Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016111.1 Corchorus olitorius cultivar O-4 contig16144, whole genome shotgun sequence
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: 10368
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1337 original size:34 final size:34
Alignment explanation
Indices: 1299--1366 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
1289 TATTATCTAA
* * *
1299 GGATTTTATTAGTTGTTTGATATATTGTGAATTG
1 GGATTTGATTAGTAGTTTGATATATTGTAAATTG
1333 GGATTTGATTAGTAGTTTGATATATTGTAAATTG
1 GGATTTGATTAGTAGTTTGATATATTGTAAATTG
1367 ATATATCGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (34 bp):
GGATTTGATTAGTAGTTTGATATATTGTAAATTG
Found at i:2455 original size:18 final size:18
Alignment explanation
Indices: 2432--2471 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
2422 CTACTGCTAC
2432 AAAACGGAAAC-GAAAAA
1 AAAACGGAAACGGAAAAA
2449 GAAAACGGAAACGGAAAAA
1 -AAAACGGAAACGGAAAAA
2468 AAAA
1 AAAA
2472 AAGAAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.70, C:0.10, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAACGGAAACGGAAAAA
Found at i:3267 original size:70 final size:71
Alignment explanation
Indices: 3184--3319 Score: 229
Period size: 71 Copynumber: 1.9 Consensus size: 71
3174 AGTCTAAAAT
*
3184 ATACTCATTATTTTTAAGTAAAAGTACAT-TTATTTTTTGAGATATTACGTTGAACAACATATTA
1 ATACTCATTATTTTTAAGTAAAAGTACATCTTATTTTTTGAGATATTACGTTAAACAACATATTA
3248 TCAATA
66 TCAATA
* * *
3254 ATACTCATTATTTTTAAGTTAAAGTACATCTTTTTTTTTTAGATATTACGTTAAACAACATATTA
1 ATACTCATTATTTTTAAGTAAAAGTACATCTTATTTTTTGAGATATTACGTTAAACAACATATTA
3319 T
66 T
3320 TATTATGATA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
70 28 0.46
71 33 0.54
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (71 bp):
ATACTCATTATTTTTAAGTAAAAGTACATCTTATTTTTTGAGATATTACGTTAAACAACATATTA
TCAATA
Found at i:3778 original size:71 final size:71
Alignment explanation
Indices: 3715--3855 Score: 203
Period size: 71 Copynumber: 2.0 Consensus size: 71
3705 ACAAAATCTA
*
3715 AAAT-ATACTCATTATTTTTAAGTTAAAGTACCTCTTTTTTTTTGAGAAATTACGTTGAATAACA
1 AAATAATACTCATTATTTTTAAGTTAAAGTACATCTTTTTTTTTGAGAAATTACGTTGAATAACA
*
3779 TATTAT
66 AATTAT
* * * * *
3785 CAATAATACTCATTATTTTTAAGTTAAAGTACATCTTTTTTTTTTAGATATTACGTTAAACAACA
1 AAATAATACTCATTATTTTTAAGTTAAAGTACATCTTTTTTTTTGAGAAATTACGTTGAATAACA
*
3850 TATTAT
66 AATTAT
3856 TATTATGATA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
70 3 0.05
71 61 0.95
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (71 bp):
AAATAATACTCATTATTTTTAAGTTAAAGTACATCTTTTTTTTTGAGAAATTACGTTGAATAACA
AATTAT
Found at i:4071 original size:49 final size:47
Alignment explanation
Indices: 3970--4111 Score: 164
Period size: 49 Copynumber: 3.0 Consensus size: 47
3960 GAGCGTGCCA
* *
3970 ATCAATTTTGTC-AAAAGATTGATAAAAAGTGCAAAG-AAAATTAAAAG
1 ATCAATTTTGTCTAAAA-ATTGAGAAAAAGTGC-AAGTAAAAATAAAAG
4017 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAAGTAAAAATAAAAG
* * *
4066 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGC-TGTAAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGTAAAAA-TAAA
4112 TGATTGCTTG
Statistics
Matches: 84, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
47 19 0.23
48 21 0.25
49 44 0.52
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG
