Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_178 ID=scaffold_178-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: 9919
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1069 original size:13 final size:13
Alignment explanation
Indices: 1033--1071 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 13
1023 ATTATTGTTT
1033 TTTATATTCATTTTG
1 TTTATATT-A-TTTG
1048 TTTAT-TTATTTG
1 TTTATATTATTTG
1060 TTTATATTATTT
1 TTTATATTATTT
1072 CTATGTCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.39
13 7 0.30
14 2 0.09
15 5 0.22
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.72
Consensus pattern (13 bp):
TTTATATTATTTG
Found at i:5546 original size:14 final size:15
Alignment explanation
Indices: 5529--5562 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
5519 AAAAAAGATG
5529 GAAAAAATG-AAAAT
1 GAAAAAATGAAAAAT
5543 G-AAAAATGAAAAAT
1 GAAAAAATGAAAAAT
5557 GAAAAA
1 GAAAAA
5563 GGAGAGGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.39
14 7 0.39
15 4 0.22
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (15 bp):
GAAAAAATGAAAAAT
Found at i:5548 original size:7 final size:7
Alignment explanation
Indices: 5531--5562 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
5521 AAAAGATGGA
5531 AAAAATG
1 AAAAATG
5538 -AAAATG
1 AAAAATG
5544 AAAAATG
1 AAAAATG
5551 AAAAATG
1 AAAAATG
5558 AAAAA
1 AAAAA
5563 GGAGAGGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:6209 original size:12 final size:12
Alignment explanation
Indices: 6192--6216 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6182 AAATTGAGAC
6192 TATCCCTTCAGA
1 TATCCCTTCAGA
6204 TATCCCTTCAGA
1 TATCCCTTCAGA
6216 T
1 T
6217 TTTGTTGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (12 bp):
TATCCCTTCAGA
Found at i:6966 original size:44 final size:44
Alignment explanation
Indices: 6902--6988 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
6892 CCCTTAGCCT
**
6902 TATCTCCCTGGTCAGTAGTGGAATAAGTT-ACAGATTATGAATCC
1 TATCTCCCTGGTCAACAGTGGAATAAGTTGA-AGATTATGAATCC
* * *
6946 TATCTCCCTGGTTAACAGTGGAATAGGTTGAAGATTGTGAATC
1 TATCTCCCTGGTCAACAGTGGAATAAGTTGAAGATTATGAATC
6989 TTACTTTCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 36 0.97
45 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (44 bp):
TATCTCCCTGGTCAACAGTGGAATAAGTTGAAGATTATGAATCC
Found at i:7211 original size:169 final size:169
Alignment explanation
Indices: 7007--7644 Score: 943
Period size: 169 Copynumber: 3.8 Consensus size: 169
6997 CTAACGTTAT
* *
7007 AGCGGAGCAGATTAAAGCTAAGGACAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCT
1 AGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCT
* * * *
7072 GAAGTAGAGCAGATTAAAGCTGTGGCCAGTGAATCCTATCTCTTTGGCATTATAGTGGAACAAAT
66 GAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTATAGTGGAACAGAT
7137 TAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGTGTTGC
131 TAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGTGTTGC
* * *
7176 AGCGGAGCAAATTAAAGCTGAGGGCAGCGAATCTTATCTCCTTGGTGTTAAGAGTTGAAATAGCT
1 AGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCT
* * * * *
7241 GAAGTGAAGCGGATTAAAGCTGTGGGCAGTGAATCTTATCTCTTTGGCATTGTAGTGGAACAGAT
66 GAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTATAGTGGAACAGAT
*
7306 TAAAGCTAAAGGTAGCAAATCTTGTTTCCCTAGTGTTGC
131 TAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGTGTTGC
* * * * *
7345 AGTGGAGCATATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTTGTGTTAAGAGTTGAAATAGCA
1 AGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCT
* * * *
7410 GAAGTGGAACAGATTAAAGCTGTGGGTAGCGAATTCTATCTCTTTGGCATTATAGTGGTACAGAT
66 GAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTATAGTGGAACAGAT
*
7475 TAAAGCTAAAGGTAGTGAATCTTGTTTCCCTAGTGTTGC
