Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012277.1 Corchorus olitorius cultivar O-4 contig12310, 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: 22128
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7674 original size:134 final size:134
Alignment explanation
Indices: 7498--8155 Score: 990
Period size: 131 Copynumber: 4.9 Consensus size: 134
7488 AACATCGAAA
*
7498 AATCTTTT-ATTTGTTTGGGAAAAAAAAAGAAAAATCTTTTCATTTAATACAATATCTCTAAAAT
1 AATCTTTTCATTT-TTTGGG-AAAAAAAAGAAAAATCTTTTCATTTAATACAATATCTTTAAAAT
* ** *
7562 TTGCTATCATCAGTACAACTTTTGTTAGGATTGAATCTAAGTGTGCGTTTAATTAGCATCACCCC
64 TTGCTATCATCAGTACAACTTTTGTTAGGATTGAATCTAAGGGTGCGTTTGGTTAGGATCACCCC
*
7627 CATATC
129 CAAATC
* *
7633 AATCTTTTCATTTTTTGGGAAAAAAAAGAAAACTCTTTTCATTTAATACAGTATCTTTAAAATTT
1 AATCTTTTCATTTTTTGGGAAAAAAAAGAAAAATCTTTTCATTTAATACAATATCTTTAAAATTT
* * * * **
7698 GCTATCAGCAGTATAACTTTTGTTAGGATTGAATCTAAGGGTGTGTTTGGTTAGAATCACCATCA
66 GCTATCATCAGTACAACTTTTGTTAGGATTGAATCTAAGGGTGCGTTTGGTTAGGATCACCCCCA
7763 AATC
131 AATC
*
7767 AATCTTTTCATTTTTT-GG-CAAAAAA-AAAAATCTTTTCATTTAATACAATATCTTTAAAATTT
1 AATCTTTTCATTTTTTGGGAAAAAAAAGAAAAATCTTTTCATTTAATACAATATCTTTAAAATTT
*
7829 GCTATCATCAGTACAACTTTTGTTATGATTGAATCTAAGGGTGCGTTTGGTTAGGATCA-CCCCA
66 GCTATCATCAGTACAACTTTTGTTAGGATTGAATCTAAGGGTGCGTTTGGTTAGGATCACCCCCA
*
7893 GATC
131 AATC
*
7897 AATCTTTTCA-TTTTTGGGAAAAAAATGAAAAATCTTTTCATTTAAATACAATATCTTTAAAATT
1 AATCTTTTCATTTTTTGGGAAAAAAAAGAAAAATCTTTTCATTT-AATACAATATCTTTAAAATT
* *
7961 TGCTATCAT--GTAGAACTTTTGTTAGGATTGAATCTAAGGGTGTGTTTGGTTAGGATCAACCCC
65 TGCTATCATCAGTACAACTTTTGTTAGGATTGAATCTAAGGGTGCGTTTGGTTAGGATC-ACCCC
8024 CAAATC
129 CAAATC
* * *
8030 AATCTTTTCACTTTTTGGGGAAAAAAAAAGAAAAATCTTTTCATTTAATATAGTATCTTTAAAAT
1 AATCTTTTCA-TTTTTTGGG-AAAAAAAAGAAAAATCTTTTCATTTAATACAATATCTTTAAAAT
*
8095 TTGCTATCATCAGTACAACTTTTGTTAGGATTGAATCTAAGGGTGCGTTTGGTTAGAATCA
64 TTGCTATCATCAGTACAACTTTTGTTAGGATTGAATCTAAGGGTGCGTTTGGTTAGGATCA
8156 TCACTCTTAA
Statistics
Matches: 474, Mismatches: 37, Indels: 23
0.89 0.07 0.04
Matches are distributed among these distances:
129 5 0.01
130 18 0.04
131 139 0.29
132 23 0.05
133 49 0.10
134 118 0.25
135 48 0.10
136 29 0.06
137 45 0.09
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (134 bp):
AATCTTTTCATTTTTTGGGAAAAAAAAGAAAAATCTTTTCATTTAATACAATATCTTTAAAATTT
GCTATCATCAGTACAACTTTTGTTAGGATTGAATCTAAGGGTGCGTTTGGTTAGGATCACCCCCA
AATC
Found at i:8057 original size:265 final size:266
Alignment explanation
Indices: 7498--8155 Score: 1013
Period size: 268 Copynumber: 2.5 Consensus size: 266
7488 AACATCGAAA
*
7498 AATCTTTT-ATTTGTTTGGGAAAAAAAAAGAAAAATCTTTTCATTTAATACAATATCTCTAAAAT
1 AATCTTTTCA-TT-TTTGGG-AAAAAAAAGAAAAATCTTTTCATTTAATACAATATCTTTAAAAT
