Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012481.1 Corchorus olitorius cultivar O-4 contig12514, 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: 41965
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2788 original size:7 final size:7
Alignment explanation
Indices: 2752--2790 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
2742 GCTCACTAAA
2752 TTTTAA-
1 TTTTAAT
2758 TTTTAAT
1 TTTTAAT
*
2765 TTTCAAT
1 TTTTAAT
2772 TTTTAAT
1 TTTTAAT
2779 TTTT-AT
1 TTTTAAT
2785 TTTTAA
1 TTTTAA
2791 CTTCTAACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 12 0.41
7 17 0.59
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTTAAT
Found at i:3896 original size:11 final size:11
Alignment explanation
Indices: 3880--3914 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
3870 ATTAAGAAAG
3880 TATGTCATGAA
1 TATGTCATGAA
3891 TATGTCATGAA
1 TATGTCATGAA
*
3902 TATGTCAAGAA
1 TATGTCATGAA
3913 TA
1 TA
3915 AGTGTGGGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (11 bp):
TATGTCATGAA
Found at i:3971 original size:17 final size:17
Alignment explanation
Indices: 3944--3976 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
3934 TAAAGGGTAG
3944 TTAAAAAAAGT-TTTTA
1 TTAAAAAAAGTGTTTTA
3960 TTAAAAAGAAGTGTTTT
1 TTAAAAA-AAGTGTTTT
3977 CATGACAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (17 bp):
TTAAAAAAAGTGTTTTA
Found at i:13411 original size:8 final size:7
Alignment explanation
Indices: 13381--13420 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
13371 GGCAACCCAA
13381 TTTTAA-
1 TTTTAAT
13387 TTTTAAT
1 TTTTAAT
13394 TTTTAAT
1 TTTTAAT
13401 TTTTAAGT
1 TTTTAA-T
13409 TTTT-AT
1 TTTTAAT
13415 TTTTAA
1 TTTTAA
13421 CTTCTAACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 11 0.35
7 15 0.48
8 5 0.16
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (7 bp):
TTTTAAT
Found at i:14604 original size:17 final size:18
Alignment explanation
Indices: 14582--14615 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
14572 TAAAGGGTAG
14582 TTAAAAAAAAGT-TTTTA
1 TTAAAAAAAAGTGTTTTA
*
14599 TTAAAAAGAAGTGTTTT
1 TTAAAAAAAAGTGTTTT
14616 CACGAAAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (18 bp):
TTAAAAAAAAGTGTTTTA
Found at i:15430 original size:348 final size:348
Alignment explanation
Indices: 15024--15725 Score: 1359
Period size: 348 Copynumber: 2.0 Consensus size: 348
15014 TACTTAAGAA
*
15024 TGATGATACTTGCTATTTCTTGATCTTTTGAATTGAGTATTATTATTATTCTTTGTTATTTAGAT
1 TGATGATAATTGCTATTTCTTGATCTTTTGAATTGAGTATTATTATTATTCTTTGTTATTTAGAT
*
15089 TTCATGATTAAAATTGATTCTTGATATTGGTGTGAATTCAAATTGATCTTTTGAAAAATTGGTTT
66 TTCATGATTAAAATTGATTCTTGATATAGGTGTGAATTCAAATTGATCTTTTGAAAAATTGGTTT
* *
15154 TACTGACTTTCACATTGATTTGCTAAGGGACTAGCAACGTTCAAGTGTGGGGGAAAATATGATCG
