Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020294.1 Corchorus olitorius cultivar O-4 contig20327, 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: 12873
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:2257 original size:28 final size:28
Alignment explanation
Indices: 2225--2283 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
2215 TTGCCTTTCC
*
2225 AATCAATTGTAGGATTAGAACTCAAGAG
1 AATCAATTGTAGGATTAAAACTCAAGAG
2253 AATCAATTGTAGGATTAAAACTCAAGAG
1 AATCAATTGTAGGATTAAAACTCAAGAG
2281 AAT
1 AAT
2284 ATATATGGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (28 bp):
AATCAATTGTAGGATTAAAACTCAAGAG
Found at i:7939 original size:22 final size:22
Alignment explanation
Indices: 7914--8117 Score: 166
Period size: 22 Copynumber: 9.3 Consensus size: 22
7904 TAGAAATACC
* *
7914 GATAATCACACTGTGAAAATTT
1 GATAACCACACTATGAAAATTT
* * *
7936 GATAACCTCATTATG-AAATCTG
1 GATAACCACACTATGAAAAT-TT
7958 GATAACCAC-CTTATGAAAATTT
1 GATAACCACAC-TATGAAAATTT
* *
7980 GATAACCACACTGTGAAATTTT
1 GATAACCACACTATGAAAATTT
*
8002 GATAACCACACTATGAAATTTT
1 GATAACCACACTATGAAAATTT
* * *
8024 GATAACCTCAGTGTG-AAATTGT
1 GATAACCACACTATGAAAATT-T
* * * * *
8046 GATAATCTCCCTATTAAATTTT
1 GATAACCACACTATGAAAATTT
* *
8068 GATAATCACATTAT-AAAA-TT
1 GATAACCACACTATGAAAATTT
*
8088 GGTAACCACACTATGAAAATTTT
1 GATAACCACACTATGAAAA-TTT
8111 GATAACC
1 GATAACC
8118 TCCTCATAAA
Statistics
Matches: 144, Mismatches: 29, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
20 13 0.09
21 15 0.10
22 99 0.69
23 17 0.12
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.33
Consensus pattern (22 bp):
GATAACCACACTATGAAAATTT
Found at i:7975 original size:44 final size:43
Alignment explanation
Indices: 7914--8119 Score: 200
Period size: 44 Copynumber: 4.7 Consensus size: 43
7904 TAGAAATACC
* *
7914 GATAATCACACTGTGAAAATTTGATAACCTCATTATGAAATCTG
1 GATAACCACACTATGAAAATTTGATAACCTCATTATGAAAT-TG
* * * *
7958 GATAACCAC-CTTATGAAAATTTGATAACCACACTGTGAAATTTT
1 GATAACCACAC-TATGAAAATTTGATAACCTCATTATGAAA-TTG
* * *
8002 GATAACCACACTATGAAATTTTGATAACCTCAGTGTGAAATTG
1 GATAACCACACTATGAAAATTTGATAACCTCATTATGAAATTG
* * * * * * * *
8045 TGATAATCTCCCTATTAAATTTTGATAATCACATTATAAAATTG
1 -GATAACCACACTATGAAAATTTGATAACCTCATTATGAAATTG
8089 G-TAACCACACTATGAAAATTTTGATAACCTC
1 GATAACCACACTATGAAAA-TTTGATAACCTC
8120 CTCATAAAAT
Statistics
Matches: 131, Mismatches: 26, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
42 12 0.09
43 14 0.11
44 103 0.79
45 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (43 bp):
GATAACCACACTATGAAAATTTGATAACCTCATTATGAAATTG
Found at i:8020 original size:66 final size:64
Alignment explanation
Indices: 7914--8117 Score: 196
Period size: 66 Copynumber: 3.1 Consensus size: 64
7904 TAGAAATACC
* * *
7914 GATAATCACACTGTGAAAATTTGATAACCTCATTATGAAATCTGGATAACCACCTTATGAAAATT
1 GATAACCACACTGTGAAATTTTGATAACCACATTATGAAAT-TGGATAACCACC-TATGAAAATT
7979 T
64 T
* * * * *
7980 GATAACCACACTGTGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCAGTGTG-AAATT
1 GATAACCACACTGTGAAATTTTGATAACCACATTATGAAA-TTGGATAACCAC-CTATGAAAATT
8044 GT
64 -T
* * * * * * *
8046 GATAATCTCCCTATTAAATTTTGATAATCACATTATAAAATTGG-TAACCACACTATGAAAATTT
1 GATAACCACACTGTGAAATTTTGATAACCACATTATGAAATTGGATAACCAC-CTATGAAAA-TT
8110 T
64 T
8111 GATAACC
1 GATAACC
8118 TCCTCATAAA
Statistics
Matches: 112, Mismatches: 21, Indels: 11
0.78 0.15 0.08
Matches are distributed among these distances:
