Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022594.1 Corchorus olitorius cultivar O-4 contig22627, 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: 42772
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1312 original size:15 final size:15
Alignment explanation
Indices: 1288--1321 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1278 TGCTGAAACT
*
1288 CTTTTTTTGTTTACA
1 CTTTTATTGTTTACA
*
1303 CTTTTATTGTTTGCA
1 CTTTTATTGTTTACA
1318 CTTT
1 CTTT
1322 AATTATCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.15, G:0.09, T:0.65
Consensus pattern (15 bp):
CTTTTATTGTTTACA
Found at i:22888 original size:42 final size:40
Alignment explanation
Indices: 22829--22912 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 40
22819 TTTAATTCCT
22829 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
22869 ATGTAATAATACTATAATAACTGAATTACTTACATTAATTAA
1 ATGTAAT-ATA-TATAATAACTAAAATACTTACATTAATTAA
22911 AT
1 AT
22913 TCTTAGATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 7 0.17
41 3 0.08
42 30 0.75
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:23386 original size:201 final size:198
Alignment explanation
Indices: 23022--23427 Score: 681
Period size: 201 Copynumber: 2.0 Consensus size: 198
23012 GTTTCCTTAA
*
23022 TAATAATTAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTCACATTGATCTAATT
1 TAATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTCACATTGATCTAATT
* *
23087 TAATTTAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTTCTATATATATAATAGTAAT
66 TAATTTAATCAACAACTAATGTTCAACTAATTTTTTTGGTATAGTTCTATATATATAATAATAAT
* *
23152 GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCAC
131 GTGTTGTATCTTATTAACTACAACTCTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCAC
23217 CAT
196 CAT
* *
23220 TAATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTGAT
1 TAATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTCACATTGATCTAAT
*
23285 TTAATTTAATAAATCAACAACTAATGTTCAACTACTTTTTTTGGTATAGTT-T-TATATATAATA
65 TTAA-TT--T-AATCAACAACTAATGTTCAACTAATTTTTTTGGTATAGTTCTATATATATAATA
23348 ATAATGTGTTGTATCTTATTAACTACAACTCTGTTAGTAATCTTAGACTTAAAAAATTAATAACA
126 ATAATGTGTTGTATCTTATTAACTACAACTCTGTTAGTAATCTTAGACTTAAAAAATTAATAACA
23413 TTCACCAT
191 TTCACCAT
23421 TAATAAA
1 TAATAAA
23428 GTTATTAAGC
Statistics
Matches: 195, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
198 17 0.09
199 48 0.25
200 2 0.01
201 88 0.45
202 2 0.01
203 38 0.19
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (198 bp):
TAATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTCACATTGATCTAATT
TAATTTAATCAACAACTAATGTTCAACTAATTTTTTTGGTATAGTTCTATATATATAATAATAAT
GTGTTGTATCTTATTAACTACAACTCTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCAC
CAT
Found at i:23947 original size:36 final size:36
Alignment explanation
Indices: 23900--23969 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
23890 GAGATTTTGG
* *
23900 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
23936 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
23970 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:25667 original size:58 final size:58
Alignment explanation
Indices: 25569--25678 Score: 159
Period size: 58 Copynumber: 1.9 Consensus size: 58
25559 ATCATGCCTC
* *
25569 GGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGTCTT
1 GGTCCGAAAACGTCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAAGTCTT
* * *
25627 GGTCCGAAAACGTCTTTTTTTATACATCTAAT-AAAGAACATGTCACTTGATA
1 GGTCCGAAAACGTC-TTTTTTAGACATCTAATAAAAAAACATGTCACTCGATA
25679 TTTGATTAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
58 31 0.67
