Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016824.1 Corchorus olitorius cultivar O-4 contig16857, 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: 27007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:627 original size:18 final size:20
Alignment explanation
Indices: 599--636 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
589 GCACCCTAGC
599 CTAACAACTAGAAGA-AAAA
1 CTAACAACTAGAAGAGAAAA
618 CTAA-AACTAGAAGAGAAAA
1 CTAACAACTAGAAGAGAAAA
637 AGAAGAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.63, C:0.13, G:0.13, T:0.11
Consensus pattern (20 bp):
CTAACAACTAGAAGAGAAAA
Found at i:3434 original size:88 final size:91
Alignment explanation
Indices: 3269--3444 Score: 277
Period size: 88 Copynumber: 1.9 Consensus size: 91
3259 GTGATGCACC
*
3269 CAAGGTTGATCATGGACTTGAAGATGGCAATGGAGAGCAAGGAAAGGATGAGCATGGGCTACAAG
1 CAAGGTTGATCATGGACTTGAAGATGACAAT-G-GAGCAAGGAAAGGATGAGCATGGGCTACAAG
*
3334 GAAGCATGAAGATGCATGAAGATTATCA
64 GAAGAATGAAGATGCATGAAGATTATCA
*
3362 CAAGGTTGATCATGGACTTGAAGATGACAAT-G-G-AAGGAAAGGATGAGCATGGGCTGCAAGGA
1 CAAGGTTGATCATGGACTTGAAGATGACAATGGAGCAAGGAAAGGATGAGCATGGGCTACAAGGA
*
3424 AGAATGAAGATGCATGGAGAT
66 AGAATGAAGATGCATGAAGAT
3445 CATGGAAATA
Statistics
Matches: 79, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
88 47 0.59
89 1 0.01
90 1 0.01
93 30 0.38
ACGTcount: A:0.38, C:0.11, G:0.34, T:0.18
Consensus pattern (91 bp):
CAAGGTTGATCATGGACTTGAAGATGACAATGGAGCAAGGAAAGGATGAGCATGGGCTACAAGGA
AGAATGAAGATGCATGAAGATTATCA
Found at i:6038 original size:2 final size:2
Alignment explanation
Indices: 6031--6089 Score: 75
Period size: 2 Copynumber: 29.5 Consensus size: 2
6021 CCTTGTCAAG
* * *
6031 AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT TT ACT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
6074 AT -T AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
6090 ATCTAGTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
1 1 0.02
2 46 0.94
3 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6055 original size:18 final size:18
Alignment explanation
Indices: 6032--6086 Score: 83
Period size: 18 Copynumber: 2.9 Consensus size: 18
6022 CTTGTCAAGA
6032 TATATATATATATATATT
1 TATATATATATATATATT
6050 TATATATATATATATATT
1 TATATATATATATATATT
*
6068 TACTAGATTATATATATAT
1 TA-TATA-TATATATATAT
6087 ATAATCTAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
18 20 0.59
19 3 0.09
20 11 0.32
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TATATATATATATATATT
Found at i:6095 original size:22 final size:21
Alignment explanation
Indices: 6029--6095 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
6019 ATCCTTGTCA
*
6029 AGATATATATATATATATATTT
1 AGATATATATATATATA-ATCT
* *
6051 ATATATATATATATAT-TTACT
1 AGATATATATATATATAAT-CT
6072 AGATTATATATATATATAATCT
1 AGA-TATATATATATATAATCT
6094 AG
1 AG
6096 TAATGCAGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 3 0.08
22 32 0.86
23 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (21 bp):
AGATATATATATATATAATCT
Found at i:7624 original size:6 final size:6
Alignment explanation
Indices: 7613--7662 Score: 50
Period size: 7 Copynumber: 8.2 Consensus size: 6
7603 TCGTTTGGCA
*
7613 TCGTTT TCGTTTT TCTGTTT TCTGTTT TTG-TT TCGTTT TCGTTT T-GTTT
1 TCGTTT TCG-TTT TC-GTTT TC-GTTT TCGTTT TCGTTT TCGTTT TCGTTT
7662 T
1 T
7663 TGTTGCGCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 9 0.23
6 13 0.33
7 16 0.41
8 1 0.03
ACGTcount: A:0.00, C:0.12, G:0.16, T:0.72
Consensus pattern (6 bp):
TCGTTT
Found at i:12209 original size:26 final size:26
Alignment explanation
Indices: 12173--12228 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
12163 ATGGAAGGCC
12173 TAATATTTTGAAGTAGTGTTGTTATA
1 TAATATTTTGAAGTAGTGTTGTTATA
12199 TAATATTTTGAAGTAGTGTTGTTATA
1 TAATATTTTGAAGTAGTGTTGTTATA
12225 TAAT
