Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023322.1 Corchorus olitorius cultivar O-4 contig23355, 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: 5267
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:2343 original size:783 final size:783
Alignment explanation
Indices: 838--2406 Score: 3048
Period size: 783 Copynumber: 2.0 Consensus size: 783
828 TCGGAGTTGC
*
838 CTAAGATGCCATTTGATCCATTGAAAATGCCATTAGGCCCAATGACAAGGGCAAGAGCTAAAAGG
1 CTAAGATGACATTTGATCCATTGAAAATGCCATTAGGCCCAATGACAAGGGCAAGAGCTAAAAGG
903 TTCAAGGAAGCTTTGTTTGGCCTCATTAGAGTTCATCTTGAAGAGTTTAAAGCCATCGGAGATCA
66 TTCAAGGAAGCTTTGTTTGGCCTCATTAGAGTTCATCTTGAAGAGTTTAAAGCCATCGGAGATCA
*
968 TTTGAAGCCCATTGGAGATCATCAACAAAGGAATATTCCTATCGATTCCAAGTTGTGCATTCTTC
131 TTTGAAGCCCATTGGAGATCATCAACAAAGGAATATTCCCATCGATTCCAAGTTGTGCATTCTTC
1033 TTGAAATCGATGAGCACTAGGTCATTAGAGTTGTAATTTGGCCATTGTGGGCTTTATTCTATCTT
196 TTGAAATCGATGAGCACTAGGTCATTAGAGTTGTAATTTGGCCATTGTGGGCTTTATTCTATCTT
1098 TAATTAGCTTATTTTTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCT
261 TAATTAGCTTATTTTTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCT
1163 TGTTTAATTATGTCTTTATTTCCTTTTCCTAGTTGGGTTTGGACTAGTTTTACCCTAGTCCATAT
326 TGTTTAATTATGTCTTTATTTCCTTTTCCTAGTTGGGTTTGGACTAGTTTTACCCTAGTCCATAT
*
1228 ATTTGGACGAAAATTAGGTTATTTTTCTAGATCTAGGGCATCACCCTATGCCTATATAAAGGCAC
391 ATTTGGACGAAAATTAGGTAATTTTTCTAGATCTAGGGCATCACCCTATGCCTATATAAAGGCAC
1293 CAAACCCCTCTTGTAAACATAAGTTGAGTTGATTAATAAAATTGAGGTTTTTACCCAAATTGATT
456 CAAACCCCTCTTGTAAACATAAGTTGAGTTGATTAATAAAATTGAGGTTTTTACCCAAATTGATT
1358 ATCTTAGCTTCTTTGTTCTAGTTTGAGCAAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCA
521 ATCTTAGCTTCTTTGTTCTAGTTTGAGCAAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCA
1423 AACAATTAAGTTATGATACTTGATTGCTTGTGAATCTTGTGATCTTAGGTGTTCAATTGCAGGTC
586 AACAATTAAGTTATGATACTTGATTGCTTGTGAATCTTGTGATCTTAGGTGTTCAATTGCAGGTC
*
1488 TAATTGGAGGTCTAAGGCCGGCGAAAGAAGAAGATTGCTTGGGTGAGATTGTCGACATACACATC
651 TAATTGGAGGTCTAAGGCCGACGAAAGAAGAAGATTGCTTGGGTGAGATTGTCGACATACACATC
1553 TAGAAGTTGAAAGTTGTTCAAGTTGATTCTTGGCGGGTCACAAGGGTGGATTTTGAATCTTAAAA
716 TAGAAGTTGAAAGTTGTTCAAGTTGATTCTTGGCGGGTCACAAGGGTGGATTTTGAATCTTAAAA
1618 CAA
781 CAA
1621 CTAAGATGACATTTGATCCATTGAAAATGCCATTAGGCCCAATGACAAGGGCAAGAGCTAAAAGG
1 CTAAGATGACATTTGATCCATTGAAAATGCCATTAGGCCCAATGACAAGGGCAAGAGCTAAAAGG
1686 TTCAAGGAAGCTTTGTTTGGCCTCATTAGAGTTCATCTTGAAGAGTTTAAAGCCATCGGAGATCA
66 TTCAAGGAAGCTTTGTTTGGCCTCATTAGAGTTCATCTTGAAGAGTTTAAAGCCATCGGAGATCA
1751 TTTGAAGCCCATTGGAGATCATCAACAAAGGAATATTCCCATCGATTCCAAGTTGTGCATTCTTC
131 TTTGAAGCCCATTGGAGATCATCAACAAAGGAATATTCCCATCGATTCCAAGTTGTGCATTCTTC
1816 TTGAAATCGATGAGCACTAGGTCATTAGAGTTGTAATTTGGCCATTGTGGGCTTTATTCTATCTT
196 TTGAAATCGATGAGCACTAGGTCATTAGAGTTGTAATTTGGCCATTGTGGGCTTTATTCTATCTT
*
1881 TAATTAGCTTATTTTTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCTAATCCT
261 TAATTAGCTTATTTTTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCT
* *
1946 TGTTTAATTATGTCTTTATTTCCTTTTTCTAGTTGGGTTTGGACTAGTTTTACCCTAGTTCATAT
326 TGTTTAATTATGTCTTTATTTCCTTTTCCTAGTTGGGTTTGGACTAGTTTTACCCTAGTCCATAT
*
2011 ATTTGGACGAAAATTATGTAATTTTTCTAGATCTAGGGCATCACCCTATGCCTATATAAAGGCAC
391 ATTTGGACGAAAATTAGGTAATTTTTCTAGATCTAGGGCATCACCCTATGCCTATATAAAGGCAC
2076 CAAACCCCTCTTGTAAACATAAGTTGAGTTGATTAATAAAATTGAGGTTTTTACCCAAATTGATT
456 CAAACCCCTCTTGTAAACATAAGTTGAGTTGATTAATAAAATTGAGGTTTTTACCCAAATTGATT
2141 ATCTTAGCTTCTTTGTTCTAGTTTGAGCAAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCA
521 ATCTTAGCTTCTTTGTTCTAGTTTGAGCAAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCA
2206 AACAATTAAGTTATGATACTTGATTGCTTGTGAATCTTGTGATCTTAGGTGTTCAATTGCAGGTC
586 AACAATTAAGTTATGATACTTGATTGCTTGTGAATCTTGTGATCTTAGGTGTTCAATTGCAGGTC
2271 TAATTGGAGGTCTAAGGCCGACGAAAGAAGAAGATTGCTTGGGTGAGATTGTCGACATACACATC
651 TAATTGGAGGTCTAAGGCCGACGAAAGAAGAAGATTGCTTGGGTGAGATTGTCGACATACACATC
**
2336 TAGAAGTTGAAAGTTGTTCAAGTTGATTCTTGGCGTTTCACAAGGGTGGATTTTGAATCTTAAAA
716 TAGAAGTTGAAAGTTGTTCAAGTTGATTCTTGGCGGGTCACAAGGGTGGATTTTGAATCTTAAAA
2401 CAA
781 CAA
2404 CTA
1 CTA
2407 TATTCGTATC
Statistics
Matches: 776, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
783 776 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (783 bp):
CTAAGATGACATTTGATCCATTGAAAATGCCATTAGGCCCAATGACAAGGGCAAGAGCTAAAAGG
TTCAAGGAAGCTTTGTTTGGCCTCATTAGAGTTCATCTTGAAGAGTTTAAAGCCATCGGAGATCA
TTTGAAGCCCATTGGAGATCATCAACAAAGGAATATTCCCATCGATTCCAAGTTGTGCATTCTTC
TTGAAATCGATGAGCACTAGGTCATTAGAGTTGTAATTTGGCCATTGTGGGCTTTATTCTATCTT
TAATTAGCTTATTTTTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCT
TGTTTAATTATGTCTTTATTTCCTTTTCCTAGTTGGGTTTGGACTAGTTTTACCCTAGTCCATAT
ATTTGGACGAAAATTAGGTAATTTTTCTAGATCTAGGGCATCACCCTATGCCTATATAAAGGCAC
CAAACCCCTCTTGTAAACATAAGTTGAGTTGATTAATAAAATTGAGGTTTTTACCCAAATTGATT
ATCTTAGCTTCTTTGTTCTAGTTTGAGCAAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCA
AACAATTAAGTTATGATACTTGATTGCTTGTGAATCTTGTGATCTTAGGTGTTCAATTGCAGGTC
TAATTGGAGGTCTAAGGCCGACGAAAGAAGAAGATTGCTTGGGTGAGATTGTCGACATACACATC
TAGAAGTTGAAAGTTGTTCAAGTTGATTCTTGGCGGGTCACAAGGGTGGATTTTGAATCTTAAAA
CAA
Found at i:3882 original size:22 final size:22
Alignment explanation
Indices: 3854--4018 Score: 86
Period size: 22 Copynumber: 8.0 Consensus size: 22
3844 TCTTTCCCTA
*
3854 AATTGAAAACTTTGAAGACTTG
1 AATTGAAAACTTTGAAAACTTG
*
3876 AATTGAATACTTTGAAAACTTG
1 AATTGAAAACTTTGAAAACTTG
** * *
3898 -A-TGGGAACTTT----CCTTA
1 AATTGAAAACTTTGAAAACTTG
*
3914 AATTGAACACTTTGAAAAACTTG
1 AATTGAAAACTTTG-AAAACTTG
* *
3937 AATTGAATACTTTGAAGACTTG
1 AATTGAAAACTTTGAAAACTTG
** * *
3959 -A-TGGGAACTTT----CCCT-
1 AATTGAAAACTTTGAAAACTTG
3974 AACTTGAAAACTTTGAAAAACTTG
1 AA-TTGAAAACTTTG-AAAACTTG
*
3998 AATTGAATACTTTGAAAACTT