59 15 0.33
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (58 bp):
GGTCCGAAAACGTCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAAGTCTT
Found at i:27669 original size:12 final size:13
Alignment explanation
Indices: 27642--27674 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
27632 GGGCTTAAAT
27642 AAATGAAAAGGAA
1 AAATGAAAAGGAA
27655 AAATGAAAA-GAA
1 AAATGAAAAGGAA
27667 AAAT-AAAA
1 AAATGAAAA
27675 AATGAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 7 0.35
13 9 0.45
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (13 bp):
AAATGAAAAGGAA
Found at i:30197 original size:6 final size:6
Alignment explanation
Indices: 30081--30193 Score: 113
Period size: 6 Copynumber: 18.8 Consensus size: 6
30071 GGCCCAAGTC
* * *
30081 AAAAAA AAAAAG AAAGAAG AAAGAA- AGAAAG -AAAAG AAAAAG GAAAAG
1 AAAAAG AAAAAG AAA-AAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG
* * * *
30129 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG GAAAAT AAAAGG AAAAAT
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* *
30177 AAAAAT AAAAAT AAAAA
1 AAAAAG AAAAAG AAAAA
30194 TAAATAGGAA
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
5 6 0.07
6 77 0.84
7 9 0.10
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:30318 original size:28 final size:28
Alignment explanation
Indices: 30262--30318 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
30252 TTGGAAAGTG
** *
30262 AAATTACTATTTTACCCTTGGAGGGGTA
1 AAATTACTAAATTACCCTTGGAGGAGTA
* *
30290 AAATTACTAAATTACCCTTTGATGAGTA
1 AAATTACTAAATTACCCTTGGAGGAGTA
30318 A
1 A
30319 TTTTAAGAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (28 bp):
AAATTACTAAATTACCCTTGGAGGAGTA
Found at i:31032 original size:27 final size:28
Alignment explanation
Indices: 30970--31033 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
30960 AAATCACGTA
*
30970 TTTGCCCTTGGTCGGCTAAAATTACCAT
1 TTTGCCCTTGGTCGACTAAAATTACCAT
* *
30998 TTTACCCTTGGTTGACT-AAATTA-CAGT
1 TTTGCCCTTGGTCGACTAAAATTACCA-T
31025 TTTGCCCTT
1 TTTGCCCTT
31034 AAGCGTCGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 2 0.06
27 15 0.48
28 14 0.45
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (28 bp):
TTTGCCCTTGGTCGACTAAAATTACCAT
Found at i:38373 original size:104 final size:104
Alignment explanation
Indices: 38193--38404 Score: 424
Period size: 104 Copynumber: 2.0 Consensus size: 104
38183 ATGAAATTAA
38193 TTCAGTCCTGAAGTTTTGCCATACTGACGAAAGCGGAGGCCATTTTGGACACAAGAAGACAGCAA
1 TTCAGTCCTGAAGTTTTGCCATACTGACGAAAGCGGAGGCCATTTTGGACACAAGAAGACAGCAA
38258 GAAAGATCTTGGATTGCGGATTTTATTGGACTACAATCT
66 GAAAGATCTTGGATTGCGGATTTTATTGGACTACAATCT
38297 TTCAGTCCTGAAGTTTTGCCATACTGACGAAAGCGGAGGCCATTTTGGACACAAGAAGACAGCAA
1 TTCAGTCCTGAAGTTTTGCCATACTGACGAAAGCGGAGGCCATTTTGGACACAAGAAGACAGCAA
38362 GAAAGATCTTGGATTGCGGATTTTATTGGACTACAATCT
66 GAAAGATCTTGGATTGCGGATTTTATTGGACTACAATCT
38401 TTCA
1 TTCA
38405 AGATTCTTAC
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 108 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (104 bp):
TTCAGTCCTGAAGTTTTGCCATACTGACGAAAGCGGAGGCCATTTTGGACACAAGAAGACAGCAA
GAAAGATCTTGGATTGCGGATTTTATTGGACTACAATCT
Found at i:39933 original size:25 final size:27
Alignment explanation
Indices: 39891--39947 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 27
39881 AGGCATGCCG
*
39891 AGCCATCCCGCGCACCAGCACCA-GCA
1 AGCCATCCCGCACACCAGCACCAGGCA
* *
39917 AGCCA-CCCGCACGCCAGCACGAGGCA
1 AGCCATCCCGCACACCAGCACCAGGCA
39943 AGCCA
1 AGCCA
39948 GAGCAGCTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.28, C:0.47, G:0.23, T:0.02
Consensus pattern (27 bp):
AGCCATCCCGCACACCAGCACCAGGCA
Done.