Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019622.1 Corchorus olitorius cultivar O-4 contig19655, 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: 8299
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:2619 original size:16 final size:16
Alignment explanation
Indices: 2598--2628 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2588 GCGAATGCAT
2598 TCATGCAAAGCATCAG
1 TCATGCAAAGCATCAG
*
2614 TCATGCAAATCATCA
1 TCATGCAAAGCATCA
2629 TAAGTATCTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (16 bp):
TCATGCAAAGCATCAG
Found at i:4912 original size:2 final size:2
Alignment explanation
Indices: 4905--4936 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4895 TTTGCTTTCC
*
4905 AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4937 TCTACTGTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6962 original size:35 final size:36
Alignment explanation
Indices: 6916--7149 Score: 203
Period size: 35 Copynumber: 6.6 Consensus size: 36
6906 AAGAGATCCT
* * *
6916 TTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTC-A
1 TTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTA
*
6951 TTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTT
1 TTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTA
** *
6987 TTCTTCAGTTTATTTCAATTGATCCA-GTTGATCGAA
1 TTCTTCAGTTTATTTCAATTGATCCAGGGCGATC-TA
** * * *
7023 GGCGATC-TTTTCTTT-AATTGATCCAGGGCGATCT-
1 TTC-TTCAGTTTATTTCAATTGATCCAGGGCGATCTA
* * *
7057 TTCCTCAATTTACTTCAATTGATCCAGGGCGATCT-
1 TTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTA
* * * *
7092 TTCCTCAATTTACTTCAGTTGATCCAGGGCGATCT-
1 TTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTA
* *
7127 TCTCTGCAGTTTGTTTCAATTGA
1 T-TCTTCAGTTTATTTCAATTGA
7150 CTGCAAATTG
Statistics
Matches: 163, Mismatches: 29, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
33 2 0.01
34 6 0.04
35 100 0.61
36 53 0.33
37 2 0.01
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.41
Consensus pattern (36 bp):
TTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTA
Found at i:7066 original size:25 final size:26
Alignment explanation
Indices: 7014--7066 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
7004 ATTGATCCAG
* * *
7014 TTGATCGAAGGCGATCTTTTCTTTAA
1 TTGATCCAAGGCGATCTTTTCCTCAA
*
7040 TTGATCCAGGGCGATC-TTTCCTCAA
1 TTGATCCAAGGCGATCTTTTCCTCAA
7065 TT
1 TT
7067 TACTTCAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (26 bp):
TTGATCCAAGGCGATCTTTTCCTCAA
Found at i:7426 original size:30 final size:30
Alignment explanation
Indices: 7392--7572 Score: 263
Period size: 30 Copynumber: 6.0 Consensus size: 30
7382 TGTTTTATCA
7392 GCTTTATTTTAATCCTGGTTGAGGATAATT
1 GCTTTATTTTAATCCTGGTTGAGGATAATT
* **
7422 GCTTTACTTTAATCCTGGTTGAGGATCGTT
1 GCTTTATTTTAATCCTGGTTGAGGATAATT
*
7452 GCTTTATTTTAATCTTGGTTGAGGATAATT
1 GCTTTATTTTAATCCTGGTTGAGGATAATT
* **
7482 GCTTTACTTTAATCCTGGTTGAGGATCGTT
1 GCTTTATTTTAATCCTGGTTGAGGATAATT
* **
7512 GCTTTATTTTAATCCTGATTGAGGATCGTT
