Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017228.1 Corchorus olitorius cultivar O-4 contig17261, 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: 8437
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.39
Found at i:840 original size:15 final size:14
Alignment explanation
Indices: 807--890 Score: 57
Period size: 15 Copynumber: 5.9 Consensus size: 14
797 TACATACCAC
*
807 TAATAATAATTATT
1 TAATAATAATAATT
821 ATAATAATAATAAGTT
1 -TAATAATAATAA-TT
* *
837 TAATAATTATAATAC
1 TAATAATAATAAT-T
* *
852 CACTAATAATAAGTT
1 TAATAATAATAA-TT
867 TAATAAT--T-ATT
1 TAATAATAATAATT
878 ATAATAATAATAA
1 -TAATAATAATAA
891 GTCTAAATTA
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
11 2 0.04
12 8 0.15
13 1 0.02
14 2 0.04
15 37 0.70
16 3 0.06
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (14 bp):
TAATAATAATAATT
Found at i:840 original size:27 final size:27
Alignment explanation
Indices: 810--892 Score: 130
Period size: 30 Copynumber: 3.0 Consensus size: 27
800 ATACCACTAA
810 TAATAATTATTATAATAATAATAAGTT
1 TAATAATTATTATAATAATAATAAGTT
*
837 TAATAATTATAATACCACTAATAATAAGTT
1 TAATAATTATTATA--A-TAATAATAAGTT
867 TAATAATTATTATAATAATAATAAGT
1 TAATAATTATTATAATAATAATAAGT
893 CTAAATTAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
27 24 0.47
28 1 0.02
29 1 0.02
30 25 0.49
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (27 bp):
TAATAATTATTATAATAATAATAAGTT
Found at i:1229 original size:11 final size:11
Alignment explanation
Indices: 1186--1223 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1176 TTCCTATATA
*
1186 AAATAAATTAT
1 AAATTAATTAT
1197 CAAA-TAATTAT
1 -AAATTAATTAT
1208 AAATTAATTAT
1 AAATTAATTAT
1219 AAATT
1 AAATT
1224 TGTTATGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:2182 original size:12 final size:12
Alignment explanation
Indices: 2165--2211 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
2155 TATACCACTA
2165 ATAATAATTATT
1 ATAATAATTATT
2177 ATAATAATAATAAGTT
1 ATAATAAT--T-A-TT
2193 -TAATAATTATT
1 ATAATAATTATT
2204 ATAATAAT
1 ATAATAAT
2212 AATAAGTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
11 2 0.07
12 16 0.53
13 1 0.03
14 1 0.03
15 8 0.27
16 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (12 bp):
ATAATAATTATT
Found at i:2183 original size:15 final size:15
Alignment explanation
Indices: 2163--2214 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
2153 AATATACCAC
2163 TAATAATAATTATTA
1 TAATAATAATTATTA
* *
2178 TAATAATAATAAGT-
1 TAATAATAATTATTA
2192 T--TAATAATTATTA
1 TAATAATAATTATTA
2205 TAATAATAAT
1 TAATAATAAT
2215 AAGTCTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
12 9 0.30
13 1 0.03
14 1 0.03
15 19 0.63
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TAATAATAATTATTA
Found at i:2197 original size:30 final size:27
Alignment explanation
Indices: 2166--2218 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
2156 ATACCACTAA
2166 TAATAATTATTATAATAATAATAAGTT
1 TAATAATTATTATAATAATAATAAGTT
2193 TAATAATTATTATAATAATAATAAGT
1 TAATAATTATTATAATAATAATAAGT
2219 CTAAATTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (27 bp):
TAATAATTATTATAATAATAATAAGTT
Found at i:3343 original size:33 final size:33
Alignment explanation
Indices: 3299--3364 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3289 TTTGACTTCA
* *
3299 ATTAATAGTGTTCCCACCTTTTTAAATTGCATG
1 ATTAATAGTGTTACCACCTTTTCAAATTGCATG
*
3332 ATTAATGGTGTTACCACCTTTTCAAATTGCATG
1 ATTAATAGTGTTACCACCTTTTCAAATTGCATG
3365 CCCTTAGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (33 bp):
ATTAATAGTGTTACCACCTTTTCAAATTGCATG
Found at i:4452 original size:39 final size:40
Alignment explanation
Indices: 4399--4479 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
4389 TTTAATTCCT
4399 ATGTAATATATATAATAACTAAAATAATTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATAATTACATTAATTAA
* * *
4439 ATGTAATA-CTATAATAACTTAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATAATTACATTAATTAA
4478 AT
1 AT
4480 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATAATTACATTAATTAA
Found at i:4974 original size:203 final size:204
Alignment explanation
Indices: 4589--5000 Score: 749
Period size: 203 Copynumber: 2.0 Consensus size: 204
4579 TTTCTTAATA
4589 ATAAATAAATTCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATTCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* *
4654 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAG
66 AATTTAATAAATCAACCACTAATGTTCAACTAACTTTTTTTGGTATAGTTCTATATATATAATAA
4719 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACAT
131 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACAT
4784 TCACCATTG
196 TCACCATTG
4793 ATAAATAAATT-GGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATT
1 ATAAATAAATTCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAA-T
*
4857 TTAATTTAATAAATCAACCACTAATGTTCAACT-ACTTTTTTTGGTATAGTTTTATATA-ATAAT
64 TTAATTTAATAAATCAACCACTAATGTTCAACTAACTTTTTTTGGTATAGTTCTATATATATAAT
*
4920 AATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAAC
129 AATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAAC
4985 ATTCACCATTG
194 ATTCACCATTG
4996 ATAAA
1 ATAAA
5001 GTTATTAAGC
Statistics
Matches: 202, Mismatches: 4, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
203 89 0.44
204 79 0.39
205 34 0.17
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (204 bp):
ATAAATAAATTCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATCAACCACTAATGTTCAACTAACTTTTTTTGGTATAGTTCTATATATATAATAA
TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACAT
TCACCATTG
Found at i:5558 original size:36 final size:36
Alignment explanation
Indices: 5511--5580 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
5501 GAGATTTTAG
* *
5511 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
5547 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
5581 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:6954 original size:58 final size:58
Alignment explanation
Indices: 6856--6965 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
6846 ATCATGCCTC
*
6856 GGTCCTAAAACGTCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAAGTCTT
1 GGTCCGAAAACGTCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAAGTCTT
* * *
6914 GGTCCGAAAACGTCTTTTTTTATG-CATCTAA-CAAAGAACATGTCACTTGATA
1 GGTCCGAAAACGTC-TTTTTTA-GACATCTAATAAAAAAACATGTCACTCGATA
6966 TTTGATTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
58 31 0.67
59 14 0.30
60 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (58 bp):
GGTCCGAAAACGTCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAAGTCTT
Done.