Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022033.1 Corchorus olitorius cultivar O-4 contig22066, 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: 14168
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2160 original size:31 final size:32
Alignment explanation
Indices: 2125--2205 Score: 110
Period size: 32 Copynumber: 2.6 Consensus size: 32
2115 CCTATCTGAT
**
2125 TATATCCTTAATTGCTTGAAAT-CGAAAACAA
1 TATATCCTTAATTGCTTGAAATAAAAAAACAA
* **
2156 TATATCCTTAATTGCGTGAAATAAAAAAACGT
1 TATATCCTTAATTGCTTGAAATAAAAAAACAA
2188 TATATCCTTAATTGCTTG
1 TATATCCTTAATTGCTTG
2206 CTTTGTAACG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 21 0.49
32 22 0.51
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (32 bp):
TATATCCTTAATTGCTTGAAATAAAAAAACAA
Found at i:2192 original size:32 final size:31
Alignment explanation
Indices: 2123--2202 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
2113 GCCCTATCTG
* **
2123 ATTATATCCTTAATTGCTTGAAATCGAAAAC
1 ATTATATCCTTAATTGCGTGAAATAAAAAAC
*
2154 AATATATCCTTAATTGCGTGAAATAAAAAAAC
1 ATTATATCCTTAATTGCGTGAAAT-AAAAAAC
*
2186 GTTATATCCTTAATTGC
1 ATTATATCCTTAATTGC
2203 TTGCTTTGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 22 0.52
32 20 0.48
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (31 bp):
ATTATATCCTTAATTGCGTGAAATAAAAAAC
Found at i:2332 original size:19 final size:19
Alignment explanation
Indices: 2302--2339 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
2292 AAAAAGAAAA
2302 ATAATTTGAATA-TTATTT
1 ATAATTTGAATATTTATTT
2320 ATAATTATGAATATTTATTT
1 ATAATT-TGAATATTTATTT
2340 TGATTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
ATAATTTGAATATTTATTT
Found at i:2970 original size:31 final size:31
Alignment explanation
Indices: 2892--2971 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
2882 TTTGCTGCCG
* *
2892 CAAGCAATTAAGGATACAACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCAATTT
* *
2923 TAAGAAATTAAGGATATAACGTTTTCAATTT
1 CAAGCAATTAAGGATATAACGTTTTCAATTT
2954 CAAGCAATTAAGGATATA
1 CAAGCAATTAAGGATATA
2972 GTCAATTAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCAATTT
Found at i:3114 original size:19 final size:19
Alignment explanation
Indices: 3090--3129 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3080 ATATCCTTAA
3090 TTGCTCGTTTTTCGTAACG
1 TTGCTCGTTTTTCGTAACG
3109 TTGCTCGTTTTTCGTAACG
1 TTGCTCGTTTTTCGTAACG
3128 TT
1 TT
3130 ATATCCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.50
Consensus pattern (19 bp):
TTGCTCGTTTTTCGTAACG
Found at i:4644 original size:18 final size:18
Alignment explanation
Indices: 4621--4705 Score: 77
Period size: 18 Copynumber: 4.9 Consensus size: 18
4611 TTGCTAGTGT
*
4621 AGGTGGTGGTGGTGGCGG
1 AGGTGGAGGTGGTGGCGG
**
4639 AGGTGGCCGTGGT---GG
1 AGGTGGAGGTGGTGGCGG
4654 AGGTGGAGGTGGTGGCGG
1 AGGTGGAGGTGGTGGCGG
* * *
4672 AGGTGGGGGTCGTGGTGG
1 AGGTGGAGGTGGTGGCGG
* *
4690 AGGGGGAGGAGGTGGC
1 AGGTGGAGGTGGTGGC
4706 AGTAGTTCAC
