Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018244.1 Corchorus olitorius cultivar O-4 contig18277, 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: 30744
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4447 original size:21 final size:22
Alignment explanation
Indices: 4421--4461 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4411 CAAAAAAAAA
*
4421 AAAAG-TGATTTGAGTCATAAT
1 AAAAGTTGAATTGAGTCATAAT
4442 AAAAGTTGAATTGAGTCATA
1 AAAAGTTGAATTGAGTCATA
4462 CGTTTTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.32
Consensus pattern (22 bp):
AAAAGTTGAATTGAGTCATAAT
Found at i:8066 original size:11 final size:12
Alignment explanation
Indices: 8050--8078 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
8040 TAGAGTAATG
8050 AAAAAAGAA-AA
1 AAAAAAGAAGAA
8061 AAAAAAGAAGAA
1 AAAAAAGAAGAA
8073 AAAAAA
1 AAAAAA
8079 AGGGTTAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAGAA
Found at i:8073 original size:14 final size:13
Alignment explanation
Indices: 8050--8079 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
8040 TAGAGTAATG
8050 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
8063 AAAAGAAGAAAAAA
1 AAAA-AAGAAAAAA
8077 AAA
1 AAA
8080 GGGTTAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:12103 original size:12 final size:12
Alignment explanation
Indices: 12086--12119 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
12076 ATGTAGTGTG
12086 TATATATATATA-
1 TATATAT-TATAC
12098 TATATATTATAC
1 TATATATTATAC
12110 TATATATTAT
1 TATATATTAT
12120 TTTTAGTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TATATATTATAC
Found at i:13778 original size:28 final size:29
Alignment explanation
Indices: 13741--13795 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
13731 TTATTATTGT
*
13741 AATTACTTA-TAATTTTGATTTAGGCTAA
1 AATTAATTATTAATTTTGATTTAGGCTAA
* *
13769 AATTAATTATTATTTTTTATTTAGGCT
1 AATTAATTATTAATTTTGATTTAGGCT
13796 GGAAGGGAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (29 bp):
AATTAATTATTAATTTTGATTTAGGCTAA
Found at i:13942 original size:27 final size:26
Alignment explanation
Indices: 13904--13959 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 26
13894 AAGGGAGAGA
*
13904 GAGGTTGAGGCTGCTCGGATGTATATG
1 GAGGCTGAGGCTGCTCGGATGTATA-G
13931 GAGGCTGAGGCTGCTCGGATGTATAG
1 GAGGCTGAGGCTGCTCGGATGTATAG
13957 GAG
1 GAG
13960 AGGGAGGCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.20, C:0.12, G:0.43, T:0.25
Consensus pattern (26 bp):
GAGGCTGAGGCTGCTCGGATGTATAG
Found at i:13966 original size:26 final size:27
Alignment explanation
Indices: 13910--13968 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
13900 GAGAGAGGTT
*
13910 GAGGCTGCTCGGATGTATATGGAGGCT
1 GAGGCTGCTCGGATGTATATGGAGGCG
13937 GAGGCTGCTCGGATGTATA-GGAGAG-G
1 GAGGCTGCTCGGATGTATATGGAG-GCG
13963 GAGGCT
1 GAGGCT
13969 ACTGCTGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 10 0.33
27 20 0.67
ACGTcount: A:0.20, C:0.14, G:0.44, T:0.22
Consensus pattern (27 bp):
GAGGCTGCTCGGATGTATATGGAGGCG
Found at i:16042 original size:10 final size:10
Alignment explanation
Indices: 16027--16067 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
16017 TTATATTTTG
*
16027 GGATTTGTAT
1 GGATTTTTAT
16037 GGATTTTTAT
1 GGATTTTTAT
* *
16047 GTATTTTTTT
1 GGATTTTTAT
16057 GGATTTTTAT
1 GGATTTTTAT
16067 G
1 G
16068 TATATTGGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.17, C:0.00, G:0.22, T:0.61
Consensus pattern (10 bp):
GGATTTTTAT
Found at i:19986 original size:57 final size:56
Alignment explanation
Indices: 19898--20012 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 56
19888 TATCTGTTTC
