Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015223.1 Corchorus olitorius cultivar O-4 contig15256, 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: 18943
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:205 original size:56 final size:56
Alignment explanation
Indices: 119--225 Score: 178
Period size: 56 Copynumber: 1.9 Consensus size: 56
109 GATTTGAATT
* *
119 GTTTTTGCAAACTTTTTTTAATAGTGGTTTAATATTAACTGGCCCATTGGCAAGTA
1 GTTTTTGCAAACTTTTTATAATAATGGTTTAATATTAACTGGCCCATTGGCAAGTA
* *
175 GTTTTTGCAAACTTTTTATAATAATGGTTTAATATTAAGTGGGCCATTGGC
1 GTTTTTGCAAACTTTTTATAATAATGGTTTAATATTAACTGGCCCATTGGC
226 CCATGAGTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.43
Consensus pattern (56 bp):
GTTTTTGCAAACTTTTTATAATAATGGTTTAATATTAACTGGCCCATTGGCAAGTA
Found at i:4581 original size:14 final size:13
Alignment explanation
Indices: 4557--4595 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
4547 CTTTACTTTA
*
4557 TTTTTTTTTTGTG
1 TTTTGTTTTTGTG
4570 TTGTTGTTTTTGTG
1 TT-TTGTTTTTGTG
*
4584 TTTTTTTTTTGT
1 TTTTGTTTTTGT
4596 AACTTTGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (13 bp):
TTTTGTTTTTGTG
Found at i:9494 original size:21 final size:21
Alignment explanation
Indices: 9442--9495 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
9432 GGGATTGGAG
*
9442 TATTTA-TTTATTTTGTTGCT
1 TATTTATTTTATTTTCTTGCT
*
9462 TAATTT-TATTATTTTCTTGCT
1 T-ATTTATTTTATTTTCTTGCT
9483 TATTTATTTTATT
1 TATTTATTTTATT
9496 GTTACTCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.70
Consensus pattern (21 bp):
TATTTATTTTATTTTCTTGCT
Found at i:15261 original size:15 final size:15
Alignment explanation
Indices: 15241--15270 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15231 ATTGCCTATC
*
15241 GAAGAAGATGAAGAG
1 GAAGAAGAAGAAGAG
15256 GAAGAAGAAGAAGAG
1 GAAGAAGAAGAAGAG
15271 CCATTACCCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (15 bp):
GAAGAAGAAGAAGAG
Found at i:16516 original size:39 final size:40
Alignment explanation
Indices: 16460--16540 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
16450 TTTAATTCCT
*
16460 ATGTAATATATATAATAACTAAAATATTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
*
16500 ATGTAATA-CTATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
16539 AT
1 AT
16541 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:16535 original size:21 final size:21
Alignment explanation
Indices: 16472--16535 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 21
16462 GTAATATATA
*
16472 TAATAACTAAAATATTTACAT
1 TAATAACTAAAATACTTACAT
* **
16493 TAATTAAATGTAATAC-T--A-
1 TAA-TAACTAAAATACTTACAT
16511 TAATAACTAAAATACTTACAT
1 TAATAACTAAAATACTTACAT
16532 TAAT
1 TAAT
16536 TAAATTCTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 10
0.65 0.15 0.21
Matches are distributed among these distances:
17 9 0.29
18 4 0.13
19 1 0.03
20 1 0.03
21 8 0.26
22 8 0.26
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.38
Consensus pattern (21 bp):
TAATAACTAAAATACTTACAT
Found at i:17019 original size:197 final size:200
Alignment explanation
Indices: 16625--17030 Score: 703
Period size: 197 Copynumber: 2.0 Consensus size: 200
16615 TTCCTTAATA
16625 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATA----TTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
* *
16690 ATTTAATAAACCAACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTTCTATATATATAATAG
62 ATTTAATAAACCAACCACTAATGTTCAACTAACTTTTTTTTGGTATAGTTCTATATATATAATAA
*
16755 TAATTTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
127 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
16820 TCACCATTG
192 TCACCATTG
16829 ATAAATAAATCGGATCTTTAATA-TATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT
1 ATAAATAAATCGGATC-TTAATATTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT
*
16893 TAATAAATCAACCACTAATGTTCAACT-ACTTTTTTTTGGTATAG-T-TATATATATAATAATAA
65 TAATAAACCAACCACTAATGTTCAACTAACTTTTTTTTGGTATAGTTCTATATATATAATAATAA
16955 TGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCA
130 TGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCA
17020 CCATTG
195 CCATTG
17026 ATAAA
1 ATAAA
17031 GTTATTAAGC
Statistics
Matches: 197, Mismatches: 4, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
197 91 0.46
198 1 0.01
199 16 0.08
200 67 0.34
204 16 0.08
205 6 0.03
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.43
Consensus pattern (200 bp):
ATAAATAAATCGGATCTTAATATTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTT
AATAAACCAACCACTAATGTTCAACTAACTTTTTTTTGGTATAGTTCTATATATATAATAATAAT
GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCAC
CATTG
Found at i:17605 original size:36 final size:36
Alignment explanation
Indices: 17544--17613 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
17534 GAGATTTTGG
* * *
17544 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATAATAACCAAAATCACAAAAAATGTAATA
* *
17580 AGAAATATAATAACCAAAGTCACAAAAGATGTAA
1 AGAAATATAATAACCAAAATCACAAAAAATGTAA
17614 GGTTATTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATAATAACCAAAATCACAAAAAATGTAATA
Done.