Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012573.1 Corchorus olitorius cultivar O-4 contig12606, 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: 18063
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:194 original size:25 final size:25
Alignment explanation
Indices: 166--219 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
156 GATACTAACC
166 TAAGGGACTAATTAGATATGCAAAG
1 TAAGGGACTAATTAGATATGCAAAG
191 TAAGGGACTAATTAGATATGCAAAG
1 TAAGGGACTAATTAGATATGCAAAG
216 TAAG
1 TAAG
220 AAAGTGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.44, C:0.07, G:0.24, T:0.24
Consensus pattern (25 bp):
TAAGGGACTAATTAGATATGCAAAG
Found at i:4028 original size:29 final size:29
Alignment explanation
Indices: 3972--4028 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
3962 AAACAAAAAT
*
3972 AATTTTTTTCTTATAGAAACGCAGAAACA
1 AATTTTTTTCTTATAGAAACGCAAAAACA
* *
4001 AATTTTTTTTTTA-AGAAAACGTAAAAAC
1 AATTTTTTTCTTATAG-AAACGCAAAAAC
4029 TTTTTTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.37
Consensus pattern (29 bp):
AATTTTTTTCTTATAGAAACGCAAAAACA
Found at i:11923 original size:21 final size:23
Alignment explanation
Indices: 11889--11933 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
11879 TTATGCCAAA
11889 AAATATGATAATAAA-TAATATT
1 AAATATGATAATAAATTAATATT
*
11911 AAAT-TGATTATAAATTAATATT
1 AAATATGATAATAAATTAATATT
11933 A
1 A
11934 TCATAGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (23 bp):
AAATATGATAATAAATTAATATT
Found at i:12285 original size:21 final size:21
Alignment explanation
Indices: 12258--12382 Score: 162
Period size: 21 Copynumber: 6.0 Consensus size: 21
12248 GTTTAACATA
*
12258 GTTTGACTATCACACTTTGGG
1 GTTTGACTATCAAACTTTGGG
*
12279 CTTTGACTATCAAACTTTGGG
1 GTTTGACTATCAAACTTTGGG
*
12300 GTTTGACTATCAAACGTTGGG
1 GTTTGACTATCAAACTTTGGG
* *
12321 GTTTGACCATCAAGCTTT-GG
1 GTTTGACTATCAAACTTTGGG
* *
12341 GTTTGACCATCAAAATTTGGG
1 GTTTGACTATCAAACTTTGGG
* *
12362 ATTTGACTATCAAAATTTGGG
1 GTTTGACTATCAAACTTTGGG
12383 TGACTGAAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
20 18 0.20
21 74 0.80
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (21 bp):
GTTTGACTATCAAACTTTGGG
Found at i:12360 original size:62 final size:63
Alignment explanation
Indices: 12258--12375 Score: 177
Period size: 62 Copynumber: 1.9 Consensus size: 63
12248 GTTTAACATA
* * * *
12258 GTTTGACTATCACACTTTGGGCTTTGACTATCAAACTTTGGGGTTTGACTATCAAACGTTGGG
1 GTTTGACCATCACACTTTGGGCTTTGACCATCAAAATTTGGGATTTGACTATCAAACGTTGGG
12321 GTTTGACCATCA-AGCTTTGGG-TTTGACCATCAAAATTTGGGATTTGACTATCAAA
1 GTTTGACCATCACA-CTTTGGGCTTTGACCATCAAAATTTGGGATTTGACTATCAAA
12376 ATTTGGGTGA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
62 32 0.64
63 18 0.36
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (63 bp):
GTTTGACCATCACACTTTGGGCTTTGACCATCAAAATTTGGGATTTGACTATCAAACGTTGGG
Found at i:12361 original size:41 final size:41
Alignment explanation
Indices: 12258--12383 Score: 162
Period size: 41 Copynumber: 3.0 Consensus size: 41
12248 GTTTAACATA
* *
12258 GTTTGACTATCACACTTTGGGCTTTGACTATCAAACTTTGGG
1 GTTTGACTATCAAACTTTGGGATTTGACTATCAAACTTT-GG
* * * *
12300 GTTTGACTATCAAACGTTGGGGTTTGACCATCAAGCTTTGG
1 GTTTGACTATCAAACTTTGGGATTTGACTATCAAACTTTGG
* * *
12341 GTTTGACCATCAAAATTTGGGATTTGACTATCAAAATTTGG
1 GTTTGACTATCAAACTTTGGGATTTGACTATCAAACTTTGG
12382 GT
1 GT
12384 GACTGAAATG
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
41 38 0.53
42 34 0.47
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.37
Consensus pattern (41 bp):
GTTTGACTATCAAACTTTGGGATTTGACTATCAAACTTTGG
