Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014077.1 Corchorus olitorius cultivar O-4 contig14110, 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: 19034
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:845 original size:20 final size:21
Alignment explanation
Indices: 805--865 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
795 GTCCTGTCCA
***
805 TCTGTACATTTTGAATTTCTT
1 TCTGTACATTTTTTTTTTCTT
826 TCTGTTA-ATTTTTTTTTCTTCTT
1 TCTG-TACA-TTTTTTTT-TTCTT
849 TCTGTACATTTTTTTTT
1 TCTGTACATTTTTTTTT
866 CTGTTGATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
21 6 0.18
22 17 0.52
23 10 0.30
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (21 bp):
TCTGTACATTTTTTTTTTCTT
Found at i:847 original size:23 final size:23
Alignment explanation
Indices: 821--867 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
811 CATTTTGAAT
821 TTCTTTCTGTTA-ATTTTTTTTTC
1 TTCTTTCTG-TACATTTTTTTTTC
844 TTCTTTCTGTACATTTTTTTTTC
1 TTCTTTCTGTACATTTTTTTTTC
867 T
1 T
868 GTTGATTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.09, C:0.15, G:0.04, T:0.72
Consensus pattern (23 bp):
TTCTTTCTGTACATTTTTTTTTC
Found at i:10834 original size:20 final size:18
Alignment explanation
Indices: 10801--10843 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
10791 GTTTTATATG
10801 TTTTTCTTCCTTTCACTTTT
1 TTTTTCTTCCTTT--CTTTT
**
10821 TTTTTCTTTTTTTCTTTT
1 TTTTTCTTCCTTTCTTTT
10839 TTTTT
1 TTTTT
10844 TTAAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTCTTCCTTTCTTTT
Found at i:13492 original size:14 final size:14
Alignment explanation
Indices: 13475--13523 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
13465 AAGATGATAA
13475 TTATTTCATGAATT
1 TTATTTCATGAATT
* *
13489 TTATTTTGATG-ATAA
1 TTA-TTTCATGAAT-T
13504 TTATTTCATGAATT
1 TTATTTCATGAATT
13518 TTATTT
1 TTATTT
13524 GGATGATGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.29, C:0.04, G:0.08, T:0.59
Consensus pattern (14 bp):
TTATTTCATGAATT
Found at i:13499 original size:29 final size:29
Alignment explanation
Indices: 13467--13530 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
13457 AGAAGTGCAA
*
13467 GATGATAATTATTTCATGAATTTTATTTT
1 GATGATAATTATTTCATGAATTTTATTTG
13496 GATGATAATTATTTCATGAATTTTATTTG
1 GATGATAATTATTTCATGAATTTTATTTG
13525 GATGAT
1 GATGAT
13531 GGATTTGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.52
Consensus pattern (29 bp):
GATGATAATTATTTCATGAATTTTATTTG
Found at i:13628 original size:29 final size:29
Alignment explanation
Indices: 13586--13641 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
13576 CCTTGCACGG
*
13586 TGTTGAAAGCTTGTAATTGTGGTGTTGAT
1 TGTTGAAAACTTGTAATTGTGGTGTTGAT
13615 TGTTGAAAACTTGTAATTGTGGTGTTG
1 TGTTGAAAACTTGTAATTGTGGTGTTG
13642 TAAACTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.04, G:0.30, T:0.45
Consensus pattern (29 bp):
TGTTGAAAACTTGTAATTGTGGTGTTGAT
Found at i:15770 original size:19 final size:19
Alignment explanation
