTTATTAAAT-A-AACTATTCTCATCA
1 AATTAAAATAAAGTTATTAAATGAGAACTATT-T-ATCA
2261 AATTA
1 AATTA
2266 CCAAAATAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
35 5 0.07
36 2 0.03
37 62 0.89
38 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.38
Consensus pattern (37 bp):
AATTAAAATAAAGTTATTAAATGAGAACTATTTATCA
Found at i:2379 original size:27 final size:27
Alignment explanation
Indices: 2356--2417 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
2346 TTTTTTTTGT
2356 ATATTTTGATAAATAAAAAATTTTATA
1 ATATTTTGATAAATAAAAAATTTTATA
**
2383 ATATTTTGATAAATAAAAAAAGTTATA
1 ATATTTTGATAAATAAAAAATTTTATA
2410 ATATTTTG
1 ATATTTTG
2418 GTTATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (27 bp):
ATATTTTGATAAATAAAAAATTTTATA
Found at i:6480 original size:15 final size:17
Alignment explanation
Indices: 6445--6477 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
6435 TGTAATGGTG
6445 GGTT-TTTTTTTGTAAT
1 GGTTATTTTTTTGTAAT
6461 GGTTATTTTTTT-TAAT
1 GGTTATTTTTTTGTAAT
6477 G
1 G
6478 TTAAAATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.15, C:0.00, G:0.18, T:0.67
Consensus pattern (17 bp):
GGTTATTTTTTTGTAAT
Found at i:6680 original size:22 final size:22
Alignment explanation
Indices: 6655--6724 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
6645 TTTATAAGAT
6655 AATTAGAAACGTTGGTAGATCG
1 AATTAGAAACGTTGGTAGATCG
** **
6677 AATTAGGGA-GTTTATAAGAT--
1 AATTAGAAACGTTGGT-AGATCG
6697 AATTAGAAACGTTGGTAGATCG
1 AATTAGAAACGTTGGTAGATCG
6719 AATTAG
1 AATTAG
6725 GGGTGTATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
20 11 0.31
21 8 0.22
22 17 0.47
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.30
Consensus pattern (22 bp):
AATTAGAAACGTTGGTAGATCG
Found at i:6702 original size:42 final size:42
Alignment explanation
Indices: 6643--6726 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
6633 GGGGTATGTA
6643 AGTTTATAAGATAATTAGAAACGTTGGTAGATCGAATTAGGG
1 AGTTTATAAGATAATTAGAAACGTTGGTAGATCGAATTAGGG
6685 AGTTTATAAGATAATTAGAAACGTTGGTAGATCGAATTAGGG
1 AGTTTATAAGATAATTAGAAACGTTGGTAGATCGAATTAGGG
6727 GTGTATTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (42 bp):
AGTTTATAAGATAATTAGAAACGTTGGTAGATCGAATTAGGG
Found at i:6716 original size:20 final size:20
Alignment explanation
Indices: 6651--6716 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
6641 TAAGTTTATA
6651 AGATAATTAGAAACGTTGGT
1 AGATAATTAGAAACGTTGGT
** **
6671 AGATCGAATTAGGGA-GTTTAT
1 AGAT--AATTAGAAACGTTGGT
6692 AAGATAATTAGAAACGTTGGT
1 -AGATAATTAGAAACGTTGGT
6713 AGAT
1 AGAT
6717 CGAATTAGGG
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
20 15 0.44
21 8 0.24
22 11 0.32
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (20 bp):
AGATAATTAGAAACGTTGGT
Found at i:6789 original size:14 final size:14
Alignment explanation
Indices: 6770--6799 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6760 TGCTCATGCA
6770 AGCTTAATCAATAG
1 AGCTTAATCAATAG
6784 AGCTTAATCAATAG
1 AGCTTAATCAATAG
6798 AG
1 AG
6800 TTTGAGCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (14 bp):
AGCTTAATCAATAG
Found at i:7589 original size:28 final size:29
Alignment explanation
Indices: 7539--7595 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
7529 TTTCCACACG
*
7539 GGCTGGACACACAGTCGTGTGTGCCAAACA
1 GGCTGGACACACAGTCG-ATGTGCCAAACA
*
7569 GGCTGGACACACGGTC-ATGTGCCAAAC
1 GGCTGGACACACAGTCGATGTGCCAAAC
7596 CATGTCGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.40
30 15 0.60
ACGTcount: A:0.26, C:0.28, G:0.30, T:0.16
Consensus pattern (29 bp):
GGCTGGACACACAGTCGATGTGCCAAACA
Found at i:9067 original size:45 final size:45
Alignment explanation
Indices: 8998--9084 Score: 158
Period size: 45 Copynumber: 1.9 Consensus size: 45
8988 GTGTATAACT
8998 TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
1 TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
9043 TATCTCATCTATTGAAT-CTGATAAGTATGATTTATCTTCCTT
1 TATCTCATCTATTGAATCCT-ATAAGTATGATTTATCTTCCTT
9085 AATAAGGTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
44 2 0.05
45 39 0.95
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.47
Consensus pattern (45 bp):
TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
Done.