Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021633.1 Corchorus olitorius cultivar O-4 contig21666, 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: 20804
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:3351 original size:78 final size:78
Alignment explanation
Indices: 3047--3400 Score: 487
Period size: 78 Copynumber: 4.5 Consensus size: 78
3037 CATTTTTATC
* * ** * * *
3047 TGTGATGAAACGGACTGATGGGAGACGTTCGTTTAATTTACTTT-TATATAGGGACACCAATGTT
1 TGTGATGAAACGGTCTCAACGGAGACGATCGTTTCATTTA-TTTCTATACAGGGACACCAATGTT
*
3111 GGTGTTCAGCCG-T
65 GGTGTTCGGCCGTT
* *
3124 TGCGATGAAACGGTCTCAACGGAGACGATCGTTTCATTTATTTCTATACGGGGACACCAATGTTG
1 TGTGATGAAACGGTCTCAACGGAGACGATCGTTTCATTTATTTCTATACAGGGACACCAATGTTG
3189 GTGTTCGGCCGTT
66 GTGTTCGGCCGTT
* * *
3202 TGTGATGAAACGGTCTTTAACGGAGACGATCATTTCATTTATTTCTGTACAGGGACACCAATGTT
1 TGTGATGAAACGGTC-TCAACGGAGACGATCGTTTCATTTATTTCTATACAGGGACACCAATGTT
3267 GGTGTTCGGCCGTT
65 GGTGTTCGGCCGTT
* * *
3281 TGTGATGAAACGGTCGCAATGGAGACGATCGTTTCATTTATTTCTATACGGGGACACCAATGTTG
1 TGTGATGAAACGGTCTCAACGGAGACGATCGTTTCATTTATTTCTATACAGGGACACCAATGTTG
* **
3346 ATGTTCGGTTGTT
66 GTGTTCGGCCGTT
* *
3359 TGTGACGAAGCGGTCTCAACGGAGACGATCGTTTCATTTATT
1 TGTGATGAAACGGTCTCAACGGAGACGATCGTTTCATTTATT
3401 CAAAATTTCT
Statistics
Matches: 246, Mismatches: 28, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
76 3 0.01
77 62 0.25
78 107 0.43
79 74 0.30
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (78 bp):
TGTGATGAAACGGTCTCAACGGAGACGATCGTTTCATTTATTTCTATACAGGGACACCAATGTTG
GTGTTCGGCCGTT
Found at i:3352 original size:157 final size:155
Alignment explanation
Indices: 3096--3400 Score: 493
Period size: 157 Copynumber: 2.0 Consensus size: 155
3086 ACTTTTATAT
*
3096 AGGGACACCAATGTTGGTGTTCAGCCGTTGCGATGAAACGGTCTCAACGGAGACGATCGTTTCAT
1 AGGGACACCAATGTTGGTGTTCAGCCGTTGCGATGAAACGGTCGCAACGGAGACGATCGTTTCAT
* * *
3161 TTATTTCTATACGGGGACACCAATGTTGGTGTTCGGCCGTTTGTGATGAAACGGTCTTTAACGGA
66 TTATTTCTATACGGGGACACCAATGTTGATGTTCGGCCGTTTGTGACGAAACGGTC-TCAACGGA
3226 GACGATCATTTCATTTATTTCTGTAC
130 GACGATCATTTCATTTATTTCTGTAC
* * *
3252 AGGGACACCAATGTTGGTGTTCGGCCGTTTGTGATGAAACGGTCGCAATGGAGACGATCGTTTCA
1 AGGGACACCAATGTTGGTGTTCAGCCG-TTGCGATGAAACGGTCGCAACGGAGACGATCGTTTCA
** *
3317 TTTATTTCTATACGGGGACACCAATGTTGATGTTCGGTTGTTTGTGACGAAGCGGTCTCAACGGA
65 TTTATTTCTATACGGGGACACCAATGTTGATGTTCGGCCGTTTGTGACGAAACGGTCTCAACGGA
*
3382 GACGATCGTTTCATTTATT
130 GACGATCATTTCATTTATT
3401 CAAAATTTCT
Statistics
Matches: 137, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
156 51 0.37
157 86 0.63
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (155 bp):
AGGGACACCAATGTTGGTGTTCAGCCGTTGCGATGAAACGGTCGCAACGGAGACGATCGTTTCAT