Indices: 15730--15770 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
15720 AGATCATAGT
* *
15730 AAAACCAAGATAATCAATC
1 AAAACCAAGATAATAAACC
*
15749 AAAACCGAGATAATAAACC
1 AAAACCAAGATAATAAACC
15768 AAA
1 AAA
15771 TCAATCAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.61, C:0.20, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAACCAAGATAATAAACC
Found at i:16003 original size:28 final size:27
Alignment explanation
Indices: 15933--16008 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 27
15923 TCCGACGTTT
*
15933 AAGGGCAAAACTGTAA-TTTAGTCAACC
1 AAGGGCAAAAC-GTAATTTTAGCCAACC
** *
15960 AAGGATAAAATGGTAATTTTAGCCAACC
1 AAGGGCAAAA-CGTAATTTTAGCCAACC
15988 AAGGGCAAATACGTAATTTTA
1 AAGGGCAAA-ACGTAATTTTA
16009 ACATCCTAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 12 0.31
28 26 0.67
29 1 0.03
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (27 bp):
AAGGGCAAAACGTAATTTTAGCCAACC
Found at i:16301 original size:98 final size:98
Alignment explanation
Indices: 15988--16289 Score: 597
Period size: 98 Copynumber: 3.1 Consensus size: 98
15978 TTAGCCAACC
15988 AAGGGCAAATACGTAATTTTAACATCCTAAGGCTGATACGGTAATCCTTTAGCCTTACATGTTCA
1 AAGGGCAAATACGTAATTTTAACATCCTAAGGCTGATACGGTAATCCTTTAGCCTTACATGTTCA
16053 ATTATCATGTTCAAAT-AACCAAATCCTTTTCT
66 ATTATCATGTTCAAATAAACCAAATCCTTTTCT
16085 AAGGGCAAATACGTAATTTTAACATCCTAAGGCTGATACGGTAATCCTTTAGCCTTACATGTTCA
1 AAGGGCAAATACGTAATTTTAACATCCTAAGGCTGATACGGTAATCCTTTAGCCTTACATGTTCA
16150 ATTATCATGTTCAAATAAACCAAATCCTTTTCT
66 ATTATCATGTTCAAATAAACCAAATCCTTTTCT
16183 AAGGGCAAATACGTAATTTTAACATCCTAAGGCTGATACGGTAATCCTTTAGCCTTACATGTTCA
1 AAGGGCAAATACGTAATTTTAACATCCTAAGGCTGATACGGTAATCCTTTAGCCTTACATGTTCA
16248 ATTATCATGTTCAAATAAACCAAATCCTTTTCT
66 ATTATCATGTTCAAATAAACCAAATCCTTTTCT
16281 AAGGGCAAA
1 AAGGGCAAA
16290 GTTGTAATTT
Statistics
Matches: 204, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
97 81 0.40
98 123 0.60
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (98 bp):
AAGGGCAAATACGTAATTTTAACATCCTAAGGCTGATACGGTAATCCTTTAGCCTTACATGTTCA
ATTATCATGTTCAAATAAACCAAATCCTTTTCT
Found at i:17165 original size:35 final size:35
Alignment explanation
Indices: 17097--17199 Score: 163
Period size: 35 Copynumber: 2.9 Consensus size: 35
17087 CCAAGCTTGA
* *
17097 GCGCTGGGCCATG-GTTGGCCCGCGCGCCAGGCCTGG
1 GCGCTGGGCCATGTGCTGG-CC-CGCGCCTGGCCTGG
17133 GCGCTGGGCCATGTGCTGGCCCGCGCCTGGCCTGG
1 GCGCTGGGCCATGTGCTGGCCCGCGCCTGGCCTGG
17168 GCGCTGGGCCATGTGCTGGCCCGCGCCTGGCC
1 GCGCTGGGCCATGTGCTGGCCCGCGCCTGGCC
17200 CAAACGGCCC
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
35 45 0.70
36 15 0.23
37 4 0.06
ACGTcount: A:0.04, C:0.38, G:0.43, T:0.16
Consensus pattern (35 bp):
GCGCTGGGCCATGTGCTGGCCCGCGCCTGGCCTGG
Found at i:17815 original size:3 final size:3
Alignment explanation
Indices: 17807--17832 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17797 GATATTTCTT
17807 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
17833 GTTTGGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.