Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009888.1 Corchorus olitorius cultivar O-4 contig09920, 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: 16808
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:970 original size:34 final size:36
Alignment explanation
Indices: 930--1011 Score: 114
Period size: 34 Copynumber: 2.3 Consensus size: 36
920 TCTTAATTAA
* *
930 ATATATAATATGATGTGTGTATGTAT-ATAT-ATAT
1 ATATATAATATGATGTATATATGTATAATATGATAT
*
964 ATATATAATATGATGTATATATGTATAATATGATGT
1 ATATATAATATGATGTATATATGTATAATATGATAT
1000 ATATATATATAT
1 ATATATA-ATAT
1012 ACATATGTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
34 24 0.57
35 4 0.10
36 10 0.24
37 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (36 bp):
ATATATAATATGATGTATATATGTATAATATGATAT
Found at i:984 original size:20 final size:20
Alignment explanation
Indices: 959--1028 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
949 TATGTATATA
959 TATATATATATAATATGATG
1 TATATATATATAATATGATG
*
979 TATATATGTATAATATGATG
1 TATATATATATAATATGATG
*
999 TATATATATATATACAT-ATG
1 TATATATATATA-ATATGATG
1019 TATATATATA
1 TATATATATA
1029 CATGGGTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 43 0.93
21 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.46
Consensus pattern (20 bp):
TATATATATATAATATGATG
Found at i:1040 original size:16 final size:16
Alignment explanation
Indices: 1003--1044 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
993 ATGATGTATA
*
1003 TATATATATACATATG
1 TATATATATACATAGG
*
1019 TATATATATACATGGG
1 TATATATATACATAGG
*
1035 TTTATATATA
1 TATATATATA
1045 ATACACCGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (16 bp):
TATATATATACATAGG
Found at i:1044 original size:2 final size:2
Alignment explanation
Indices: 953--1028 Score: 75
Period size: 2 Copynumber: 38.0 Consensus size: 2
943 TGTGTGTATG
* *
953 TA TA TA TA TA TA TA TA TA -A TA TGA TG TA TA TA TG TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
* * *
994 TGA TG TA TA TA TA TA TA TA CA TA TG TA TA TA TA TA
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1029 CATGGGTTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
1 2 0.03
2 54 0.90
3 4 0.07
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1316 original size:20 final size:20
Alignment explanation
Indices: 1291--1329 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1281 CGAACCAAAT
1291 TCGTATTTTCTTTAAATCAG
1 TCGTATTTTCTTTAAATCAG
1311 TCGTATTTTCTTTAAATCA
1 TCGTATTTTCTTTAAATCA
1330 AACTCGTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (20 bp):
TCGTATTTTCTTTAAATCAG
Found at i:5718 original size:11 final size:10
Alignment explanation
Indices: 5700--5728 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
5690 GAAGTATTTG
5700 TCTTTTTTTT
1 TCTTTTTTTT
5710 TCTTTTTTTT
1 TCTTTTTTTT
5720 TCTTTTTTT
1 TCTTTTTTT
5729 CTTATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:7644 original size:13 final size:13
Alignment explanation
Indices: 7626--7650 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7616 AGAGTATTTC
7626 TTACTAATTGTTG
1 TTACTAATTGTTG
7639 TTACTAATTGTT
1 TTACTAATTGTT
7651 ACTCCCTCCG
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:0.24, C:0.08, G:0.12, T:0.56
Consensus pattern (13 bp):
TTACTAATTGTTG
Found at i:8759 original size:199 final size:197
Alignment explanation
Indices: 8435--8819 Score: 517
Period size: 199 Copynumber: 1.9 Consensus size: 197
8425 TTTTGTGGGT
* * * *
8435 AATTATTTGATACACCGGTGGTTTAAATTTTGGACTCCATAAACGGGTTGTGGAGTTGACATATG
1 AATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAACGGGTTGTGGAGTTGACATATC
8500 TTCATTTTCTGAATTAATTAAATTTAAATATTTCAACCGAGTCCCTAGGGGACACATGTCACCCT
66 TTCATTTTCTGAATTAATTAAATTTAAATATTTCAACCGAGTCCCTAGGGGACACATGTCACCCT
* *
8565 TCAAGACCTGCTTGTGCAG-CTTATTAAACTCCACTGACGGTGTATTATATATAAACTCTTTTAG
131 TCAAGACCTGCTTGTGCAGTC-CACTAAACTCCACTGACGGTGTATTATATATAAACTCTTTTAG
8629 GGC
195 GGC
** *
8632 AATTATTTGATACATTGGCGGTGTAAATTTTGGATTCCACAAACGGGTT-TGGAGTTGACACATA
1 AATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAACGGGTTGTGGAGTTG--ACATA
* * * * * * *
8696 TCTAT-TTTTTTTTAATT-ATTGAAATTTTAAATATTTCAATCTAGTCTCTAGGGGATACATGTC
64 TCT-TCATTTTCTGAATTAATT-AAA-TTTAAATATTTCAACCGAGTCCCTAGGGGACACATGTC
* * *
8759 ACCCTTCAAGACTTGCTTGTGCAGTCCGCTAAACTTCACTGACGGTGTATTATATATAAAC
126 ACCCTTCAAGACCTGCTTGTGCAGTCCACTAAACTCCACTGACGGTGTATTATATATAAAC
8820 ACTTATAATA
Statistics
Matches: 163, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
196 8 0.05
197 46 0.28
198 19 0.12
199 89 0.55
200 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37
Consensus pattern (197 bp):
AATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAACGGGTTGTGGAGTTGACATATC
TTCATTTTCTGAATTAATTAAATTTAAATATTTCAACCGAGTCCCTAGGGGACACATGTCACCCT
TCAAGACCTGCTTGTGCAGTCCACTAAACTCCACTGACGGTGTATTATATATAAACTCTTTTAGG
GC
Found at i:10416 original size:19 final size:19
Alignment explanation
Indices: 10392--10428 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
10382 CCAAAACTTG
*
10392 AAAACATCAAACTAAACCC
1 AAAACAGCAAACTAAACCC
10411 AAAACAGCAAACTAAACC
1 AAAACAGCAAACTAAACC
10429 AGTAAACAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.30, G:0.03, T:0.08
Consensus pattern (19 bp):
AAAACAGCAAACTAAACCC
Found at i:13002 original size:49 final size:50
Alignment explanation
Indices: 12935--13069 Score: 177
Period size: 49 Copynumber: 2.8 Consensus size: 50
12925 CACTCAAAGC
*
12935 AATCATTTACTTTTCCTTGCACCTATTTCTCAATTTTTACAACAAAATTG
1 AATCATTTACTTTTCCTTGCACCTATTTATCAATTTTTACAACAAAATTG
* * **
12985 AATC-TTTAATTTTCCTTGCACCTTTTTATCAATTTTTATGACAAAATTG
1 AATCATTTACTTTTCCTTGCACCTATTTATCAATTTTTACAACAAAATTG
* * *
13034 AA-CATTTACTTTTCATTGCA-TTTTTTATCAATTTTT
1 AATCATTTACTTTTCCTTGCACCTATTTATCAATTTTT
13070 GTACAAAATT
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
48 16 0.21
49 56 0.74
50 4 0.05
ACGTcount: A:0.28, C:0.18, G:0.04, T:0.50
Consensus pattern (50 bp):
AATCATTTACTTTTCCTTGCACCTATTTATCAATTTTTACAACAAAATTG
Found at i:15970 original size:2 final size:2
Alignment explanation
Indices: 15963--15990 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15953 GCATTCACAT
15963 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15991 CACACACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.