Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009678.1 Corchorus olitorius cultivar O-4 contig09710, 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: 4522
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Found at i:1523 original size:22 final size:21
Alignment explanation
Indices: 1498--1538 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1488 CTATTTCAAG
*
1498 AACCTTTTTATAAAAATTTTTA
1 AACCTTCTTAT-AAAATTTTTA
*
1520 AACCTTCTTATGAAATTTT
1 AACCTTCTTATAAAATTTT
1539 GTTAATCTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (21 bp):
AACCTTCTTATAAAATTTTTA
Found at i:1721 original size:22 final size:22
Alignment explanation
Indices: 1696--1935 Score: 98
Period size: 22 Copynumber: 11.1 Consensus size: 22
1686 GAATTGTTAG
*
1696 TAATTACACTCTGAAATTTTGA
1 TAATTACACTATGAAATTTTGA
* *
1718 TAATCACACTATGAAATTGTGA
1 TAATTACACTATGAAATTTTGA
* *
1740 TAACCT-CGCTATGAAATTTTGA
1 TAA-TTACACTATGAAATTTTGA
*
1762 TAAACCTT-C-CTATAAAATTTTGA
1 T-AA--TTACACTATGAAATTTTGA
* *
1785 TAAATCT-CCCTATAAAATTTTGA
1 T-AAT-TACACTATGAAATTTTGA
*
1808 TAATCT-C-CTTATGAAATCTTG-
1 TAAT-TACAC-TATGAAATTTTGA
*
1829 --A-TA-ACTA-CAAATTTTGA
1 TAATTACACTATGAAATTTTGA
* * *
1846 TAACCT-CATTATGAAATTTTGT
1 TAA-TTACACTATGAAATTTTGA
*
1868 TAATCT-CCCTATGAAATTTTGA
1 TAAT-TACACTATGAAATTTTGA
*
1890 T--CTACATACTATGAAATTTTGA
1 TAATTAC--ACTATGAAATTTTGA
* * *
1912 AAACTAAACTATGAAATTTTGA
1 TAATTACACTATGAAATTTTGA
1934 TA
1 TA
1936 TCCTGCCTGA
Statistics
Matches: 172, Mismatches: 25, Indels: 42
0.72 0.10 0.18
Matches are distributed among these distances:
16 7 0.04
17 3 0.02
18 1 0.01
19 3 0.02
20 1 0.01
21 6 0.03
22 111 0.65
23 34 0.20
24 6 0.03
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
TAATTACACTATGAAATTTTGA
Found at i:1755 original size:44 final size:44
Alignment explanation
Indices: 1707--1935 Score: 163
Period size: 44 Copynumber: 5.3 Consensus size: 44
1697 AATTACACTC
* * *
1707 TGAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAATCTCCCTA
* * *
1751 TGAAATTTTGATAAAC-CTTCCTATAAAATTTTGATAAATCTCCCTA
1 TGAAATTTTGATAATCAC--ACTATGAAATTTTGAT-AATCTCCCTA
* * *
1797 TAAAATTTTGATAATCTC-CTTATGAAATCTTGATAA-----CTA
1 TGAAATTTTGATAATCACAC-TATGAAATTTTGATAATCTCCCTA
* * * * *
1836 -CAAATTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAATCTCCCTA
* * * **
1879 TGAAATTTTGAT-CTACATACTATGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAAT-CACACTATGAAATTTTGATAATCT-CCCTA
1923 TGAAATTTTGATA
1 TGAAATTTTGATA
1936 TCCTGCCTGA
Statistics
Matches: 145, Mismatches: 25, Indels: 29
0.73 0.13 0.15
Matches are distributed among these distances:
38 29 0.20
39 3 0.02
43 8 0.06
44 57 0.39
45 25 0.17
46 22 0.15
47 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (44 bp):
TGAAATTTTGATAATCACACTATGAAATTTTGATAATCTCCCTA
Found at i:1774 original size:23 final size:23
Alignment explanation
Indices: 1726--1956 Score: 106
Period size: 22 Copynumber: 10.7 Consensus size: 23
1716 GATAATCACA
*
1726 CTATGAAATTGTGAT-AACC-TC
1 CTATGAAATTTTGATAAACCTTC
1747 GCTATGAAATTTTGATAAACCTTC
1 -CTATGAAATTTTGATAAACCTTC
* * *
1771 CTATAAAATTTTGATAAATCTCC
1 CTATGAAATTTTGATAAACCTTC
* *
1794 CTATAAAATTTTGAT-AATC-TC
1 CTATGAAATTTTGATAAACCTTC
*
1815 CTTATGAAATCTTGAT-AA-----
1 C-TATGAAATTTTGATAAACCTTC
*
1833 CTA-CAAATTTTGATA-ACC-TC
1 CTATGAAATTTTGATAAACCTTC
* * * *
1853 ATTATGAAATTTTG-TTAATCTCC
1 -CTATGAAATTTTGATAAACCTTC
** * *
1876 CTATGAAATTTTGATCTA-CATA
1 CTATGAAATTTTGATAAACCTTC
**
1898 CTATGAAATTTTGA-AAA-CTAAA
1 CTATGAAATTTTGATAAACCT-TC
* *
1920 CTATGAAATTTTGAT-ATCCTGC
1 CTATGAAATTTTGATAAACCTTC
1942 C--TGAAATTTTGATAA
1 CTATGAAATTTTGATAA
1957 CTCCATAATA
Statistics
Matches: 165, Mismatches: 27, Indels: 35
0.73 0.12 0.15
Matches are distributed among these distances:
16 10 0.06
17 2 0.01
18 1 0.01
20 12 0.07
21 8 0.05
22 86 0.52
23 44 0.27
24 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (23 bp):