Found at i:12947 original size:21 final size:21
Alignment explanation
Indices: 12903--13051 Score: 203
Period size: 21 Copynumber: 7.1 Consensus size: 21
12893 TTAACGTGTG
* *
12903 GACTATCAAA-TTTTGGGTTA
1 GACTATCAAACTTTGGGGTTT
*
12923 GACTATCAAACATTGGGGTTT
1 GACTATCAAACTTTGGGGTTT
*
12944 GACTATCGAACTTTGGGGTTT
1 GACTATCAAACTTTGGGGTTT
*
12965 GACAATCAAACTTTGGGGTTT
1 GACTATCAAACTTTGGGGTTT
*
12986 GACAATCAAACTTT-GGGTTT
1 GACTATCAAACTTTGGGGTTT
*
13006 GACTATCAAATTTTGGGGTTT
1 GACTATCAAACTTTGGGGTTT
*
13027 GACTATCAAACTTTTAGGGTTT
1 GACTATCAAAC-TTTGGGGTTT
13049 GAC
1 GAC
13052 CATGCATGTA
Statistics
Matches: 115, Mismatches: 11, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
20 28 0.24
21 75 0.65
22 12 0.10
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (21 bp):
GACTATCAAACTTTGGGGTTT
Found at i:12960 original size:41 final size:41
Alignment explanation
Indices: 12903--13051 Score: 208
Period size: 41 Copynumber: 3.6 Consensus size: 41
12893 TTAACGTGTG
* * *
12903 GACTATCAAATTTTGGGTTAGACTATCAAACATTGGGGTTT
1 GACTATCAAACTTTGGGTTTGACTATCAAACTTTGGGGTTT
* *
12944 GACTATCGAACTTTGGGGTTTGACAATCAAACTTTGGGGTTT
1 GACTATCAAACTTT-GGGTTTGACTATCAAACTTTGGGGTTT
* *
12986 GACAATCAAACTTTGGGTTTGACTATCAAATTTTGGGGTTT
1 GACTATCAAACTTTGGGTTTGACTATCAAACTTTGGGGTTT
13027 GACTATCAAACTTTTAGGGTTTGAC
1 GACTATCAAAC-TTT-GGGTTTGAC
13052 CATGCATGTA
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
41 47 0.49
42 39 0.41
43 9 0.09
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (41 bp):
GACTATCAAACTTTGGGTTTGACTATCAAACTTTGGGGTTT
Found at i:13004 original size:62 final size:63
Alignment explanation
Indices: 12907--13051 Score: 195
Period size: 62 Copynumber: 2.3 Consensus size: 63
12897 CGTGTGGACT
* * * *
12907 ATCAAA-TTTTGGGTTAGACTATCAAACATTGGGGTTTGACTATCGAACTTTGGGGTTTGACA
1 ATCAAACTTTAGGGTTTGACAATCAAACATTGGGGTTTGACTATCAAACTTTGGGGTTTGACA
* * * *
12969 ATCAAACTTTGGGGTTTGACAATCAAAC-TTTGGGTTTGACTATCAAATTTTGGGGTTTGACT
1 ATCAAACTTTAGGGTTTGACAATCAAACATTGGGGTTTGACTATCAAACTTTGGGGTTTGACA
13031 ATCAAACTTTTAGGGTTTGAC
1 ATCAAAC-TTTAGGGTTTGAC
13052 CATGCATGTA
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
62 43 0.59
63 30 0.41
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (63 bp):
ATCAAACTTTAGGGTTTGACAATCAAACATTGGGGTTTGACTATCAAACTTTGGGGTTTGACA
Found at i:13105 original size:21 final size:21
Alignment explanation
Indices: 13076--13127 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
13066 GAAATGTTTT
*
13076 TTTGTGGTTTCACAATCAAAC
1 TTTGGGGTTTCACAATCAAAC
* * **
13097 TTTGGGGTTTGACTATCATCC
1 TTTGGGGTTTCACAATCAAAC
13118 TTTGGGGTTT
1 TTTGGGGTTT
13128 GACCATACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.44
Consensus pattern (21 bp):
TTTGGGGTTTCACAATCAAAC
Found at i:13107 original size:80 final size:78
Alignment explanation
Indices: 12997--13149 Score: 207
Period size: 79 Copynumber: 1.9 Consensus size: 78
12987 ACAATCAAAC
* * * * *
12997 TTTGGGTTTGACTATCAAATTTTGGGGTTTGACTATCAAACTTTTAGGGTTTGACCATGCATGTA
1 TTTGGGTTTCACAATCAAACTTTGGGGTTTGACTATC-AACCTTTAGGGTTTGACCATACATGTA
*
13062 CAATGAAATGTTTT
65 CAAAGAAATGTTTT
* *
13076 TTTGTGGTTTCACAATCAAACTTTGGGGTTTGACTATCATCCTTTGGGGTTTGACCATACATGTA
1 TTTG-GGTTTCACAATCAAACTTTGGGGTTTGACTATCAACCTTTAGGGTTTGACCATACATGTA
*
13141 TAAAGAAAT
65 CAAAGAAAT
13150 AATTTTTGCT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 34 0.53
80 30 0.47
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (78 bp):
TTTGGGTTTCACAATCAAACTTTGGGGTTTGACTATCAACCTTTAGGGTTTGACCATACATGTAC
AAAGAAATGTTTT
Done.