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
15 13 0.25
18 39 0.75
ACGTcount: A:0.09, C:0.07, G:0.66, T:0.18
Consensus pattern (18 bp):
AGGTGGAGGTGGTGGCGG
Found at i:4652 original size:21 final size:21
Alignment explanation
Indices: 4626--4665 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4616 AGTGTAGGTG
*
4626 GTGGTGGTGGCGGAGGTGGCC
1 GTGGTGGAGGCGGAGGTGGCC
*
4647 GTGGTGGAGGTGGAGGTGG
1 GTGGTGGAGGCGGAGGTGG
4666 TGGCGGAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.65, T:0.20
Consensus pattern (21 bp):
GTGGTGGAGGCGGAGGTGGCC
Found at i:4665 original size:15 final size:15
Alignment explanation
Indices: 4625--4668 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4615 TAGTGTAGGT
* *
4625 GGTGGTGGTGGCGGA
1 GGTGGAGGTGGTGGA
**
4640 GGTGGCCGTGGTGGA
1 GGTGGAGGTGGTGGA
4655 GGTGGAGGTGGTGG
1 GGTGGAGGTGGTGG
4669 CGGAGGTGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.07, C:0.07, G:0.66, T:0.20
Consensus pattern (15 bp):
GGTGGAGGTGGTGGA
Found at i:6955 original size:24 final size:24
Alignment explanation
Indices: 6880--6961 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
6870 CATGCGCAGT
*
6880 GGTGGAGGAAGAGGTATTGGTAGA
1 GGTGGAGGAAGAGGTCTTGGTAGA
* * * * *
6904 GGTGGCAGTGAGGAAGACGTGGCAGTAGT
1 GGTGG-AG-GAAGAGGTC-TTG--GTAGA
6933 GGTGGAGGAAGAGGTCTTGGTAGA
1 GGTGGAGGAAGAGGTCTTGGTAGA
6957 GGTGG
1 GGTGG
6962 CAACGCTGCC
Statistics
Matches: 42, Mismatches: 11, Indels: 10
0.67 0.17 0.16
Matches are distributed among these distances:
24 14 0.33
25 2 0.05
26 7 0.17
27 8 0.19
28 2 0.05
29 9 0.21
ACGTcount: A:0.24, C:0.05, G:0.51, T:0.20
Consensus pattern (24 bp):
GGTGGAGGAAGAGGTCTTGGTAGA
Found at i:8435 original size:11 final size:11
Alignment explanation
Indices: 8415--8449 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
8405 TTGACAGCGC
8415 AACAAAAACAA
1 AACAAAAACAA
*
8426 AACGAAAACAA
1 AACAAAAACAA
8437 AACAAAAACAA
1 AACAAAAACAA
8448 AA
1 AA
8450 AACTGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:11988 original size:20 final size:22
Alignment explanation
Indices: 11959--12016 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
11949 AAGGGATCAA
* *
11959 TTCCAAAGCTTCAAACA-C-GC
1 TTCCACAGCTACAAACACCAGC
*
11979 TTCCACAGCTACACACACCAGC
1 TTCCACAGCTACAAACACCAGC
*
12001 TTCTACAGCTACAAAC
1 TTCCACAGCTACAAAC
12017 TTGCTCCGCG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 14 0.45
21 1 0.03
22 16 0.52
ACGTcount: A:0.34, C:0.38, G:0.09, T:0.19
Consensus pattern (22 bp):
TTCCACAGCTACAAACACCAGC
Found at i:12075 original size:22 final size:23
Alignment explanation
Indices: 12044--12087 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
12034 TCAAGCTTTG
12044 TGCTTATTTCTCTCAAAGCTCCA
1 TGCTTATTTCTCTCAAAGCTCCA
* *
12067 TGCTT-TTTCTCTGAAATCTCC
1 TGCTTATTTCTCTCAAAGCTCC
12088 GCGATTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.18, C:0.30, G:0.09, T:0.43
Consensus pattern (23 bp):
TGCTTATTTCTCTCAAAGCTCCA
Done.