Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019502.1 Corchorus olitorius cultivar O-4 contig19535, 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: 26289
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Found at i:108 original size:41 final size:42
Alignment explanation
Indices: 7--182 Score: 221
Period size: 43 Copynumber: 4.2 Consensus size: 42
1 TTTGGG
*
7 GGACTTTTG-ATATAGATGCCTCTGTGTTATATATGTGTTTGA
1 GGAC-TTTGAATATAGATGCCCCTGTGTTATATATGTGTTTGA
* * *
49 GGACTTTGTAATAAAGGTGCCCCTGTGTTATATATGTGTTTGG
1 GGACTTTG-AATATAGATGCCCCTGTGTTATATATGTGTTTGA
* *
92 GGAC-TTGAATATAGGTGCCTCTGTGTTATATATGTGTTTGA
1 GGACTTTGAATATAGATGCCCCTGTGTTATATATGTGTTTGA
* * * *
133 GGACTTTGGAATAGAGATACCCTTGTGTTATATATGTGTTTGG
1 GGACTTT-GAATATAGATGCCCCTGTGTTATATATGTGTTTGA
176 GGACTTT
1 GGACTTT
183 TTGGTTATTG
Statistics
Matches: 117, Mismatches: 13, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
41 39 0.33
42 9 0.08
43 69 0.59
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.41
Consensus pattern (42 bp):
GGACTTTGAATATAGATGCCCCTGTGTTATATATGTGTTTGA
Found at i:160 original size:84 final size:84
Alignment explanation
Indices: 16--181 Score: 278
Period size: 84 Copynumber: 2.0 Consensus size: 84
6 GGGACTTTTG
* * *
16 ATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGTGCCCCTGTGTTATA
1 ATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAATAAAGATACCCCTGTGTTATA
81 TATGTGTTTGGGGACTTGA
66 TATGTGTTTGGGGACTTGA
* * *
100 ATATAGGTGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAGATACCCTTGTGTTATA
1 ATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAATAAAGATACCCCTGTGTTATA
165 TATGTGTTTGGGGACTT
66 TATGTGTTTGGGGACTT
182 TTTGGTTATT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.41
Consensus pattern (84 bp):
ATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAATAAAGATACCCCTGTGTTATA
TATGTGTTTGGGGACTTGA
Found at i:4323 original size:16 final size:16
Alignment explanation
Indices: 4302--4332 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4292 CAATGTTATT
4302 TGATTTGAGAGAGAGC
1 TGATTTGAGAGAGAGC
4318 TGATTTGAGAGAGAG
1 TGATTTGAGAGAGAG
4333 GGTCCAGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.39, T:0.26
Consensus pattern (16 bp):
TGATTTGAGAGAGAGC
Found at i:6230 original size:27 final size:28
Alignment explanation
Indices: 6199--6272 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 28
6189 AAGTGAACTT
*
6199 AAAATGACCAAAATGCCCTTAGA-CGTG
1 AAAATGACCAAAATGCCCCTAGATCGTG
* * *
6226 CAAATGACTAAAATGCCCCTAGATCTTG
1 AAAATGACCAAAATGCCCCTAGATCGTG
6254 AAAATGACCAAAATGCCCC
1 AAAATGACCAAAATGCCCC
6273 CTAGTTGATC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 20 0.50
28 20 0.50
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.19
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTAGATCGTG
Found at i:14660 original size:2 final size:2
Alignment explanation
Indices: 14648--14687 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
14638 CCCTTGTCAC
*
14648 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14688 GGAATTTGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:14843 original size:43 final size:42
Alignment explanation
Indices: 14796--15208 Score: 530
Period size: 43 Copynumber: 9.8 Consensus size: 42
14786 ATAAGGAGAA
*
14796 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTG-AATAGAG
* * *
14839 ATGCCCCTGTGTTATATTTGTGTTTGGGGACTTTG-ATATAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAG
*
14880 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTG-AATAGAG
* * * *
14923 TTGCCCCTGTGTTATATATGTGTTTGGGGACTCTG-ATATAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAG
*
14964 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTG-AATAGAG
* * * * *
15007 TTTCCCCTGTGTTATATATGTATTTGGGGACTTTCATATA-A-
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGA-ATAGAG
* *
15048 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGCAATAAAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTG-AATAGAG
* * *
15091 GTGCCCCTGTGTTATATATGTGTTTGGGGAC-TTGAATATAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAG
* *
15132 GTGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTT-GAATAGAG
*
15175 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTT
15209 TGGTTATTGG
Statistics
Matches: 320, Mismatches: 40, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
41 140 0.44
42 9 0.03
43 171 0.53
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.42
Consensus pattern (42 bp):
ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAG
Found at i:14908 original size:84 final size:84
Alignment explanation
Indices: 14796--15208 Score: 693
Period size: 84 Copynumber: 4.9 Consensus size: 84
