Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013646.1 Corchorus olitorius cultivar O-4 contig13679, 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: 22151
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Found at i:3907 original size:73 final size:75
Alignment explanation
Indices: 3809--3953 Score: 240
Period size: 76 Copynumber: 1.9 Consensus size: 75
3799 AGAGAGGTTT
*
3809 AACCAAGCAAGAGCAACATGAGATGGCAATG-TT-GCCAACAAAAAATAATATCAACATGTGCCT
1 AACCAAGCAAGAGCAACATGAGATGGCAATGTTTAGCCAACAAAAAATAATATCAACATCTGCCT
3872 AAGGTTTTTC
66 AAGGTTTTTC
* *
3882 AACCAAGCAAGAGCAATATGCGATGGCAATGTTTAAGCCAACAAAAAATAATATCAACATCTGCC
1 AACCAAGCAAGAGCAACATGAGATGGCAATGTTT-AGCCAACAAAAAATAATATCAACATCTGCC
3947 TAAGGTT
65 TAAGGTT
3954 CAATTAAGCA
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
73 29 0.44
74 2 0.03
76 35 0.53
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.21
Consensus pattern (75 bp):
AACCAAGCAAGAGCAACATGAGATGGCAATGTTTAGCCAACAAAAAATAATATCAACATCTGCCT
AAGGTTTTTC
Found at i:3956 original size:73 final size:72
Alignment explanation
Indices: 3803--4009 Score: 251
Period size: 73 Copynumber: 2.8 Consensus size: 72
3793 CAACTGAGAG
* *
3803 AGGTTTAACCAAGCAAGAGCAACATGAGATGGCAATG-TT--GCCAACAAAAAATAATATCAACA
1 AGGTTCAACCAAGCAAGAGCAATATG-GATGGCAATGTTTAAGCCAACAAAAAATAATATCAACA
*
3865 TGTGCCTA
65 TCTGCCTA
3873 AGGTTTTTCAACCAAGCAAGAGCAATATGCGATGGCAATGTTTAAGCCAACAAAAAATAATATCA
1 AGG---TTCAACCAAGCAAGAGCAATATG-GATGGCAATGTTTAAGCCAACAAAAAATAATATCA
3938 ACATCTGCCTA
62 ACATCTGCCTA
** * * *
3949 AGGTTCAATTAAGCAAG-GCCTATATAGGATGGAAATGTTTAAGCCAACAATAAATAATATC
1 AGGTTCAACCAAGCAAGAG-CAATAT-GGATGGCAATGTTTAAGCCAACAAAAAATAATATC
4010 GGCATGTGCC
Statistics
Matches: 120, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
70 3 0.03
72 1 0.01
73 80 0.67
74 3 0.03
76 33 0.28
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (72 bp):
AGGTTCAACCAAGCAAGAGCAATATGGATGGCAATGTTTAAGCCAACAAAAAATAATATCAACAT
CTGCCTA
Found at i:4203 original size:17 final size:17
Alignment explanation
Indices: 4158--4205 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
4148 CATATCACAT
*
4158 GACTAGTAATGGTTTAG
1 GACTAGTAATGTTTTAG
* *
4175 GACTAGTCATGTTTTAT
1 GACTAGTAATGTTTTAG
*
4192 TACTAGTAATGTTT
1 GACTAGTAATGTTT
4206 CTCAAATCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (17 bp):
GACTAGTAATGTTTTAG
Found at i:7525 original size:3 final size:3
Alignment explanation
Indices: 7517--7610 Score: 152
Period size: 3 Copynumber: 31.0 Consensus size: 3
7507 TATTTAGCCG
* * *
7517 TTA TTA TTA TTA TTA TTTA TTA TTA TTG TTG TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
7563 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
7611 AAACAAACGT
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
3 85 0.97
4 3 0.03
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:8108 original size:21 final size:21
Alignment explanation
