Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024604.1 Corchorus olitorius cultivar O-4 contig24637, 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: 24286
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:3968 original size:23 final size:22
Alignment explanation
Indices: 3942--3989 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 22
3932 TTTACTATCT
3942 TAAAT-ATAATATATATTATTAAA
1 TAAATAATAA-ATATATT-TTAAA
3965 TAAATAATAAATATATTTTAAA
1 TAAATAATAAATATATTTTAAA
3987 TAA
1 TAA
3990 TAAATAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 8 0.33
23 12 0.50
24 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATAATAAATATATTTTAAA
Found at i:3973 original size:21 final size:21
Alignment explanation
Indices: 3947--4029 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
3937 TATCTTAAAT
3947 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
3968 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
3989 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
4011 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
4030 TTACTAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:8408 original size:26 final size:27
Alignment explanation
Indices: 8356--8408 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
8346 CTTTTCCAAT
8356 ATATTTCTAATTTGCCATTATTAAAAA
1 ATATTTCTAATTTGCCATTATTAAAAA
*
8383 ATATTT-TAATTATTCCATTATTAAAA
1 ATATTTCTAATT-TGCCATTATTAAAA
8409 TAATGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (27 bp):
ATATTTCTAATTTGCCATTATTAAAAA
Found at i:10366 original size:22 final size:21
Alignment explanation
Indices: 10341--10418 Score: 84
Period size: 22 Copynumber: 3.6 Consensus size: 21
10331 CATATGGAGT
* *
10341 TTATCACAATTTCATAGCTAAA
1 TTATCAAAATTTAATAGCT-AA
**
10363 TTATCAAAATTTAATAGCTTGG
1 TTATCAAAATTTAATAGC-TAA
*
10385 TTATCAAAATTTAATAGGGTAA
1 TTATCAAAATTTAATA-GCTAA
10407 TTATCAAAATTT
1 TTATCAAAATTT
10419 CATAAAAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
22 45 0.96
23 2 0.04
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (21 bp):
TTATCAAAATTTAATAGCTAA
Found at i:10372 original size:66 final size:65
Alignment explanation
Indices: 10297--10422 Score: 148
Period size: 66 Copynumber: 1.9 Consensus size: 65
10287 TAGAAAAGGT
* * * * *
10297 TTATTAAAATTTCATA-ATTAGGTTATCAAAGTTTCATATGGAGT-TTATCACAATTTCATAGCT
1 TTATCAAAATTTAATAGATT-GGTTATCAAAATTTAATA-GG-GTATTATCAAAATTTCATAGCT
10360 AAA
63 AAA
*
10363 TTATCAAAATTTAATAGCTTGGTTATCAAAATTTAATAGGGTAATTATCAAAATTTCATA
1 TTATCAAAATTTAATAGATTGGTTATCAAAATTTAATAGGGT-ATTATCAAAATTTCATA
10423 AAAATATTCA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
64 2 0.04
65 2 0.04
66 45 0.88
67 2 0.04
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (65 bp):
TTATCAAAATTTAATAGATTGGTTATCAAAATTTAATAGGGTATTATCAAAATTTCATAGCTAAA
Found at i:10807 original size:89 final size:89
Alignment explanation
Indices: 10656--10819 Score: 274
Period size: 89 Copynumber: 1.8 Consensus size: 89
10646 TTCATTACTA
10656 ACAAAAGACTCTTTGAAAAAAATTAAGATTTTGTGTGAAGTCTAAAAAAAATACAATTGAATTCT
1 ACAAAAGACTCTTTGAAAAAAATTAAGATTTTGTGTGAAGTCTAAAAAAAATACAATTGAATTCT
10721 CCACGATTAGGTAGTTATTATAAT
66 CCACGATTAGGTAGTTATTATAAT
* * * * *
10745 ACAAAAGACTCTTTGAAAGAAATTAAGCTTTTGTGTGAATTCTAAGAAAAATACTATTGAATTCT
1 ACAAAAGACTCTTTGAAAAAAATTAAGATTTTGTGTGAAGTCTAAAAAAAATACAATTGAATTCT
*
10810 CCACGGTTAG
66 CCACGATTAG
10820 TAAATCTCAA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 69 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (89 bp):
ACAAAAGACTCTTTGAAAAAAATTAAGATTTTGTGTGAAGTCTAAAAAAAATACAATTGAATTCT
CCACGATTAGGTAGTTATTATAAT
Found at i:11556 original size:159 final size:159
