Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024059.1 Corchorus olitorius cultivar O-4 contig24092, 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: 9114
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Found at i:1177 original size:30 final size:30
Alignment explanation
Indices: 1141--1197 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1131 GTTTGGATAA
* *
1141 TCCCAAAAGAAGGTTTTTGAAAATAAAGGT
1 TCCCAAAAGAAGATTTTGGAAAATAAAGGT
* *
1171 TCCCAAAAGGAGATTTTGGAAATTAAA
1 TCCCAAAAGAAGATTTTGGAAAATAAA
1198 TGGGTAAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (30 bp):
TCCCAAAAGAAGATTTTGGAAAATAAAGGT
Found at i:4080 original size:21 final size:22
Alignment explanation
Indices: 4056--4097 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
4046 TTTGCCTCAT
*
4056 GCATTCATTCAT-CATGCCATG
1 GCATTCATTCATGCATCCCATG
4077 GCATTCATTCATGCATCCCAT
1 GCATTCATTCATGCATCCCAT
4098 TAAAGCCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.33
Consensus pattern (22 bp):
GCATTCATTCATGCATCCCATG
Found at i:6643 original size:26 final size:24
Alignment explanation
Indices: 6597--6661 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 24
6587 AAAAAGAAAA
6597 AAATCAAAAATC-AAAAATCAAATC
1 AAATC-AAAATCAAAAAATCAAATC
*
6621 AAAGTCAATAATTAAAAAATCAAATC
1 AAA-TCAA-AATCAAAAAATCAAATC
6647 AAATCAAAATCAAAA
1 AAATCAAAATCAAAA
6662 GAGAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
24 12 0.33
25 9 0.25
26 15 0.42
ACGTcount: A:0.66, C:0.14, G:0.02, T:0.18
Consensus pattern (24 bp):
AAATCAAAATCAAAAAATCAAATC
Found at i:7333 original size:50 final size:50
Alignment explanation
Indices: 7258--7407 Score: 255
Period size: 50 Copynumber: 3.0 Consensus size: 50
7248 AGTTTTACAA
*
7258 TAAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
* *
7308 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCTAAATTTGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
* *
7358 TAAAATTGCATTCCATTTGTGAGTTCAAAATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
7408 GACATTGAAG
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 93 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (50 bp):
TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
Found at i:7947 original size:79 final size:79
Alignment explanation
Indices: 7854--8003 Score: 282
Period size: 79 Copynumber: 1.9 Consensus size: 79
7844 CAAGTTATCA
7854 AAGTTGACTGCACATTGGTCCTCTTTCATCATTAATCAAGAAATTTTCAGTTACAACATCAGACT
1 AAGTTGACTGCACATTGGTCCTCTTTCATCATTAATCAAGAAATTTTCAGTTACAACATCAGACT
7919 CAGAGTTATTTTTC
66 CAGAGTTATTTTTC
* *
7933 AAGTTGACTGCACATTGGTCCTCTTTCATCATTAATCAAGAAATTTTCAGTTGCAACATCAGATT
1 AAGTTGACTGCACATTGGTCCTCTTTCATCATTAATCAAGAAATTTTCAGTTACAACATCAGACT
7998 CAGAGT
66 CAGAGT
8004 CATTGTCCAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (79 bp):
AAGTTGACTGCACATTGGTCCTCTTTCATCATTAATCAAGAAATTTTCAGTTACAACATCAGACT
CAGAGTTATTTTTC
Found at i:8260 original size:50 final size:50
Alignment explanation
Indices: 8076--8244 Score: 311
Period size: 50 Copynumber: 3.4 Consensus size: 50
8066 TCCGAATGCT
*
8076 CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAAA
1 CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
8126 CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
1 CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
8176 CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
1 CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
**
8226 TGGGCTTTTCCACAAGCCA
1 CAGGCTTTTCCACAAGCCA
8245 CATCCGGTTC
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 116 1.00
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.26
Consensus pattern (50 bp):
CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
Found at i:8398 original size:50 final size:50
Alignment explanation
Indices: 8272--8528 Score: 451
Period size: 50 Copynumber: 5.1 Consensus size: 50
8262 TGCATTACCT
8272 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
8322 TTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
1 -TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
8373 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
*
8423 CTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
* * * **
8473 TTTTAAGATTGAATTGGTAGACAATTCAAATGATAAGCGGAAGATAGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
8523 TTTTAA
1 TTTTAA
8529 TATGTTAGAT
Statistics
Matches: 199, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
50 149 0.75
51 50 0.25
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.28
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
Found at i:8868 original size:27 final size:28
Alignment explanation
Indices: 8795--8874 Score: 101
Period size: 29 Copynumber: 2.9 Consensus size: 28
8785 TTAGGATTAC
8795 CTAGGGGCATTTTGGTCATTTTCAAAAAT
1 CTAGGGGCATTTTGGTCATTTT-AAAAAT
* * *
8824 CTAGGGGCATTTTAGTCATTTGT-ATATT
1 CTAGGGGCATTTTGGTCATTT-TAAAAAT
8852 C-AGGGGCATTTTGGTCATTTTAA
1 CTAGGGGCATTTTGGTCATTTTAA
8875 GTCCATGCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 1 0.02
27 19 0.42
28 4 0.09
29 20 0.44
30 1 0.02
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.41
Consensus pattern (28 bp):
CTAGGGGCATTTTGGTCATTTTAAAAAT
Done.