19898 CTTTCACACAATAAATATTATAATAAATCATATCCCCTCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTATAATAAATCATATCCCC-CTATCTCTACTTAATTATT
* *
19955 CTTTCACACAATAAATGTTATAATAAATCATATCCTCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
20011 CT
1 CT
20013 ACAAAATAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 21 0.38
57 35 0.62
ACGTcount: A:0.36, C:0.23, G:0.01, T:0.41
Consensus pattern (56 bp):
CTTTCACACAATAAATATTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
Found at i:20103 original size:21 final size:21
Alignment explanation
Indices: 20079--20143 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
20069 AAGACTTAGG
20079 ATTTGAGTTGAGTATTTCTTA
1 ATTTGAGTTGAGTATTTCTTA
*** * *
20100 ATTT-A-CAAAGAATTTTCTATG
1 ATTTGAGTTGAGTA-TTTCT-TA
20121 ATTTGAGTTGAGTATTTCTTA
1 ATTTGAGTTGAGTATTTCTTA
20142 AT
1 AT
20144 GTACAGAGAA
Statistics
Matches: 30, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
19 3 0.10
20 6 0.20
21 12 0.40
22 6 0.20
23 3 0.10
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.49
Consensus pattern (21 bp):
ATTTGAGTTGAGTATTTCTTA
Found at i:20137 original size:42 final size:42
Alignment explanation
Indices: 20078--20158 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
20068 TAAGACTTAG
*
20078 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATGTACAAAGAATTTTCTAT
*
20120 GATTTGAGTTGAGTATTTCTTAATGTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATGTACAAAGAATTTTC
20159 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATGTACAAAGAATTTTCTAT
Found at i:20740 original size:150 final size:150
Alignment explanation
Indices: 20525--20794 Score: 522
Period size: 150 Copynumber: 1.8 Consensus size: 150
20515 TTCTTAAGAG
*
20525 ATCACAAACCATTTGTTTCCAGTGATGCAATGTCTTATCAAACAACTAATAACAATTTCAAAATG
1 ATCACAAACCATTTGTTTCCAGAGATGCAATGTCTTATCAAACAACTAATAACAATTTCAAAATG
20590 TCCATATGAAGAAGAGAGTAAACTTAGTTTTTGTTTTAAGTGCTACACACTTTAGCACTTATCAA
66 TCCATATGAAGAAGAGAGTAAACTTAGTTTTTGTTTTAAGTGCTACACACTTTAGCACTTATCAA
20655 ACAACTATTTGTTATGTCTT
131 ACAACTATTTGTTATGTCTT
*
20675 ATCACAAACCATTTGTTTCCAGAGATGCAATGTCTTATCAAACAACTAATAACAATTTCTAAATG
1 ATCACAAACCATTTGTTTCCAGAGATGCAATGTCTTATCAAACAACTAATAACAATTTCAAAATG
20740 TCCATATGAAGAAGAGAGTAAACTTAGTTTTTGTTTTAAGTGCTACACACTTTAG
66 TCCATATGAAGAAGAGAGTAAACTTAGTTTTTGTTTTAAGTGCTACACACTTTAG
20795 AGGAGGAAAC
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
150 118 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (150 bp):
ATCACAAACCATTTGTTTCCAGAGATGCAATGTCTTATCAAACAACTAATAACAATTTCAAAATG
TCCATATGAAGAAGAGAGTAAACTTAGTTTTTGTTTTAAGTGCTACACACTTTAGCACTTATCAA
ACAACTATTTGTTATGTCTT
Found at i:23710 original size:20 final size:20
Alignment explanation
Indices: 23658--23715 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
23648 AGGGAGATTA
*
23658 ACAAAATCTCACAGAAAGGTT
1 ACAAAAT-TCATAGAAAGGTT
* *
23679 ATCAAAAATCATAGGAAGGTT
1 A-CAAAATTCATAGAAAGGTT
23700 ACAAAATTCATAGAAA
1 ACAAAATTCATAGAAA
23716 AGTTTATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 13 0.42
21 13 0.42
22 5 0.16
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.21
Consensus pattern (20 bp):
ACAAAATTCATAGAAAGGTT
Found at i:23810 original size:22 final size:21
Alignment explanation
Indices: 23763--23843 Score: 90
Period size: 22 Copynumber: 3.8 Consensus size: 21
23753 CTTATGGAGT
* * *
23763 TTATCACAATTTTATAGGTAA
1 TTATCAAAATTTCATAGGTGA
*
23784 TTATCAAAATTTCATATGGTGG
1 TTATCAAAATTTCATA-GGTGA
* *
23806 TTATCAACATTTAATAGGATGA
1 TTATCAAAATTTCATAGG-TGA
23828 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
23844 AAAATATTCA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 16 0.33