1 GCTTTATTTTAATCCTGGTTGAGGATAATT
*
7542 GCTTTAATTTAATCCTGGTTGAGGATAATT
1 GCTTTATTTTAATCCTGGTTGAGGATAATT
7572 G
1 G
7573 ATAGGCACTT
Statistics
Matches: 134, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 134 1.00
ACGTcount: A:0.21, C:0.12, G:0.22, T:0.45
Consensus pattern (30 bp):
GCTTTATTTTAATCCTGGTTGAGGATAATT
Found at i:7458 original size:60 final size:60
Alignment explanation
Indices: 7392--7567 Score: 307
Period size: 60 Copynumber: 2.9 Consensus size: 60
7382 TGTTTTATCA
7392 GCTTTATTTTAATCCTGGTTGAGGATAATTGCTTTACTTTAATCCTGGTTGAGGATCGTT
1 GCTTTATTTTAATCCTGGTTGAGGATAATTGCTTTACTTTAATCCTGGTTGAGGATCGTT
*
7452 GCTTTATTTTAATCTTGGTTGAGGATAATTGCTTTACTTTAATCCTGGTTGAGGATCGTT
1 GCTTTATTTTAATCCTGGTTGAGGATAATTGCTTTACTTTAATCCTGGTTGAGGATCGTT
* ** *
7512 GCTTTATTTTAATCCTGATTGAGGATCGTTGCTTTAATTTAATCCTGGTTGAGGAT
1 GCTTTATTTTAATCCTGGTTGAGGATAATTGCTTTACTTTAATCCTGGTTGAGGAT
7568 AATTGATAGG
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 110 1.00
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.45
Consensus pattern (60 bp):
GCTTTATTTTAATCCTGGTTGAGGATAATTGCTTTACTTTAATCCTGGTTGAGGATCGTT
Found at i:7545 original size:90 final size:90
Alignment explanation
Indices: 7392--7572 Score: 299
Period size: 90 Copynumber: 2.0 Consensus size: 90
7382 TGTTTTATCA
* *
7392 GCTTTATTTTAATCCTGGTTGAGGATAATTGCTTTACTTTAATCCTGGTTGAGGATCGTTGCTTT
1 GCTTTACTTTAATCCTGGTTGAGGATAATTGCTTTACTTTAATCCTGATTGAGGATCGTTGCTTT
* *
7457 ATTTTAATCTTGGTTGAGGATAATT
66 AATTTAATCCTGGTTGAGGATAATT
** *
7482 GCTTTACTTTAATCCTGGTTGAGGATCGTTGCTTTATTTTAATCCTGATTGAGGATCGTTGCTTT
1 GCTTTACTTTAATCCTGGTTGAGGATAATTGCTTTACTTTAATCCTGATTGAGGATCGTTGCTTT
7547 AATTTAATCCTGGTTGAGGATAATT
66 AATTTAATCCTGGTTGAGGATAATT
7572 G
1 G
7573 ATAGGCACTT
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 84 1.00
ACGTcount: A:0.21, C:0.12, G:0.22, T:0.45
Consensus pattern (90 bp):
GCTTTACTTTAATCCTGGTTGAGGATAATTGCTTTACTTTAATCCTGATTGAGGATCGTTGCTTT
AATTTAATCCTGGTTGAGGATAATT
Found at i:7858 original size:21 final size:21
Alignment explanation
Indices: 7832--7895 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
7822 AGTTCTGAGG
7832 CTACCCGGCCCCGGGTACCCC
1 CTACCCGGCCCCGGGTACCCC
*
7853 CTACCCGGCCCTGGGTACCCCCC
1 CTACCCGGCCCCGGGTA--CCCC
* *
7876 CTACCCAGCCCCAGGTACCC
1 CTACCCGGCCCCGGGTACCC
7896 TAAGGAACGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 19 0.51
23 18 0.49
ACGTcount: A:0.12, C:0.56, G:0.20, T:0.11
Consensus pattern (21 bp):
CTACCCGGCCCCGGGTACCCC
Found at i:7879 original size:23 final size:23
Alignment explanation
Indices: 7832--7895 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
7822 AGTTCTGAGG
7832 CTACCCGGCCCCGGGTA--CCCC
1 CTACCCGGCCCCGGGTACCCCCC
*
7853 CTACCCGGCCCTGGGTACCCCCC
1 CTACCCGGCCCCGGGTACCCCCC
* *
7876 CTACCCAGCCCCAGGTACCC
1 CTACCCGGCCCCGGGTACCC
7896 TAAGGAACGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 16 0.43
23 21 0.57
ACGTcount: A:0.12, C:0.56, G:0.20, T:0.11
Consensus pattern (23 bp):
CTACCCGGCCCCGGGTACCCCCC
Done.