64 10 0.09
65 18 0.16
66 83 0.74
67 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.33
Consensus pattern (64 bp):
GATAACCACACTGTGAAATTTTGATAACCACATTATGAAATTGGATAACCACCTATGAAAATTT
Found at i:8441 original size:44 final size:44
Alignment explanation
Indices: 8345--8448 Score: 113
Period size: 44 Copynumber: 2.4 Consensus size: 44
8335 ATAACCACAC
* * *
8345 TATAAAATTTCGATAATCTTCGTATGAAATTTTGTTAACATCTC
1 TATAAAATTTTGATAATCTTCGTACGAAATTTTGTTAACATCTA
** **
8389 TA-AGAAATTTTGATAATCTTTTTACGAAAATTTTG-TAATTTCTA
1 TATA-AAATTTTGATAATCTTCGTACG-AAATTTTGTTAACATCTA
8433 TATAAAATTTTGATAA
1 TATAAAATTTTGATAA
8449 CTATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.02
44 40 0.80
45 9 0.18
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (44 bp):
TATAAAATTTTGATAATCTTCGTACGAAATTTTGTTAACATCTA
Found at i:8512 original size:44 final size:44
Alignment explanation
Indices: 8415--8514 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 44
8405 TCTTTTTACG
* * * *
8415 AAAATTTTG-TAATTTCTATATAAAATTTTGATAACTATACTAT
1 AAAATTTTGATAAATTCCATATAAAATTTTGATAACCACACTAT
* * * *
8458 GAAGTTTTGATAAATTCCATATGAAATTTTGGTAACCACACTAT
1 AAAATTTTGATAAATTCCATATAAAATTTTGATAACCACACTAT
*
8502 AAAATATTGATAA
1 AAAATTTTGATAA
8515 CCTTCCTATG
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
43 7 0.16
44 38 0.84
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (44 bp):
AAAATTTTGATAAATTCCATATAAAATTTTGATAACCACACTAT
Found at i:11110 original size:11 final size:11
Alignment explanation
Indices: 11096--11142 Score: 55
Period size: 10 Copynumber: 4.5 Consensus size: 11
11086 GGGAAAAAGG
11096 GAAAAGGAAAA
1 GAAAAGGAAAA
11107 GAAAA-GAAAA
1 GAAAAGGAAAA
11117 GAAAAAGGAAAA
1 G-AAAAGGAAAA
*
11129 -AAAAGTAAAA
1 GAAAAGGAAAA
11139 -AAAA
1 GAAAA
11143 AAAAATAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
10 19 0.58
11 9 0.27
12 5 0.15
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (11 bp):
GAAAAGGAAAA
Found at i:11117 original size:16 final size:15
Alignment explanation
Indices: 11097--11171 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 15
11087 GGAAAAAGGG
*
11097 AAAAGGAAAAGAAAA
1 AAAAGAAAAAGAAAA
11112 GAAAAGAAAAAGGAAAA
1 -AAAAGAAAAA-GAAAA
*
11129 AAAAGTAAAAAAAAAAA
1 AAAAG--AAAAAGAAAA
*
11146 AATAAGAAATAAGAGAA
1 AA-AAGAAA-AAGAAAA
*
11163 AATAGAAAA
1 AAAAGAAAA
11172 TTATGGATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
15 1 0.02
16 22 0.45
17 18 0.37
18 8 0.16
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (15 bp):
AAAAGAAAAAGAAAA
Found at i:11125 original size:22 final size:22
Alignment explanation
Indices: 11097--11144 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
11087 GGAAAAAGGG
*
11097 AAAAGGAAAAGAAAAG-AAAAGA
1 AAAAGGAAAA-AAAAGTAAAAAA
11119 AAAAGGAAAAAAAAGTAAAAAA
1 AAAAGGAAAAAAAAGTAAAAAA
11141 AAAA
1 AAAA
11145 AAATAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (22 bp):
AAAAGGAAAAAAAAGTAAAAAA
Found at i:11143 original size:11 final size:10
Alignment explanation
Indices: 11097--11147 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 10
11087 GGAAAAAGGG
*
11097 AAAAGGAAAA
1 AAAAAGAAAA
*
11107 GAAAAGAAAA
1 AAAAAGAAAA
*
11117 GAAAAAGGAAA
1 -AAAAAGAAAA
11128 AAAAAGTAAAA
1 AAAAAG-AAAA
11139 AAAAA-AAAA
1 AAAAAGAAAA
11148 TAAGAAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
9 4 0.12
10 14 0.41
11 16 0.47
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Done.