* ** *
7562 TTGCTATCATCAGTACAACTTTTGTTAGGATTGAATCTAAGTGTGCGTTTAATTAGCATCACCCC
63 TTGCTATCATCAGTACAACTTTTGTTAGGATTGAATCTAAGGGTGCGTTTGGTTAGAATCACCCC
* * *
7627 CATATCAATCTTTTCATTTTTTGGGAAAAAAAAGAAAACTCTTTTCATTTAATACAGTATCTTTA
128 CAGATCAATCTTTTCATTTTTTGGGAAAAAAAAGAAAAATCTTTTCATTTAATACAATATCTTTA
*
7692 AAATTTGCTATCAGCAGTATAACTTTTGTTAGGATTGAATCTAAGGGTGTGTTTGGTTAGAATCA
193 AAATTTGCTATCA-CAGTAGAACTTTTGTTAGGATTGAATCTAAGGGTGTGTTTGGTTAGAATCA
*
7757 CCATCAAATC
257 CCACCAAATC
* *
7767 AATCTTTTCATTTTTTGG-CAAAAAA-AAAAATCTTTTCATTTAATACAATATCTTTAAAATTTG
1 AATCTTTTCATTTTTGGGAAAAAAAAGAAAAATCTTTTCATTTAATACAATATCTTTAAAATTTG
* *
7830 CTATCATCAGTACAACTTTTGTTATGATTGAATCTAAGGGTGCGTTTGGTTAGGATCA-CCCCAG
66 CTATCATCAGTACAACTTTTGTTAGGATTGAATCTAAGGGTGCGTTTGGTTAGAATCACCCCCAG
*
7894 ATCAATCTTTTCA-TTTTTGGGAAAAAAATGAAAAATCTTTTCATTTAAATACAATATCTTTAAA
131 ATCAATCTTTTCATTTTTTGGGAAAAAAAAGAAAAATCTTTTCATTT-AATACAATATCTTTAAA
* *
7958 ATTTGCTATCA-TGTAGAACTTTTGTTAGGATTGAATCTAAGGGTGTGTTTGGTTAGGATCAACC
195 ATTTGCTATCACAGTAGAACTTTTGTTAGGATTGAATCTAAGGGTGTGTTTGGTTAGAATC-ACC
*
8022 CCCAAATC
259 ACCAAATC
* *
8030 AATCTTTTCACTTTTTGGGGAAAAAAAAAGAAAAATCTTTTCATTTAATATAGTATCTTTAAAAT
1 AATCTTTTCA-TTTTT-GGG-AAAAAAAAGAAAAATCTTTTCATTTAATACAATATCTTTAAAAT
8095 TTGCTATCATCAGTACAACTTTTGTTAGGATTGAATCTAAGGGTGCGTTTGGTTAGAATCA
63 TTGCTATCATCAGTACAACTTTTGTTAGGATTGAATCTAAGGGTGCGTTTGGTTAGAATCA
8156 TCACTCTTAA
Statistics
Matches: 358, Mismatches: 23, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
262 46 0.13
263 50 0.14
264 50 0.14
265 92 0.26
266 6 0.02
267 6 0.02
268 97 0.27
269 10 0.03
270 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (266 bp):
AATCTTTTCATTTTTGGGAAAAAAAAGAAAAATCTTTTCATTTAATACAATATCTTTAAAATTTG
CTATCATCAGTACAACTTTTGTTAGGATTGAATCTAAGGGTGCGTTTGGTTAGAATCACCCCCAG
ATCAATCTTTTCATTTTTTGGGAAAAAAAAGAAAAATCTTTTCATTTAATACAATATCTTTAAAA
TTTGCTATCACAGTAGAACTTTTGTTAGGATTGAATCTAAGGGTGTGTTTGGTTAGAATCACCAC
CAAATC
Found at i:8988 original size:14 final size:15
Alignment explanation
Indices: 8971--9004 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
8961 AAATCTAAAA
*
8971 AGAAAAAA-AAACGC
1 AGAAAAAAGAAACCC
8985 AGAAAAAAGAAACCC
1 AGAAAAAAGAAACCC
9000 AGAAA
1 AGAAA
9005 CAGCGGGTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.71, C:0.15, G:0.15, T:0.00
Consensus pattern (15 bp):
AGAAAAAAGAAACCC
Found at i:18414 original size:5 final size:5
Alignment explanation
Indices: 18406--18440 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
18396 CAAGGAAAAC
*
18406 GAAAG GAAAG AGAAAG GAAAG GAAAA GAAAG GAAA
1 GAAAG GAAAG -GAAAG GAAAG GAAAG GAAAG GAAA
18441 TTGAGAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (5 bp):
GAAAG
Done.