Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018815.1 Corchorus olitorius cultivar O-4 contig18848, 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: 3343
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Found at i:87 original size:21 final size:22
Alignment explanation
Indices: 45--87 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
35 AAGGAAATTG
***
45 TGAAAATAAAAAAATCGTCTTT
1 TGAAAATAAAAAAATAAACTTT
67 TGAAAATAAAAAAA-AAACTTT
1 TGAAAATAAAAAAATAAACTTT
88 AAGAAAACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.28
Consensus pattern (22 bp):
TGAAAATAAAAAAATAAACTTT
Found at i:250 original size:22 final size:21
Alignment explanation
Indices: 210--250 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
200 AAGAAAAACA
**
210 TTTTTTTATTTTTTTATTATT
1 TTTTTTTATTTTTGAATTATT
231 TTTTATTTATTTTTGAATTA
1 TTTT-TTTATTTTTGAATTA
251 AACTAAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTTTTATTTTTGAATTATT
Found at i:1344 original size:10 final size:10
Alignment explanation
Indices: 1331--1355 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1321 CCACCACTGT
1331 CGGCCACCGC
1 CGGCCACCGC
1341 CGGCCACCGC
1 CGGCCACCGC
1351 CGGCC
1 CGGCC
1356 GCCGGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.60, G:0.32, T:0.00
Consensus pattern (10 bp):
CGGCCACCGC
Found at i:1650 original size:14 final size:13
Alignment explanation
Indices: 1628--1662 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
1618 CTACCCGAAA
1628 TTTTTTTTTTTTG
1 TTTTTTTTTTTTG
1641 TTTTTGTTTTTTTG
1 TTTTT-TTTTTTTG
1655 TTTTTTTT
1 TTTTTTTT
1663 GTTATTGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:1652 original size:17 final size:17
Alignment explanation
Indices: 1629--1665 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1619 TACCCGAAAT
*
1629 TTTTTTTTTTTGTTTTTG
1 TTTTTTTGTTT-TTTTTG
1647 TTTTTTTGTTTTTTTTG
1 TTTTTTTGTTTTTTTTG
1664 TT
1 TT
1666 ATTGTGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (17 bp):
TTTTTTTGTTTTTTTTG
Found at i:1662 original size:23 final size:22
Alignment explanation
Indices: 1628--1670 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1618 CTACCCGAAA
*
1628 TTTTTTTTTTTTGTTTTTGTTT
1 TTTTTTTTTTTTGTTATTGTTT
1650 TTTTGTTTTTTTTGTTATTGT
1 TTTT-TTTTTTTTGTTATTGT
1671 GTTGCTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (22 bp):
TTTTTTTTTTTTGTTATTGTTT
Found at i:1804 original size:12 final size:12
Alignment explanation
Indices: 1787--1811 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1777 CCTTTGTTTT
1787 TTGGGTTGAATG
1 TTGGGTTGAATG
1799 TTGGGTTGAATG
1 TTGGGTTGAATG
1811 T
1 T
1812 ATTTTTTTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.40, T:0.44
Consensus pattern (12 bp):
TTGGGTTGAATG
Found at i:1901 original size:14 final size:14
Alignment explanation
Indices: 1882--1910 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1872 TTTTTTGCTC
1882 TGTGGACCTTTTTT
1 TGTGGACCTTTTTT
1896 TGTGGACCTTTTTT
1 TGTGGACCTTTTTT
1910 T
1 T
1911 TTGACTGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.14, G:0.21, T:0.59
Consensus pattern (14 bp):
TGTGGACCTTTTTT
Found at i:2215 original size:3 final size:3
Alignment explanation
Indices: 2209--2327 Score: 193
Period size: 3 Copynumber: 38.3 Consensus size: 3
2199 TTTTTTTAAC
2209 ATA ATA ATA TATA ATA ATA ATA ATAA ATA ATA TATA TATA ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA -ATA -ATA ATA ATA ATA
2258 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
2306 ATA ATA ATA ATA ATA AGA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
2328 GACCCAAAAC
Statistics
Matches: 111, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
3 98 0.88
4 13 0.12
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2840 original size:1 final size:1
