Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015597.1 Corchorus olitorius cultivar O-4 contig15630, 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: 11946
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Found at i:1287 original size:13 final size:13
Alignment explanation
Indices: 1269--1293 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1259 TGTTGCTCCT
1269 AATCAAATTCAAA
1 AATCAAATTCAAA
1282 AATCAAATTCAA
1 AATCAAATTCAA
1294 GTCAGTAAAA
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:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (13 bp):
AATCAAATTCAAA
Found at i:2649 original size:121 final size:121
Alignment explanation
Indices: 2406--2805 Score: 472
Period size: 121 Copynumber: 3.3 Consensus size: 121
2396 AACAAGATGA
* * ** * *
2406 AATTCATTTAAGATATAAGTAAATCTTTAATCAAATTTGAAATTAAGGTTAAGT-AACCT--AAC
1 AATTCATTTAAGATTTAAGTGAATCTTTAATTGAATTTGAAATCAAGGTTAAGTGACCCTAAAAC
*
2468 TTAAGGTTTAATTAA-TTGATTATAACCTTTAGTT--TGAAAACTTTGGAAATTTCCAT
66 TTAAGGTTTAATTAAGTT-ATTATAACCTTTAGTTAAT-AAAA-TTTGGAAATTTTCAT
* *
2524 AATTCATTTAAGATTTAAGTGAATCCTTAATTGAATTTGAAATCAAGGTTAAGTGACCCTAAAAA
1 AATTCATTTAAGATTTAAGTGAATCTTTAATTGAATTTGAAATCAAGGTTAAGTGACCCTAAAAC
* *
2589 TTAAGGTTTAATTAAGTTATTAAAACCTTTAGTTAATAAAATTTGGGAATTTTCAT
66 TTAAGGTTTAATTAAGTTATTATAACCTTTAGTTAATAAAATTTGGAAATTTTCAT
* * * * *
2645 AATTCATTTAAGATTTAAGTGAATCTTTAACTGAATTTGGAATCGAGGTTAAGTGACCTTAAATC
1 AATTCATTTAAGATTTAAGTGAATCTTTAATTGAATTTGAAATCAAGGTTAAGTGACCCTAAAAC
* * * * * *
2710 TTTAGTTTTAATTAAGTGATTATAACC-TTAGTCAATAAACTTTTTGGAAACTTTCAT
66 TTAAGGTTTAATTAAGTTATTATAACCTTTAGTTAATAAA--ATTTGGAAATTTTCAT
* * * *
2767 AATTCTTTTGAGATTTAAGTGAATCATTAAATGAATTTG
1 AATTCATTTAAGATTTAAGTGAATCTTTAATTGAATTTG
2806 GTATGTTCTA
Statistics
Matches: 244, Mismatches: 30, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
118 48 0.20
119 4 0.02
120 11 0.05
121 126 0.52
122 54 0.22
123 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (121 bp):
AATTCATTTAAGATTTAAGTGAATCTTTAATTGAATTTGAAATCAAGGTTAAGTGACCCTAAAAC
TTAAGGTTTAATTAAGTTATTATAACCTTTAGTTAATAAAATTTGGAAATTTTCAT
Found at i:4235 original size:6 final size:6
Alignment explanation
Indices: 4224--4250 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4214 TTCGAAGCAA
4224 GGTTTG GGTTTG GGTTTG GGTTTG GGT
1 GGTTTG GGTTTG GGTTTG GGTTTG GGT
4251 GAAGTGATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (6 bp):
GGTTTG
Found at i:4412 original size:13 final size:14
Alignment explanation
Indices: 4383--4412 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4373 AGATTTAGAC
4383 ATGTTAATATCTGA
1 ATGTTAATATCTGA
4397 ATGTTAATAT-TGA
1 ATGTTAATATCTGA
4410 ATG
1 ATG
4413 CTTGGCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.43
Consensus pattern (14 bp):
ATGTTAATATCTGA
Found at i:4651 original size:35 final size:35
Alignment explanation
Indices: 4612--4690 Score: 122
Period size: 35 Copynumber: 2.3 Consensus size: 35
4602 TTTTGTTAGA
****
4612 TTTGAGCATGTTTCTGATTTTGCTTTGTGACTATG
1 TTTGAGCATGTTTCTGATCACCCTTTGTGACTATG
4647 TTTGAGCATGTTTCTGATCACCCTTTGTGACTATG
1 TTTGAGCATGTTTCTGATCACCCTTTGTGACTATG
4682 TTTGAGCAT
1 TTTGAGCAT
4691 ATCTAATGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.16, C:0.15, G:0.22, T:0.47
Consensus pattern (35 bp):
TTTGAGCATGTTTCTGATCACCCTTTGTGACTATG
Found at i:6483 original size:25 final size:25
Alignment explanation
Indices: 6455--6519 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
6445 TACAAGTTTA
*
6455 TAACTTTCTTTTTTTTATAAGCATC
1 TAACTTTCTGTTTTTTATAAGCATC
* *
6480 TAACTTTCTGTTTTTTATCAGTATC
1 TAACTTTCTGTTTTTTATAAGCATC
6505 TAACTTTCTGTTTTT
1 TAACTTTCTGTTTTT
6520 GGTCGATGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.20, C:0.15, G:0.06, T:0.58
Consensus pattern (25 bp):
TAACTTTCTGTTTTTTATAAGCATC
Found at i:7680 original size:15 final size:15
Alignment explanation
Indices: 7660--7701 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
7650 AAGAAACTCC
* *
7660 CACTGCCTAGCACCA
1 CACTGCCCAACACCA
*
7675 CACTGCCCAACACCC
1 CACTGCCCAACACCA
7690 CACTGCCCAACA
1 CACTGCCCAACA
7702 GTCATTAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.29, C:0.52, G:0.10, T:0.10
Consensus pattern (15 bp):
CACTGCCCAACACCA
Found at i:11892 original size:26 final size:27
Alignment explanation
Indices: 11863--11921 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
11853 TATTCCCAAA
* * *
11863 CTTTTTTTCCTTTTCTCTTC-CTTTTT
1 CTTTTTTTACTTTTCCCTTCTATTTTT
*
11889 CTTTTCTTACTTTTCCCTTCTATTTTT
1 CTTTTTTTACTTTTCCCTTCTATTTTT
11916 CTTTTT
1 CTTTTT
11922 CTTTTTCCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.71
Consensus pattern (27 bp):
CTTTTTTTACTTTTCCCTTCTATTTTT
Found at i:11940 original size:12 final size:12
Alignment explanation
Indices: 11866--11946 Score: 60
Period size: 12 Copynumber: 6.9 Consensus size: 12
11856 TCCCAAACTT
*
11866 TTTTTCCTTTTC
1 TTTTCCCTTTTC
* *
11878 TCTTCCTTTTTC
1 TTTTCCCTTTTC
*
11890 TTTT--C-TTAC
1 TTTTCCCTTTTC
* *
11899 TTTTCCCTTCTA
1 TTTTCCCTTTTC
* *
11911 TTTTTCTTTTTC
1 TTTTCCCTTTTC
11923 TTTTTCCCTTTTC
1 -TTTTCCCTTTTC
11936 TTTTCCCTTTT
1 TTTTCCCTTTT
Statistics
Matches: 50, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
9 7 0.14
11 1 0.02
12 32 0.64
13 10 0.20
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTCCCTTTTC
Done.