Found at i:6751 original size:30 final size:30
Alignment explanation
Indices: 6710--6817 Score: 103
Period size: 30 Copynumber: 3.6 Consensus size: 30
6700 TCATCACCAC
*
6710 TTTCAGTGCCATCATCTTTAGTGCCGTCAA
1 TTTCGGTGCCATCATCTTTAGTGCCGTCAA
* * * *
6740 TTTCGGTGCCATCA-GTTTCGATGCCATCAG
1 TTTCGGTGCCATCATCTTTAG-TGCCGTCAA
* * * *
6770 TTTTGGTGCCATCATCTTTGGTGTCGTCGA
1 TTTCGGTGCCATCATCTTTAGTGCCGTCAA
6800 TATT-GGTGCCATCATCTT
1 T-TTCGGTGCCATCATCTT
6818 CTTCCATGAC
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
29 4 0.06
30 53 0.84
31 6 0.10
ACGTcount: A:0.16, C:0.24, G:0.21, T:0.39
Consensus pattern (30 bp):
TTTCGGTGCCATCATCTTTAGTGCCGTCAA
Found at i:6789 original size:15 final size:14
Alignment explanation
Indices: 6715--6814 Score: 74
Period size: 15 Copynumber: 6.7 Consensus size: 14
6705 ACCACTTTCA
*
6715 GTGCCATCATCTTTA
1 GTGCCATCAT-TTTG
* *
6730 GTGCCGTCAATTTCG
1 GTGCCATC-ATTTTG
*
6745 GTGCCATCAGTTTCG
1 GTGCCATCA-TTTTG
*
6760 ATGCCATCAGTTTTG
1 GTGCCATCA-TTTTG
6775 GTGCCATCATCTTTG
1 GTGCCATCAT-TTTG
* * *
6790 GTGTCGTCGATATTG
1 GTGCCATC-ATTTTG
6805 GTGCCATCAT
1 GTGCCATCAT
6815 CTTCTTCCAT
Statistics
Matches: 69, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
14 4 0.06
15 61 0.88
16 4 0.06
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (14 bp):
GTGCCATCATTTTG
Found at i:8066 original size:18 final size:18
Alignment explanation
Indices: 8045--8114 Score: 104
Period size: 18 Copynumber: 3.9 Consensus size: 18
8035 AGGTGTGGCA
8045 ACTTGGTGCGGTGCGACC
1 ACTTGGTGCGGTGCGACC
*
8063 ACTTGGTGTGGTGCGACC
1 ACTTGGTGCGGTGCGACC
* **
8081 ATTTGGTGCGGTGCGAAT
1 ACTTGGTGCGGTGCGACC
8099 ACTTGGTGCGGTGCGA
1 ACTTGGTGCGGTGCGA
8115 TATGTTGTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.13, C:0.20, G:0.40, T:0.27
Consensus pattern (18 bp):
ACTTGGTGCGGTGCGACC
Found at i:8901 original size:49 final size:47
Alignment explanation
Indices: 8807--8948 Score: 180
Period size: 49 Copynumber: 3.0 Consensus size: 47
8797 GAGCGTGCCA
* * *
8807 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCAAAG-AAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGC-AAGTAAAAATAAAAG
8854 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAAGTAAAAATAAAAG
* *
8903 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGC-AGTAAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGTAAAAA-TAAA
8949 GGATTGCTTA
Statistics
Matches: 85, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
47 20 0.24
48 25 0.29
49 40 0.47
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG
Found at i:10245 original size:9 final size:9
Alignment explanation
Indices: 10225--10262 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
10215 TTAATTCATT
10225 TAATTTCC-
1 TAATTTCCA
10233 TAATTTCCA
1 TAATTTCCA
*
10242 TAATTTCCC
1 TAATTTCCA
10251 TAATTTCCA
1 TAATTTCCA
10260 TAA
1 TAA
10263 GTAATTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:10254 original size:18 final size:17
Alignment explanation
Indices: 10225--10262 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
10215 TTAATTCATT
10225 TAATTTCCTAATTTCCA
1 TAATTTCCTAATTTCCA
10242 TAATTTCCCTAATTTCCA
1 TAATTT-CCTAATTTCCA
10260 TAA
1 TAA
10263 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATTTCCTAATTTCCA
Done.