131 TAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGTGTTGC
* * * * *
7514 AGCAGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTAGCGTTAAGACTTGGATTAGCT
1 AGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCT
** * * * * *
7579 GAAGTGGAGTGGATTGAAGCTGTGGGTAGCGAATCCTATCTCTTTGGCATTACAGTGAAAAAGAT
66 GAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTATAGTGGAACAGAT
7644 T
131 T
7645 GAAGTCGCAA
Statistics
Matches: 422, Mismatches: 47, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
169 422 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (169 bp):
AGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCT
GAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTATAGTGGAACAGAT
TAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGTGTTGC
Found at i:7224 original size:51 final size:51
Alignment explanation
Indices: 7078--7225 Score: 125
Period size: 51 Copynumber: 2.9 Consensus size: 51
7068 AGCTGAAGTA
* * * * * * ** * *
7078 GAGCAGATTAAAGCTGTGGCCAGTGAATCCTATCTCTTTGGCATTATAGTG
1 GAGCAAATTAAAGCTGAGGGCAGCGAATCTTATCTCCTTGGTGTTACAGCG
* * * * * * * * *
7129 GAACAAATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGTGTTGCAGCG
1 GAGCAAATTAAAGCTGAGGGCAGCGAATCTTATCTCCTTGGTGTTACAGCG
7180 GAGCAAATTAAAGCTGAGGGCAGCGAATCTTATCTCCTTGGTGTTA
1 GAGCAAATTAAAGCTGAGGGCAGCGAATCTTATCTCCTTGGTGTTA
7226 AGAGTTGAAA
Statistics
Matches: 69, Mismatches: 28, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (51 bp):
GAGCAAATTAAAGCTGAGGGCAGCGAATCTTATCTCCTTGGTGTTACAGCG
Found at i:7378 original size:51 final size:51
Alignment explanation
Indices: 7294--7393 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 51
7284 TTGGCATTGT
* * *
7294 AGTGGAACAGATTAAAGCTAAAGGTAGCAAATCTTGTTTCCCTAGTGTTGC
1 AGTGGAACAGATTAAAGCTAAAGGCAGCAAATCTTATCTCCCTAGTGTTGC
* * * * * *
7345 AGTGGAGCATATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTTGTGTT
1 AGTGGAACAGATTAAAGCTAAAGGCAGCAAATCTTATCTCCCTAGTGTT
7394 AAGAGTTGAA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (51 bp):
AGTGGAACAGATTAAAGCTAAAGGCAGCAAATCTTATCTCCCTAGTGTTGC
Found at i:8094 original size:44 final size:43
Alignment explanation
Indices: 8022--8143 Score: 129
Period size: 44 Copynumber: 2.8 Consensus size: 43
8012 GAAGATGGCG
* * * * * *
8022 AATCTTATCTCCCTAAAGTTGCAATAGAGCAGATTGAAGCCAC
1 AATCTTATCTCCCTGAAGATGCAGTAGAGTAGATTAAAACCAC
*
8065 TAATCTTATCTCCCTGAAG-TGCCAGTAGAGTGGATTAAAACCAC
1 -AATCTTATCTCCCTGAAGATG-CAGTAGAGTAGATTAAAACCAC
**
8109 AGATCTTATCTCTTTGAAGATGCAGTAGAGTAGAT
1 A-ATCTTATCTCCCTGAAGATGCAGTAGAGTAGAT
8144 CACATCGGGT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
43 3 0.05
44 61 0.92
45 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGATGCAGTAGAGTAGATTAAAACCAC
Found at i:8203 original size:45 final size:44
Alignment explanation
Indices: 8152--8268 Score: 135
Period size: 45 Copynumber: 2.6 Consensus size: 44
8142 ATCACATCGG
* *
8152 GTCTTATCTCCCTGAAGTTCCAGTGGAGCAGACTCAAGAAAGCAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAA-CAA
* * * *
8197 GTCTTATCCCCCTGAAATTGCAGTGGGGCAGACTAAATAAACAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAACAA
* * * *
8241 ATCCTATCTCCCTAAAGTTGTAGTGGAG
1 GTCTTATCTCCCTGAAGTTGCAGTGGAG
8269 TAGATTAGAA
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
44 24 0.41
45 35 0.59
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (44 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAACAA
Found at i:9845 original size:19 final size:18
Alignment explanation
Indices: 9823--9858 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9813 AATTAATTAA
*
9823 TATGTAATTATTATTTTTT
1 TATGAAATTATT-TTTTTT
9842 TATGAAATTATTTTTTT
1 TATGAAATTATTTTTTT
9859 AAATTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (18 bp):
TATGAAATTATTTTTTTT
Done.