131 TACTGACTTACACATTGATTTACTAAGGGACTAGCAACGTTCAAGTGTGGGGGAAAATATGATCG
15219 AGCTAAAAACAACCCTATTTGTATAGCTATTTTATTATGTTTTTAGATGAATTTATGCTCTAATA
196 AGCTAAAAACAACCCTATTTGTATAGCTATTTTATTATGTTTTTAGATGAATTTATGCTCTAATA
15284 TATCTTATTTTGTTAATATTTGTGATTTGAGTCTTTAAGTGATGTAAAACTGGAAACTTGCAAAT
261 TATCTTATTTTGTTAATATTTGTGATTTGAGTCTTTAAGTGATGTAAAACTGGAAACTTGCAAAT
15349 TTTCACTACTTTTGGAGCTATTT
326 TTTCACTACTTTTGGAGCTATTT
15372 TGATGATAATTGCTATTTCTTGATCTTTTGAATTGAGTATTATTATTATTCTTTGTTATTTAGAT
1 TGATGATAATTGCTATTTCTTGATCTTTTGAATTGAGTATTATTATTATTCTTTGTTATTTAGAT
15437 TTCATGATTAAAATTGATTCTTGATATAGGTGTGAATTCAAATTGATCTTTTGAAAAATTGGTTT
66 TTCATGATTAAAATTGATTCTTGATATAGGTGTGAATTCAAATTGATCTTTTGAAAAATTGGTTT
15502 TACTGACTTACACATTGATTTACTAAGGGACTAGCAACGTTCAAGTGTGGGGGAAAATATGATCG
131 TACTGACTTACACATTGATTTACTAAGGGACTAGCAACGTTCAAGTGTGGGGGAAAATATGATCG
*
15567 AGCTAAGAACAACCCTATTTGTATAGCTATTTTATTATGTTTTTAGATGAATTTATGCTCTAATA
196 AGCTAAAAACAACCCTATTTGTATAGCTATTTTATTATGTTTTTAGATGAATTTATGCTCTAATA
15632 TATCTTATTTTGTTAATATTTGTGATTTGAGTCTTTAAGTGATGTAAAACTGGAAACTTGCAAAT
261 TATCTTATTTTGTTAATATTTGTGATTTGAGTCTTTAAGTGATGTAAAACTGGAAACTTGCAAAT
15697 TTTCACTACTTTTGGAGCTATTT
326 TTTCACTACTTTTGGAGCTATTT
15720 TGATGA
1 TGATGA
15726 CTTTTTACAC
Statistics
Matches: 349, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
348 349 1.00
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (348 bp):
TGATGATAATTGCTATTTCTTGATCTTTTGAATTGAGTATTATTATTATTCTTTGTTATTTAGAT
TTCATGATTAAAATTGATTCTTGATATAGGTGTGAATTCAAATTGATCTTTTGAAAAATTGGTTT
TACTGACTTACACATTGATTTACTAAGGGACTAGCAACGTTCAAGTGTGGGGGAAAATATGATCG
AGCTAAAAACAACCCTATTTGTATAGCTATTTTATTATGTTTTTAGATGAATTTATGCTCTAATA
TATCTTATTTTGTTAATATTTGTGATTTGAGTCTTTAAGTGATGTAAAACTGGAAACTTGCAAAT
TTTCACTACTTTTGGAGCTATTT
Found at i:20869 original size:19 final size:18
Alignment explanation
Indices: 20836--20871 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20826 TTGAGACAAT
20836 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
20854 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
20872 TAAGCCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:37119 original size:5 final size:5
Alignment explanation
Indices: 37111--37207 Score: 74
Period size: 5 Copynumber: 18.8 Consensus size: 5
37101 TTACTTTCCT
** *
37111 TTTTC TTTTC TTTTC TCCTA TTTGTC TTTTC TTTTC TTTCTTC TTTT-
1 TTTTC TTTTC TTTTC TTTTC TTT-TC TTTTC TTTTC -TT-TTC TTTTC
* *
37158 TTTT- ATTTC TTTTCC TTCTC TTTTC TTTTTC TTTTTC TTTT- TTTTC
1 TTTTC TTTTC TTTT-C TTTTC TTTTC -TTTTC -TTTTC TTTTC TTTTC
37204 TTTT
1 TTTT
37208 TATTTTTTTA
Statistics
Matches: 75, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
4 11 0.15
5 38 0.51
6 23 0.31
7 3 0.04
