Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011460.1 Corchorus capsularis cultivar CVL-1 contig11481, 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: 19994
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:8125 original size:209 final size:209
Alignment explanation
Indices: 7765--8184 Score: 840
Period size: 209 Copynumber: 2.0 Consensus size: 209
7755 CTTCCAACTA
7765 TTGACTCTCTGAGTAATTCTCTCCTTGATAAACTGAAACTCCTAGGCCTTAGACTTGCCAATCAT
1 TTGACTCTCTGAGTAATTCTCTCCTTGATAAACTGAAACTCCTAGGCCTTAGACTTGCCAATCAT
7830 GATAGGCAAACCTAAGTACTTATCACGTTCCATGATTCTCTGAATTCCAAGCCTTTCTTTGATTG
66 GATAGGCAAACCTAAGTACTTATCACGTTCCATGATTCTCTGAATTCCAAGCCTTTCTTTGATTG
7895 CTTCCTTGACATTATCCATCGTGTTTACACTGAACAAAATTGAATATTTGTCAATATTTACCTGC
131 CTTCCTTGACATTATCCATCGTGTTTACACTGAACAAAATTGAATATTTGTCAATATTTACCTGC
7960 TGGCCTGTTGCATT
196 TGGCCTGTTGCATT
7974 TTGACTCTCTGAGTAATTCTCTCCTTGATAAACTGAAACTCCTAGGCCTTAGACTTGCCAATCAT
1 TTGACTCTCTGAGTAATTCTCTCCTTGATAAACTGAAACTCCTAGGCCTTAGACTTGCCAATCAT
8039 GATAGGCAAACCTAAGTACTTATCACGTTCCATGATTCTCTGAATTCCAAGCCTTTCTTTGATTG
66 GATAGGCAAACCTAAGTACTTATCACGTTCCATGATTCTCTGAATTCCAAGCCTTTCTTTGATTG
8104 CTTCCTTGACATTATCCATCGTGTTTACACTGAACAAAATTGAATATTTGTCAATATTTACCTGC
131 CTTCCTTGACATTATCCATCGTGTTTACACTGAACAAAATTGAATATTTGTCAATATTTACCTGC
8169 TGGCCTGTTGCATT
196 TGGCCTGTTGCATT
8183 TT
1 TT
8185 CAAATTGATG
Statistics
Matches: 211, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
209 211 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (209 bp):
TTGACTCTCTGAGTAATTCTCTCCTTGATAAACTGAAACTCCTAGGCCTTAGACTTGCCAATCAT
GATAGGCAAACCTAAGTACTTATCACGTTCCATGATTCTCTGAATTCCAAGCCTTTCTTTGATTG
CTTCCTTGACATTATCCATCGTGTTTACACTGAACAAAATTGAATATTTGTCAATATTTACCTGC
TGGCCTGTTGCATT
Found at i:13036 original size:18 final size:18
Alignment explanation
Indices: 13005--13039 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12995 TGAAGATTTC
* *
13005 TTGAAGATATTTGAAGAT
1 TTGAAGACAATTGAAGAT
13023 TTGAAGACAATTGAAGA
1 TTGAAGACAATTGAAGA
13040 ATTATTTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.31
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:17668 original size:13 final size:11
Alignment explanation
Indices: 17650--17687 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
17640 TTTTTAGTTT
17650 TTTTCTTTTTCC
1 TTTTCTTTTT-C
17662 GTTTTCTTTTTC
1 -TTTTCTTTTTC
17674 TTTTCTTTTT-
1 TTTTCTTTTTC
17684 TTTT
1 TTTT
17688 TTAATTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 10 0.40
12 1 0.04
13 10 0.40
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.82
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:19258 original size:28 final size:28
Alignment explanation
Indices: 19199--19274 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 28
19189 TAAGGTCATC
19199 CAGGGGCATTTTGGTCA-TTTTTACATT
1 CAGGGGCATTTTGGTCATTTTTTACATT
* *
19226 CAGGGGCATTTAGGTCATTTTTTGCATT
1 CAGGGGCATTTTGGTCATTTTTTACATT
* *
19254 TAGGGGCATTTTGGTTATTTT
1 CAGGGGCATTTTGGTCATTTT
19275 AAGCTCACTT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 16 0.37
28 27 0.63
ACGTcount: A:0.17, C:0.12, G:0.25, T:0.46
Consensus pattern (28 bp):
CAGGGGCATTTTGGTCATTTTTTACATT
Done.