Indices: 8063--8116 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
8053 ATATGCATGG
*
8063 TCAAACCCCAAATGATGATAG
1 TCAAACCCCAAATGATGATAA
*
8084 TCAAACCCCAAA-GTTTGATAA
1 TCAAACCCCAAATG-ATGATAA
*
8105 TCAAACCACAAA
1 TCAAACCCCAAA
8117 AATCATTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.46, C:0.26, G:0.09, T:0.19
Consensus pattern (21 bp):
TCAAACCCCAAATGATGATAA
Found at i:8157 original size:78 final size:78
Alignment explanation
Indices: 8052--8368 Score: 476
Period size: 78 Copynumber: 4.1 Consensus size: 78
8042 TGAATTGACT
* *
8052 TATATGCATGGTCAAACCCCAAATGATGATAGTCAAACCCCAAAGTTTGATAATCAAACCACAAA
1 TATATGCATGGTCAAACCCCAAATGATGATAGTCAAACCCCAAAATTTGATAGTCAAACCACAAA
8117 AATCATTTCATTG
66 AATCATTTCATTG
* * * *
8130 TATATGCATGATCAAACCCCAAATGATGATAGTCAAAGCTCAAAGTTTGATAGTCAAACCACAAA
1 TATATGCATGGTCAAACCCCAAATGATGATAGTCAAACCCCAAAATTTGATAGTCAAACCACAAA
8195 AATCATTTCATTG
66 AATCATTTCATTG
* *
8208 TATATGCATGGTCAAACCCCAAATGATGATAGTCAAACCCCAAAATTTGATAGTCAAATCATAAA
1 TATATGCATGGTCAAACCCCAAATGATGATAGTCAAACCCCAAAATTTGATAGTCAAACCACAAA
8273 AATCATTTCATTG
66 AATCATTTCATTG
* * * * * *
8286 TACATGCATTGTCAAATCCCAAA-GAATCAT-CTGAAACCCCAAAATTTGATAGTCAAACCACAA
1 TATATGCATGGTCAAACCCCAAATG-ATGATAGTCAAACCCCAAAATTTGATAGTCAAACCACAA
*
8349 AAATCATTTTATTG
65 AAATCATTTCATTG
8363 TATATG
1 TATATG
8369 AATTCTTTGG
Statistics
Matches: 218, Mismatches: 20, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
77 48 0.22
78 170 0.78
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.27
Consensus pattern (78 bp):
TATATGCATGGTCAAACCCCAAATGATGATAGTCAAACCCCAAAATTTGATAGTCAAACCACAAA
AATCATTTCATTG
Found at i:8166 original size:21 final size:21
Alignment explanation
Indices: 8141--8194 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
8131 ATATGCATGA
*
8141 TCAAACCCCAAA-TGATGATAG
1 TCAAACCACAAAGT-ATGATAG
* * *
8162 TCAAAGCTCAAAGTTTGATAG
1 TCAAACCACAAAGTATGATAG
8183 TCAAACCACAAA
1 TCAAACCACAAA
8195 AATCATTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.20
Consensus pattern (21 bp):
TCAAACCACAAAGTATGATAG
Found at i:8244 original size:21 final size:21
Alignment explanation
Indices: 8209--8265 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
8199 ATTTCATTGT
*
8209 ATATGCATGGTCAAACCCC-AA
1 ATATG-ATAGTCAAACCCCAAA
8230 ATGATGATAGTCAAACCCCAAA
1 AT-ATGATAGTCAAACCCCAAA
*
8252 ATTTGATAGTCAAA
1 ATATGATAGTCAAA
8266 TCATAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 25 0.78
22 7 0.22
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (21 bp):
ATATGATAGTCAAACCCCAAA
Found at i:8562 original size:21 final size:20
Alignment explanation
Indices: 8550--8607 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
8540 AATCATAAAT
* *
8550 TTTGATAGTCAAAAGCAAAAG
1 TTTGATAGTC-AAACCAAAAA
* *
8571 TTTAATAGTCAAACCCCAAAA
1 TTTGATAGTCAAA-CCAAAAA
8592 TTTGATAGTCAAACCA
1 TTTGATAGTCAAACCA
8608 TGTTAAACCT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (20 bp):
TTTGATAGTCAAACCAAAAA
Done.