ACGTcount: A:0.02, C:0.20, G:0.01, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:37138 original size:21 final size:19
Alignment explanation
Indices: 37107--37204 Score: 69
Period size: 21 Copynumber: 5.1 Consensus size: 19
37097 TTCCTTACTT
37107 TCCTTTTTCTTTTCTTTTC
1 TCCTTTTTCTTTTCTTTTC
37126 TCCTATTTGTCTTTTCTTTTC
1 TCCT-TTT-TCTTTTCTTTTC
* * * *
37147 TTTCTTCTTTTTTTTATTTCTTT
1 -TCCTT-TTTCTTTT-CTT-TTC
*
37170 TCC-TTCTCTTTTCTTTT-
1 TCCTTTTTCTTTTCTTTTC
37187 T-CTTTTTCTTTT-TTTTC
1 TCCTTTTTCTTTTCTTTTC
37204 T
1 T
37205 TTTTATTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
16 5 0.08
17 10 0.16
18 2 0.03
19 6 0.10
20 9 0.15
21 19 0.31
22 9 0.15
23 2 0.03
ACGTcount: A:0.02, C:0.21, G:0.01, T:0.76
Consensus pattern (19 bp):
TCCTTTTTCTTTTCTTTTC
Found at i:37181 original size:22 final size:20
Alignment explanation
Indices: 37135--37192 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 20
37125 CTCCTATTTG
*
37135 TCTTTTCTTTTC-TTTCTTC
1 TCTTTTTTTTTCTTTTCTTC
*
37154 TTTTTTTTATTTCTTTTCCTTC
1 TCTTTTTT-TTTCTTTT-CTTC
37176 TCTTTTCTTTTTCTTTT
1 TCTTTT-TTTTTCTTTT
37193 TCTTTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 6 0.19
20 4 0.12
21 3 0.09
22 17 0.53
23 2 0.06
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.78
Consensus pattern (20 bp):
TCTTTTTTTTTCTTTTCTTC
Found at i:37208 original size:22 final size:21
Alignment explanation
Indices: 37147--37214 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
37137 TTTTCTTTTC
*
37147 TTTCTTCTTTTTTTTATTTCTT
1 TTTCTT-TTTTTTTTTTTTCTT
* * *
37169 TTCCTTCTCTTTTCTTTTTCTT
1 TTTCTT-TTTTTTTTTTTTCTT
* *
37191 TTTCTTTTTTTTCTTTTTATT
1 TTTCTTTTTTTTTTTTTTCTT
37212 TTT
1 TTT
37215 TTATTTGGGC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 16 0.41
22 23 0.59
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTCTTTTTTTTTTTTTTCTT
Found at i:37213 original size:15 final size:15
Alignment explanation
Indices: 37183--37216 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
37173 TTCTCTTTTC
*
37183 TTTTTCTTTTTCTTT
1 TTTTTCTTTTTATTT
37198 TTTTTCTTTTTATTT
1 TTTTTCTTTTTATTT
37213 TTTT
1 TTTT
37217 ATTTGGGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTCTTTTTATTT
Found at i:37215 original size:22 final size:22
Alignment explanation
Indices: 37142--37215 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 22
37132 TTGTCTTTTC
37142 TTTTCTTTCTTCTTT-TTTTTATTT
1 TTTTCTTT-TT-TTTCTTTTTA-TT
* *
37166 CTTTTCCTTCTCTTTTCTTTTT-CT
1 -TTTT-CTT-TTTTTTCTTTTTATT
37190 TTTTCTTTTTTTTCTTTTTATT
1 TTTTCTTTTTTTTCTTTTTATT
37212 TTTT
1 TTTT
37216 TATTTGGGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.27
22 8 0.20
23 4 0.10
24 1 0.02
25 7 0.17
26 9 0.22
27 1 0.02
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTCTTTTTTTTCTTTTTATT
Done.