22 33 0.67
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGTGA
Found at i:23963 original size:13 final size:13
Alignment explanation
Indices: 23945--23970 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23935 AGTATTCCTG
23945 TAATAATATAATA
1 TAATAATATAATA
23958 TAATAATATAATA
1 TAATAATATAATA
23971 ATCATAAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATAATATAATA
Found at i:24638 original size:178 final size:178
Alignment explanation
Indices: 24313--24695 Score: 448
Period size: 178 Copynumber: 2.1 Consensus size: 178
24303 CCATAAGCGC
* ** * **
24313 AAATTATGTAATATTAAGTAGACCGTCTATTTTCGTTAACCGAAACAATTAATTCTTTGGAAGCA
1 AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTCTTTGGAAGCA
* ** *
24378 TTTTTTATACCTTGAACAATAAATTTAGTTTTCGAGTCCTTCATCAAATTTGTAAATCATAGAAC
66 TTTTTGATACCTTGAACAATAAATTTAGTTTTCGAGTCCCGCATCAAAGTTGTAAATCATAGAAC
* * * *
24443 AACCTTTCAAGAGACACTTGAATCATCTCAATTAGACAACTGAAGCA-A
131 AACCTTTAAAGAGACACTTAAATCACCTCAATCAGACAACTGAAG-AGA
* *
24491 AAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCAAAACAACAAATT-TTTCGGAAGC
1 AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTCTTT-GGAAGC
* * * * * *
24555 ATTTTTGATA-CTTGAAACATTAATTTTAGTTTTTGAGTCCCGCATGAAAGTTGTAGATCATGGA
65 ATTTTTGATACCTTG-AACAATAAATTTAGTTTTCGAGTCCCGCATCAAAGTTGTAAATCATAGA
* * * * *
24619 ACAATCTTTAAATAGACACTTAAATCACCTTAATCGGATAACTGAAGAGA
129 ACAACCTTTAAAGAGACACTTAAATCACCTCAATCAGACAACTGAAGAGA
* *
24669 AAATTATATAATGTTAAAATAGACCGT
1 AAATTATATAATATT-AAGTAGACCGT
24696 TTAGCCAAAC
Statistics
Matches: 170, Mismatches: 31, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
177 8 0.05
178 153 0.90
179 9 0.05
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (178 bp):
AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTCTTTGGAAGCA
TTTTTGATACCTTGAACAATAAATTTAGTTTTCGAGTCCCGCATCAAAGTTGTAAATCATAGAAC
AACCTTTAAAGAGACACTTAAATCACCTCAATCAGACAACTGAAGAGA
Found at i:25744 original size:21 final size:24
Alignment explanation
Indices: 25715--25765 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
25705 TTTTGAACTC
25715 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
25738 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
25761 ATTAT
1 ATTAT
25766 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:25760 original size:25 final size:25
Alignment explanation
Indices: 25715--25763 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
25705 TTTTGAACTC
*
25715 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
25740 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
25764 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:27091 original size:18 final size:21
Alignment explanation
Indices: 27068--27110 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
27058 ACAAGATCTA
27068 AACAAG-AA-AAATT-TGATG
1 AACAAGTAAGAAATTGTGATG
*
27086 AACAAGTAAGAACTTGTGATG
1 AACAAGTAAGAAATTGTGATG
27107 AACA
1 AACA
27111 GGGTGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 2 0.10
20 4 0.19
21 9 0.43
ACGTcount: A:0.51, C:0.09, G:0.19, T:0.21
Consensus pattern (21 bp):
AACAAGTAAGAAATTGTGATG
Found at i:27244 original size:16 final size:17
Alignment explanation
Indices: 27196--27246 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
27186 TAGGAGCTGA
27196 ATTTTGAGATGAGTGAT
1 ATTTTGAGATGAGTGAT
**
27213 ATCACTGAGA-GA-TGAT
1 AT-TTTGAGATGAGTGAT
27229 -TTTTGAGATGAGTGAT
1 ATTTTGAGATGAGTGAT
27245 AT
1 AT
27247 CTGCCTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
14 5 0.19
15 3 0.12
16 8 0.31
17 5 0.19
18 5 0.19
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.37
Consensus pattern (17 bp):
ATTTTGAGATGAGTGAT
Done.