Alignment explanation
Indices: 2834--2908 Score: 69
Period size: 1 Copynumber: 75.0 Consensus size: 1
2824 TTCTTATAAA
* * * * * * * * *
2834 TTTTTTTCTGTTTTTTTTTGTTTTTTTTGTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTGTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2899 TTTTTTTTTT
1 TTTTTTTTTT
2909 GGAAGATCAG
Statistics
Matches: 56, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.00, C:0.01, G:0.11, T:0.88
Consensus pattern (1 bp):
T
Found at i:2857 original size:8 final size:8
Alignment explanation
Indices: 2846--2908 Score: 92
Period size: 9 Copynumber: 7.6 Consensus size: 8
2836 TTTTTCTGTT
2846 TTTTTTTG
1 TTTTTTTG
2854 TTTTTTTTG
1 -TTTTTTTG
2863 TTTTTTTTG
1 -TTTTTTTG
2872 TTTTTTTG
1 TTTTTTTG
2880 TTTTTTTG
1 TTTTTTTG
2888 TTTTTGTTG
1 TTTTT-TTG
2897 TTTTTTT-
1 TTTTTTTG
2904 TTTTT
1 TTTTT
2909 GGAAGATCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
7 5 0.09
8 23 0.43
9 25 0.47
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTTTTG
Found at i:2866 original size:17 final size:17
Alignment explanation
Indices: 2835--2908 Score: 98
Period size: 18 Copynumber: 4.2 Consensus size: 17
2825 TCTTATAAAT
2835 TTTTTTCTGTTTTTTTTTG
1 TTTTTT-TG-TTTTTTTTG
2854 TTTTTTTTGTTTTTTTTG
1 -TTTTTTTGTTTTTTTTG
2872 TTTTTTTG-TTTTTTTG
1 TTTTTTTGTTTTTTTTG
2888 TTTTTGTTGTTTTTTTT-
1 TTTTT-TTGTTTTTTTTG
2905 TTTT
1 TTTT
2909 GGAAGATCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
16 13 0.25
17 15 0.29
18 16 0.31
19 2 0.04
20 6 0.12
ACGTcount: A:0.00, C:0.01, G:0.11, T:0.88
Consensus pattern (17 bp):
TTTTTTTGTTTTTTTTG
Found at i:2883 original size:25 final size:27
Alignment explanation
Indices: 2834--2902 Score: 88
Period size: 25 Copynumber: 2.6 Consensus size: 27
2824 TTCTTATAAA
*
2834 TTTTTTTCTGTTTTTTTTTGTTTTTTTTG
1 TTTTTTT-TGTTTTTTGTTG-TTTTTTTG
2863 TTTTTTTTG-TTTTT-TTGTTTTTTTG
1 TTTTTTTTGTTTTTTGTTGTTTTTTTG
*
2888 TTTTTGTTGTTTTTT
1 TTTTTTTTGTTTTTT
2903 TTTTTTGGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
25 16 0.42
26 8 0.21
27 5 0.13
28 2 0.05
29 7 0.18
ACGTcount: A:0.00, C:0.01, G:0.12, T:0.87
Consensus pattern (27 bp):
TTTTTTTTGTTTTTTGTTGTTTTTTTG
Found at i:3086 original size:43 final size:43
Alignment explanation
Indices: 2932--3094 Score: 120
Period size: 43 Copynumber: 3.8 Consensus size: 43
2922 AGATCTTTGA
* * * * **
2932 AAGATAATTCGAAGATCAGCCTAGATCTCC-GAATATTATTAA-
1 AAGACAATTCGAAGATCAACATAGAT-TCCTGAAAATTAACAAG
* * * * * *
2974 AATGACAACTCGAAGATCATCGTAGA-CCTCTGAAAGTTGACAAG
1 AA-GACAATTCGAAGATCAACATAGATTC-CTGAAAATTAACAAG
*
3018 AAGACAATTCGCAGATCAACATAGATCTCC-GAAAATTAACAAG
1 AAGACAATTCGAAGATCAACATAGAT-TCCTGAAAATTAACAAG
*
3061 AAGACGATTC-AAGAATCAACATAGATTCCTGAAA
1 AAGACAATTCGAAG-ATCAACATAGATTCCTGAAA
3095 TTGAATGAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 15
0.73 0.15 0.12
Matches are distributed among these distances:
41 1 0.01
42 8 0.09
43 81 0.86
44 3 0.03
45 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (43 bp):
AAGACAATTCGAAGATCAACATAGATTCCTGAAAATTAACAAG
Found at i:3208 original size:53 final size:53
Alignment explanation
Indices: 3092--3214 Score: 140
Period size: 53 Copynumber: 2.3 Consensus size: 53
3082 TAGATTCCTG
* * * * **
3092 AAATTGAA-TGAAAGGCCGCCCAGGACCATCAGAAAATCAGCTTAGATTTTTGA
1 AAATT-AATTGAAAGGTCACCCAAGACCATCAGAAAATCAGCTTAGATCTACGA
* * *
3145 AAATTTATTGAAAGGTCACCCAAGACCATCAGAAAATCAGTTTAGATCTACGT
1 AAATTAATTGAAAGGTCACCCAAGACCATCAGAAAATCAGCTTAGATCTACGA
*
3198 ATATTAATTGAAAGGTC
1 AAATTAATTGAAAGGTC
3215 GAACTTGAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
52 1 0.02
53 57 0.98
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (53 bp):
AAATTAATTGAAAGGTCACCCAAGACCATCAGAAAATCAGCTTAGATCTACGA
Done.