Alignment explanation
Indices: 11303--11621 Score: 602
Period size: 159 Copynumber: 2.0 Consensus size: 159
11293 TATCTACATC
11303 TATAAAATGCTTAAATGAAGAACGTGTAATGACCCTTTTATCCACTACTTTCCAATTTTTTGGGA
1 TATAAAATGCTTAAATGAAGAACGTGTAATGACCCTTTTATCCACTACTTTCCAATTTTTTGGGA
* * *
11368 TTTTCGGTTGGATTTTAAGCTAGTCTCATTTGTCTAATAAAAGTTGGTTAAGTTGTAATTTTTGA
66 TTTTCGGTTGGATTTTAAGCTAGTCTCATTTGTCTAATAAAAATTGGTTAAATTATAATTTTTGA
11433 CTTAATAGAGTCAGGGTTAAATGAGGTTT
131 CTTAATAGAGTCAGGGTTAAATGAGGTTT
11462 TATAAAATGCTTAAATGAAGAACGTGTAATGACCCTTTTATCCACTACTTTCCAATTTTTTGGGA
1 TATAAAATGCTTAAATGAAGAACGTGTAATGACCCTTTTATCCACTACTTTCCAATTTTTTGGGA
11527 TTTTCGGTTGGATTTTAAGCTAGTCTCATTTGTCTAATAAAAATTGGTTAAATTATAATTTTTGA
66 TTTTCGGTTGGATTTTAAGCTAGTCTCATTTGTCTAATAAAAATTGGTTAAATTATAATTTTTGA
*
11592 CTTAATAGAGTCAGGGTTAAATGGGGTTT
131 CTTAATAGAGTCAGGGTTAAATGAGGTTT
11621 T
1 T
11622 GGCACCTGTT
Statistics
Matches: 156, Mismatches: 4, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
159 156 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.41
Consensus pattern (159 bp):
TATAAAATGCTTAAATGAAGAACGTGTAATGACCCTTTTATCCACTACTTTCCAATTTTTTGGGA
TTTTCGGTTGGATTTTAAGCTAGTCTCATTTGTCTAATAAAAATTGGTTAAATTATAATTTTTGA
CTTAATAGAGTCAGGGTTAAATGAGGTTT
Found at i:12279 original size:13 final size:13
Alignment explanation
Indices: 12261--12285 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12251 AGGCTTTTGA
12261 CTTTTTCTCAATT
1 CTTTTTCTCAATT
12274 CTTTTTCTCAAT
1 CTTTTTCTCAAT
12286 CCTCTGTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (13 bp):
CTTTTTCTCAATT
Found at i:13058 original size:13 final size:13
Alignment explanation
Indices: 13040--13065 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13030 GAGTTTCTGA
13040 AGTGTTTTACATT
1 AGTGTTTTACATT
13053 AGTGTTTTACATT
1 AGTGTTTTACATT
13066 CTATCTTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
AGTGTTTTACATT
Found at i:16967 original size:7 final size:8
Alignment explanation
Indices: 16948--16978 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
16938 AAGGAAAATA
*
16948 AAAAAAAT
1 AAAAAAAC
16956 AAAAAAAC
1 AAAAAAAC
16964 AAAAAAAC
1 AAAAAAAC
16972 AAAAAAA
1 AAAAAAA
16979 AACCTGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.90, C:0.06, G:0.00, T:0.03
Consensus pattern (8 bp):
AAAAAAAC
Found at i:16970 original size:18 final size:18
Alignment explanation
Indices: 16942--16981 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
16932 TAAGAAAAGG
* *
16942 AAAATAAAAAAA-ATAAA
1 AAAACAAAAAAACAAAAA
16959 AAAACAAAAAAACAAAAA
1 AAAACAAAAAAACAAAAA
16977 AAAAC
1 AAAAC
16982 CTGAAAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.88, C:0.07, G:0.00, T:0.05
Consensus pattern (18 bp):
AAAACAAAAAAACAAAAA
Found at i:17248 original size:16 final size:17
Alignment explanation
Indices: 17227--17259 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
17217 TCCAAACTAA
17227 ATATTAATTA-ATAAAT
1 ATATTAATTACATAAAT
17243 ATATTAATTACATAAAT
1 ATATTAATTACATAAAT
17260 TTTTTTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTAATTACATAAAT
Found at i:23246 original size:51 final size:50
Alignment explanation
Indices: 23145--23247 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
23135 GTTCTTCATA
** *
23145 TTTTTCTTGTTTAGATCTTGTCTCAGGACACCCAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
* * * *
23195 TTTTCTCTTGTTTCA-ATCTTGTCTCTGGACATAAAAACACTGTATTCGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
23246 TT
1 TT
23248 CTCTTTCAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
50 4 0.09
51 39 0.89
52 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
Done.