1 TAAT
12229 GATGGATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (26 bp):
TAATATTTTGAAGTAGTGTTGTTATA
Found at i:12985 original size:28 final size:28
Alignment explanation
Indices: 12948--13007 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
12938 CACACTTTCC
12948 CACTACTTTTCACCTATCAAATTTACCA
1 CACTACTTTTCACCTATCAAATTTACCA
12976 CACTACTTTTCACCTATCAAATTTACCA
1 CACTACTTTTCACCTATCAAATTTACCA
13004 CACT
1 CACT
13008 TTTCCACTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.33, G:0.00, T:0.35
Consensus pattern (28 bp):
CACTACTTTTCACCTATCAAATTTACCA
Found at i:15868 original size:11 final size:11
Alignment explanation
Indices: 15852--15900 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
15842 GAAGTTCGTG
15852 TTTGAAGATCA
1 TTTGAAGATCA
*
15863 TTTGAAGATAA
1 TTTGAAGATCA
15874 TTTGAAGA-C-
1 TTTGAAGATCA
*
15883 -TTGAAGACCA
1 TTTGAAGATCA
15893 -TTGAAGAT
1 TTTGAAGAT
15901 TTTGATGCCG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 7 0.21
11 18 0.55
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (11 bp):
TTTGAAGATCA
Found at i:17289 original size:15 final size:16
Alignment explanation
Indices: 17258--17297 Score: 73
Period size: 15 Copynumber: 2.6 Consensus size: 16
17248 TTACTTTGTT
17258 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
17274 TTGTTTTCTA-TTTAA
1 TTGTTTTCTAGTTTAA
17289 TTGTTTTCT
1 TTGTTTTCT
17298 GTCAACCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:20891 original size:10 final size:11
Alignment explanation
Indices: 20866--20891 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20856 TCATCTTTTA
20866 TTTTTCTCTAG
1 TTTTTCTCTAG
20877 TTTTTCTCTAG
1 TTTTTCTCTAG
20888 TTTT
1 TTTT
20892 AGAAGAGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTTCTCTAG
Found at i:24156 original size:69 final size:69
Alignment explanation
Indices: 24037--24177 Score: 185
Period size: 69 Copynumber: 2.0 Consensus size: 69
24027 TTTCACATCA
* ** * *
24037 AAGGAATTTTATTATGAGAGGACGATTAGGGGAGGAGAGGGAGGTATTATAGGGAGGGTTTTGTC
1 AAGGAATTTTATTATGAGAGAACGATTAGGAAAGCAGAGGGAGGTATTATAGGGAGGGTTTAGTC
24102 GGCT
66 GGCT
* * * *
24106 AAGGAATTTTATTATGAGATAATGATTAGGAAAGCAGAGGG-GCTTCTTATAGGGAGGGTTTAGT
1 AAGGAATTTTATTATGAGAGAACGATTAGGAAAGCAGAGGGAG-GTATTATAGGGAGGGTTTAGT
24170 CGGCT
65 CGGCT
24175 AAG
1 AAG
24178 TTTAAATAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
68 1 0.02
69 61 0.98
ACGTcount: A:0.30, C:0.06, G:0.36, T:0.28
Consensus pattern (69 bp):
AAGGAATTTTATTATGAGAGAACGATTAGGAAAGCAGAGGGAGGTATTATAGGGAGGGTTTAGTC
GGCT
Found at i:24724 original size:114 final size:114
Alignment explanation
Indices: 24519--24750 Score: 446
Period size: 114 Copynumber: 2.0 Consensus size: 114
24509 GTTTGTTTCT
24519 AATGCAATCATATATTATATACTAGATTACATTATCTTCCTCTCCTAATTCCCTTATCTTGCTTT
1 AATGCAATCATATATTATATACTAGATTACATTATCTTCCTCTCCTAATTCCCTTATCTTGCTTT
24584 TGCTTTGTAAGATAACATCGCACTAGTTCTTGAATTATGGGATTCCAAG
66 TGCTTTGTAAGATAACATCGCACTAGTTCTTGAATTATGGGATTCCAAG
*
24633 AATGTAATCATATATTATATACTAGATTACATTATCTTCCTCTCCTAATTCCCTTATCTTGCTTT
1 AATGCAATCATATATTATATACTAGATTACATTATCTTCCTCTCCTAATTCCCTTATCTTGCTTT
*
24698 TGCTTTGTAAGATAACATCGCACTAGTTCTTGAATTATGGGATTTCAAG
66 TGCTTTGTAAGATAACATCGCACTAGTTCTTGAATTATGGGATTCCAAG
24747 AATG
1 AATG
24751 ATTCACGAAT
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 116 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (114 bp):
AATGCAATCATATATTATATACTAGATTACATTATCTTCCTCTCCTAATTCCCTTATCTTGCTTT
TGCTTTGTAAGATAACATCGCACTAGTTCTTGAATTATGGGATTCCAAG
Found at i:25945 original size:2 final size:2
Alignment explanation
Indices: 25938--25974 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25928 TGGCCGAATC
25938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25975 ACCAATTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.