TTATTTCTATACGGGGACACCAATGTTGATGTTCGGCCGTTTGTGACGAAACGGTCTCAACGGAG
ACGATCATTTCATTTATTTCTGTAC
Found at i:10485 original size:1 final size:1
Alignment explanation
Indices: 10481--10506 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
10471 GCTTTTTTAC
10481 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
10507 TTGGTACTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11039 original size:124 final size:124
Alignment explanation
Indices: 10819--11066 Score: 460
Period size: 124 Copynumber: 2.0 Consensus size: 124
10809 CAAGTTAAAT
* *
10819 TACGATTTTGGGGTAGTTAATGTGGCCTGTAATTTGCCACGTCATTGCCCTTACCAAACTTTTCA
1 TACGATTTTGGGGCAGTTAATGTGGCCTATAATTTGCCACGTCATTGCCCTTACCAAACTTTTCA
* *
10884 AATTTGCTAGATCTATTCCCACTGAGCACGTTCCCATTTTCAGCTTTACTCTCTGTTTG
66 AATTTGCTAGATCAATTCCCACTGAGCACGTTCCCATTTTCAGCTTTACTCTCTCTTTG
10943 TACGATTTTGGGGCAGTTAATGTGGCCTATAATTTGCCACGTCATTGCCCTTACCAAACTTTTCA
1 TACGATTTTGGGGCAGTTAATGTGGCCTATAATTTGCCACGTCATTGCCCTTACCAAACTTTTCA
11008 AATTTGCTAGATCAATTCCCACTGAGCACGTTCCCATTTTCAGCTTTACTCTCTCTTTG
66 AATTTGCTAGATCAATTCCCACTGAGCACGTTCCCATTTTCAGCTTTACTCTCTCTTTG
11067 CTCTGTCTCC
Statistics
Matches: 120, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 120 1.00
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (124 bp):
TACGATTTTGGGGCAGTTAATGTGGCCTATAATTTGCCACGTCATTGCCCTTACCAAACTTTTCA
AATTTGCTAGATCAATTCCCACTGAGCACGTTCCCATTTTCAGCTTTACTCTCTCTTTG
Found at i:14670 original size:28 final size:28
Alignment explanation
Indices: 14633--14691 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
14623 TACACATCAA
14633 AATTTCTTTGA-ACAAAAAATAATTTTAC
1 AATTTCTTTGAGA-AAAAAATAATTTTAC
*
14661 AATTTTTTTGAGGAAAAAAATAATTTTAC
1 AATTTCTTTGA-GAAAAAAATAATTTTAC
14690 AA
1 AA
14692 CTGATTTGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 10 0.36
29 17 0.61
30 1 0.04
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (28 bp):
AATTTCTTTGAGAAAAAAATAATTTTAC
Found at i:14699 original size:29 final size:29
Alignment explanation
Indices: 14646--14702 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
14636 TTCTTTGAAC
* **
14646 AAAAAATAATTTTACAATTTTTTTGAGGA
1 AAAAAATAATTTTACAACTGATTTGAGGA
14675 AAAAAATAATTTTACAACTGATTTGAGG
1 AAAAAATAATTTTACAACTGATTTGAGG
14703 GTAAATTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (29 bp):
AAAAAATAATTTTACAACTGATTTGAGGA
Found at i:15059 original size:13 final size:13
Alignment explanation
Indices: 15041--15065 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15031 GAAAGCTGTA
15041 AAAAATAAAAAAT
1 AAAAATAAAAAAT
15054 AAAAATAAAAAA
1 AAAAATAAAAAA
15066 ATTATCCCCT
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Done.