Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021831.1 Corchorus olitorius cultivar O-4 contig21864, 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: 24121
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:2169 original size:21 final size:21
Alignment explanation
Indices: 2145--2186 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2135 ACATCTTAGG
2145 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
*
2166 CAACTCTGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
2187 TTCTTCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:2830 original size:76 final size:76
Alignment explanation
Indices: 2697--2844 Score: 174
Period size: 76 Copynumber: 1.9 Consensus size: 76
2687 GGACCCCGAG
** * *
2697 TCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGTGGGC
1 TCCACCTGGGCGCCCACATGGTTGCCTTGAAAACCCATGTGGTTTGCCTGAGAACCCAGATGGGC
2762 AGTGTCACGAC
66 AGTGTCACGAC
* * * **
2773 TCCAGCTGGGTGCCCACATGGTTTGTC-TGAAAACCCATGT-GTTTCGCCTGATCACCCAGATGG
1 TCCACCTGGGCGCCCACATGG-TTGCCTTGAAAACCCATGTGGTTT-GCCTGAGAACCCAGATGG
*
2836 GCTGTGTCA
64 GCAGTGTCA
2845 TAGCTCATCA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
75 4 0.07
76 52 0.87
77 4 0.07
ACGTcount: A:0.18, C:0.29, G:0.28, T:0.25
Consensus pattern (76 bp):
TCCACCTGGGCGCCCACATGGTTGCCTTGAAAACCCATGTGGTTTGCCTGAGAACCCAGATGGGC
AGTGTCACGAC
Found at i:5927 original size:30 final size:30
Alignment explanation
Indices: 5893--5953 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
5883 TAAAAACTTC
5893 AATTACCCTAAATCTAACTATATATACCTT
1 AATTACCCTAAATCTAACTATATATACCTT
*
5923 AATTACCCTAAATTTAACTATATATACCTT
1 AATTACCCTAAATCTAACTATATATACCTT
5953 A
1 A
5954 CATATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (30 bp):
AATTACCCTAAATCTAACTATATATACCTT
Found at i:7000 original size:11 final size:10
Alignment explanation
Indices: 6984--7030 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
6974 AAACTCATGT
6984 TTGAAGACTCA
1 TTGAAGA-TCA
*
6995 TTGAAGATAA
1 TTGAAGATCA
7005 TTTGAAGAT--
1 -TTGAAGATCA
7014 TTGAAGATCA
1 TTGAAGATCA
7024 TTGAAGA
1 TTGAAGA
7031 ATTATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:7019 original size:19 final size:18
Alignment explanation
Indices: 6995--7030 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6985 TGAAGACTCA
6995 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
7014 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
7031 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:9119 original size:20 final size:19
Alignment explanation
Indices: 9091--9130 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
9081 GTGGCTTTTT
*
9091 ATATTTGAAAAAAAACTGAA
1 ATATATGAAAAAAAA-TGAA
9111 ATATATGAAAAAAAATGAA
1 ATATATGAAAAAAAATGAA
9130 A
1 A
9131 AGAAAAGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.65, C:0.03, G:0.10, T:0.23
Consensus pattern (19 bp):
ATATATGAAAAAAAATGAA
Found at i:10938 original size:2 final size:2
Alignment explanation
Indices: 10933--10977 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
10923 TATAAAAAAA
* *
10933 AT AT AT AT AT AT AT AT AT AC AT AT AA AT AT AT -T AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10973 AT AT A
1 AT AT A
10978 ATCATATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10973 original size:28 final size:28
Alignment explanation
Indices: 10931--10995 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
10921 AATATAAAAA
10931 AAATATA-TA-TATATATAT-ATACATAT
1 AAATATATTATTATATATATAAT-CATAT
10957 AAATATATTATTATATATATAATCATAT
1 AAATATATTATTATATATATAATCATAT
10985 AAA-ATGATTAT
1 AAATAT-ATTAT
10996 CTAAAGTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 7 0.20
27 4 0.11
28 22 0.63
29 2 0.06
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (28 bp):
AAATATATTATTATATATATAATCATAT
Found at i:10984 original size:12 final size:11
Alignment explanation
Indices: 10935--10985 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 11
10925 TAAAAAAAAT
10935 ATATATATATA
1 ATATATATATA
*
10946 TATATACATATA
1 -ATATATATATA
10958 A-ATATAT-TA
1 ATATATATATA
*
10967 TTATATATATA
1 ATATATATATA
10978 ATCATATA
1 AT-ATATA
10986 AAATGATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 2 0.06
10 11 0.34
11 4 0.12
12 15 0.47
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (11 bp):
ATATATATATA
Found at i:12269 original size:4 final size:4
Alignment explanation
Indices: 12260--12291 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
12250 AAAACATAAA
12260 TATT TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT
12292 ATTATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:15626 original size:30 final size:30
Alignment explanation
Indices: 15554--15627 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
15544 GACCCAAATC
* *
15554 TGTAAGTACAGGGACTAAATTGATCATTTT
1 TGTAAGTACATGGACCAAATTGATCATTTT
* *
15584 T-TAAGTAGATGGACCAAATTGA-CTTTTCT
1 TGTAAGTACATGGACCAAATTGATCATTT-T
15613 TGTAAGTACATGGAC
1 TGTAAGTACATGGAC
15628 TTATCAGGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.11
29 20 0.54
30 13 0.35
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.35
Consensus pattern (30 bp):
TGTAAGTACATGGACCAAATTGATCATTTT
Found at i:20524 original size:12 final size:12
Alignment explanation
Indices: 20489--20529 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
20479 AATAATGTAG
20489 CATATAT-ATATA
1 CATATATGATA-A
*
20501 TATATATG-TAA
1 CATATATGATAA
20512 CATATATGATAA
1 CATATATGATAA
20524 CATATA
1 CATATA
20530 ATAAGAACGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (12 bp):
CATATATGATAA
Found at i:20528 original size:23 final size:23
Alignment explanation
Indices: 20483--20529 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
20473 AGTGATAATA
* *
20483 ATGTAGCATATATATATATATAT
1 ATGTAACATATATATATACATAT
20506 ATGTAACATATATGATA-ACATAT
1 ATGTAACATATAT-ATATACATAT
20529 A
1 A
20530 ATAAGAACGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (23 bp):
ATGTAACATATATATATACATAT
Found at i:21303 original size:12 final size:12
Alignment explanation
Indices: 21285--21325 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
21275 TGCAACTAAA
21285 ATATATAATATT
1 ATATATAATATT
*
21297 CTATATAAT-TT
1 ATATATAATATT
*
21308 AT-TATAATATA
1 ATATATAATATT
21319 ATATATA
1 ATATATA
21326 TAAATTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
10 6 0.25
11 6 0.25
12 12 0.50
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATATAATATT
Done.