1 AATTGAAAACTTTGAAAACTT
4019 TGAAGGAAAT
Statistics
Matches: 103, Mismatches: 24, Indels: 32
0.65 0.15 0.20
Matches are distributed among these distances:
16 6 0.06
17 1 0.01
18 15 0.15
20 14 0.14
21 2 0.02
22 34 0.33
23 29 0.28
24 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (22 bp):
AATTGAAAACTTTGAAAACTTG
Found at i:3962 original size:61 final size:61
Alignment explanation
Indices: 3831--4018 Score: 306
Period size: 61 Copynumber: 3.1 Consensus size: 61
3821 CTTTGAAAAG
* * *
3831 AAACTGGATGGGATCTTTCCCTAAATTGAAAACTTTG-AAGACTTGAATTGAATACTTTGA
1 AAACTTGATGGGAACTTTCCCTAAATTGAAAACTTTGAAAAACTTGAATTGAATACTTTGA
* *
3891 AAACTTGATGGGAACTTTCCTTAAATTGAACACTTTGAAAAACTTGAATTGAATACTTTGA
1 AAACTTGATGGGAACTTTCCCTAAATTGAAAACTTTGAAAAACTTGAATTGAATACTTTGA
* *
3952 AGACTTGATGGGAACTTTCCCTAACTTGAAAACTTTGAAAAACTTGAATTGAATACTTTGA
1 AAACTTGATGGGAACTTTCCCTAAATTGAAAACTTTGAAAAACTTGAATTGAATACTTTGA
4013 AAACTT
1 AAACTT
4019 TGAAGGAAAT
Statistics
Matches: 117, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
60 33 0.28
61 84 0.72
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.34
Consensus pattern (61 bp):
AAACTTGATGGGAACTTTCCCTAAATTGAAAACTTTGAAAAACTTGAATTGAATACTTTGA
Found at i:4049 original size:10 final size:10
Alignment explanation
Indices: 4034--4067 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
4024 GAAATTCTTT
4034 TTTTTTTTGA
1 TTTTTTTTGA
*
4044 TTTTTTTTAA
1 TTTTTTTTGA
*
4054 TTTTTTTGGA
1 TTTTTTTTGA
4064 TTTT
1 TTTT
4068 GAAAACTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:4970 original size:57 final size:56
Alignment explanation
Indices: 4879--4993 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 56
4869 TATGTGTTTC
4879 CTTTCACACAATAAATGTTATAATAAATCATATCCCTCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCC-CCTATCTCTACTTAATTATT
* * *
4936 CTTTCACACAATAAATTTTATATTAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
4992 CT
1 CT
4994 AAAAAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 22 0.40
57 33 0.60
ACGTcount: A:0.33, C:0.24, G:0.01, T:0.42
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
Found at i:5006 original size:57 final size:57
Alignment explanation
Indices: 4888--5012 Score: 153
Period size: 57 Copynumber: 2.2 Consensus size: 57
4878 CCTTTCACAC
* *** * *
4888 AATAAATGTTATAATAAATCATATCCCTCCTATCTCTACTTAATTATTCTTTCACAC
1 AATAAATTTTATAATAAATCATATCCCTCCTATCTCTACTTAATTATTCTAAAAAAA
* *
4945 AATAAATTTTATATTAAATCCTATCCC-CCTATCTCTACTTAATTATTCTAAAAAATA
1 AATAAATTTTATAATAAATCATATCCCTCCTATCTCTACTTAATTATTCTAAAAAA-A
5002 AATAATATTTT
1 AATAA-ATTTT
5013 CTTTTAAGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
56 24 0.41
57 29 0.50
58 5 0.09
ACGTcount: A:0.38, C:0.19, G:0.01, T:0.42
Consensus pattern (57 bp):
AATAAATTTTATAATAAATCATATCCCTCCTATCTCTACTTAATTATTCTAAAAAAA
Done.