14786 ATAAGGAGAA
*
14796 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATTTGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
14861 TTTGGGGACTTTGATATAG
66 TTTGGGGACTTTGATATAG
*
14880 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
*
14945 TTTGGGGACTCTGATATAG
66 TTTGGGGACTTTGATATAG
* * *
14964 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTTCCCCTGTGTTATATATGTA
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
* *
15029 TTTGGGGACTTTCATATAA
66 TTTGGGGACTTTGATATAG
* * *
15048 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGCAATAAAGGTGCCCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
15113 TTTGGGGAC-TTGAATATAG
66 TTTGGGGACTTTG-ATATAG
* *
15132 GTGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAGATGCCCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
15197 TTTGGGGACTTT
66 TTTGGGGACTTT
15209 TGGTTATTGG
Statistics
Matches: 308, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
83 2 0.01
84 304 0.99
85 2 0.01
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.42
Consensus pattern (84 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
TTTGGGGACTTTGATATAG
Found at i:15479 original size:3 final size:3
Alignment explanation
Indices: 15471--15520 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
15461 CAACATTTGT
*
15471 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTA TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
15519 TT
1 TT
15521 AGACCGAAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:17832 original size:17 final size:18
Alignment explanation
Indices: 17810--17843 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17800 AAAGTTGCTT
17810 AAAATTATTT-CTATTTG
1 AAAATTATTTCCTATTTG
*
17827 AAAATTTTTTCCTATTT
1 AAAATTATTTCCTATTT
17844 TAATTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.56
Consensus pattern (18 bp):
AAAATTATTTCCTATTTG
Found at i:18258 original size:29 final size:29
Alignment explanation
Indices: 18225--18420 Score: 184
Period size: 29 Copynumber: 6.8 Consensus size: 29
18215 CACGTTCAGA
18225 GGCATTTTGGTCATTTTTGCATATCCAGG
1 GGCATTTTGGTCATTTTTGCATATCCAGG
*
18254 GGCATTTTGGTCATTTTGGC-TCATCCAGTG
1 GGCATTTTGGTCATTTTTGCAT-ATCCAG-G
* **
18284 GGCATTTTGGTCATTTTTGCATGTTTAGG
1 GGCATTTTGGTCATTTTTGCATATCCAGG
* * *
18313 TGCATTTTGGTCATTTTTGCACATCTAGG
1 GGCATTTTGGTCATTTTTGCATATCCAGG
* * * ** **
18342 GGTATTATAGTCATTTTTGCGCATCCAAA
1 GGCATTTTGGTCATTTTTGCATATCCAGG
* *
18371 GGCATTTTGGTCATCTTTGCATTAT--A-C
1 GGCATTTTGGTCATTTTTGCA-TATCCAGG
*
18398 GGCAGTTTGGTCATTTTTGCATA
1 GGCATTTTGGTCATTTTTGCATA
18421 CTTTAGGTTC
Statistics
Matches: 137, Mismatches: 26, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
26 2 0.01
27 19 0.14
28 2 0.01
29 88 0.64
30 25 0.18
31 1 0.01
ACGTcount: A:0.18, C:0.16, G:0.23, T:0.43
Consensus pattern (29 bp):
GGCATTTTGGTCATTTTTGCATATCCAGG
Found at i:18270 original size:9 final size:9
Alignment explanation
Indices: 18256--18329 Score: 51
Period size: 9 Copynumber: 7.7 Consensus size: 9
18246 TATCCAGGGG
18256 CATTTTGGT
1 CATTTTGGT
18265 CATTTTGGCT
1 CATTTTGG-T
** *
18275 CATCCAGTGGG
1 CAT--TTTGGT
18286 CATTTTGGT
1 CATTTTGGT
*
18295 CATTTTTG-
1 CATTTTGGT
18303 CATGTTTAGGT
1 CAT-TTT-GGT
18314 GCATTTTGGT
1 -CATTTTGGT
18324 CATTTT
1 CATTTT
18330 TGCACATCTA
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
8 3 0.06
9 27 0.54
10 8 0.16
11 6 0.12
12 6 0.12
ACGTcount: A:0.14, C:0.15, G:0.23, T:0.49
Consensus pattern (9 bp):
CATTTTGGT
Found at i:18318 original size:59 final size:58
Alignment explanation
Indices: 18225--18389 Score: 186
Period size: 59 Copynumber: 2.8 Consensus size: 58
18215 CACGTTCAGA
*
18225 GGCATTTTGGTCATTTTTGCATATCCAGGGGCATTTTGGTCATTTTGGCTCATCCAGTG
1 GGCATTTTGGTCATTTTTGCATATCCAGGGGCATTTTGGTCATTTTGGCACATCCAG-G
* ** * * *
18284 GGCATTTTGGTCATTTTTGCATGTTTAGGTGCATTTTGGTCATTTTTGCACATCTAGG
1 GGCATTTTGGTCATTTTTGCATATCCAGGGGCATTTTGGTCATTTTGGCACATCCAGG
* * * ** **
18342 GGTATTATAGTCATTTTTGCGCATCCAAAGGCATTTTGGTCATCTTTG
1 GGCATTTTGGTCATTTTTGCATATCCAGGGGCATTTTGGTCAT-TTTG
18390 CATTATACGG
Statistics
Matches: 86, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
58 33 0.38
59 53 0.62
ACGTcount: A:0.17, C:0.16, G:0.24, T:0.43
Consensus pattern (58 bp):
GGCATTTTGGTCATTTTTGCATATCCAGGGGCATTTTGGTCATTTTGGCACATCCAGG
Found at i:26076 original size:16 final size:16
Alignment explanation
Indices: 26043--26076 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
26033 CCCTAAAATT
*
26043 CCGAAACCCAGATAAC
1 CCGAAACCCAAATAAC
*
26059 CCGAAACCCAAATGAC
1 CCGAAACCCAAATAAC
26075 CC
1 CC
26077 AAAGCCTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.41, G:0.12, T:0.06
Consensus pattern (16 bp):
CCGAAACCCAAATAAC
Done.