CTATGAAATTTTGATAAACCTTC
Found at i:1872 original size:60 final size:61
Alignment explanation
Indices: 1776--1890 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 61
1766 CCTTCCTATA
* * *
1776 AAATTTTGATAAATCTCCCTATAAAATTTTGATAATCTCCTTATGAAATCTTGATAACTAC
1 AAATTTTGATAAACCTCACTATAAAATTTTGATAATCTCCCTATGAAATCTTGATAACTAC
* * * *
1837 AAATTTTGAT-AACCTCATTATGAAATTTTGTTAATCTCCCTATGAAATTTTGAT
1 AAATTTTGATAAACCTCACTATAAAATTTTGATAATCTCCCTATGAAATCTTGAT
1891 CTACATACTA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
60 37 0.79
61 10 0.21
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (61 bp):
AAATTTTGATAAACCTCACTATAAAATTTTGATAATCTCCCTATGAAATCTTGATAACTAC
Found at i:1903 original size:82 final size:84
Alignment explanation
Indices: 1753--1917 Score: 196
Period size: 82 Copynumber: 2.0 Consensus size: 84
1743 CCTCGCTATG
*
1753 AAATTTTGATAAACCTTCCTATAAAATTTTGATAAATCTCCCTATAAAATTTTGATAATCTCCTT
1 AAATTTTGATAAACCTTCCTATAAAATTTTGATAAATCTCCCTATAAAATTTTGATAATCTACTT
*
1818 ATGAAATCTTGATAACTAC
66 ATGAAATCTTGAAAACTAC
* * * * *
1837 AAATTTTGAT-AACC-TCATTATGAAATTTTG-TTAATCTCCCTATGAAATTTTGAT-CTACATA
1 AAATTTTGATAAACCTTC-CTATAAAATTTTGATAAATCTCCCTATAAAATTTTGATAAT-C-TA
*
1898 C-TATGAAATTTTGAAAACTA
63 CTTATGAAATCTTGAAAACTA
1918 AACTATGAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
81 1 0.01
82 42 0.60
83 17 0.24
84 10 0.14
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (84 bp):
AAATTTTGATAAACCTTCCTATAAAATTTTGATAAATCTCCCTATAAAATTTTGATAATCTACTT
ATGAAATCTTGAAAACTAC
Found at i:2127 original size:22 final size:22
Alignment explanation
Indices: 2036--2205 Score: 98
Period size: 22 Copynumber: 7.8 Consensus size: 22
2026 AAAACACCAC
*
2036 TATGAAATTTTGGTAATCACAT
1 TATGAAATTTTGATAATCACAT
* * * * *
2058 TTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCACAT
* * *
2080 TATGAAATTTTAATAAACTC-T
1 TATGAAATTTTGATAATCACAT
*
2101 CTATGAAATTTTGATGATCACAT
1 -TATGAAATTTTGATAATCACAT
* *** *
2124 TATGTAATTAAAATAACCTCGC-T
1 TATGAAATTTTGATAA--TCACAT
* *
2147 T-TGAAATTTTGATAATAACAC
1 TATGAAATTTTGATAATCACAT
* *
2168 TATAAAATTTTGATAATCTTC-T
1 TATGAAATTTTGATAATC-ACAT
2190 TAT-AAATTTTGATAAT
1 TATGAAATTTTGATAAT
2206 TTGATCTTTA
Statistics
Matches: 110, Mismatches: 31, Indels: 15
0.71 0.20 0.10
Matches are distributed among these distances:
20 2 0.02
21 15 0.14
22 86 0.78
23 4 0.04
24 3 0.03
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAT
Found at i:2127 original size:44 final size:44
Alignment explanation
Indices: 2079--2205 Score: 123
Period size: 44 Copynumber: 2.9 Consensus size: 44
2069 GATAACCTCT
* *
2079 TTATGAAATTTTAATAAACTCTCTATGAAATTTTGATGATCACA
1 TTATGAAATTTTAATAAACTCTCTATGAAATTTTGATAATAACA
* ** * * *
2123 TTATGTAATTAAAATAACCTCGCTTTGAAATTTTGATAATAACA
1 TTATGAAATTTTAATAAACTCTCTATGAAATTTTGATAATAACA
* * * *
2167 CTATAAAATTTTGATAATCT-TCTTAT-AAATTTTGATAAT
1 TTATGAAATTTTAATAAACTCTC-TATGAAATTTTGATAAT
2206 TTGATCTTTA
Statistics
Matches: 65, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
43 14 0.22
44 51 0.78
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (44 bp):
TTATGAAATTTTAATAAACTCTCTATGAAATTTTGATAATAACA
Found at i:2141 original size:66 final size:66
Alignment explanation
Indices: 2035--2185 Score: 155
Period size: 66 Copynumber: 2.3 Consensus size: 66
2025 AAAAACACCA
* * ** *
2035 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTC-TTTATGAAATTTTAATAAACT
1 CTATGAAATTTTGATAATCACATTATGAAAATTAAATAACCTCGCTT-TGAAATTTTAATAAACT
2099 CT
65 CT
* * *
2101 CTATGAAATTTTGATGATCACATTATG-TAATTAAAATAACCTCGCTTTGAAATTTTGATAATA-
1 CTATGAAATTTTGATAATCACATTATGAAAATT-AAATAACCTCGCTTTGAAATTTTAATAA-AC
* *
2164 ACA
64 TCT
*
2167 CTATAAAATTTTGATAATC
1 CTATGAAATTTTGATAATC
2186 TTCTTATAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
65 4 0.06
66 63 0.90
67 3 0.04
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (66 bp):
CTATGAAATTTTGATAATCACATTATGAAAATTAAATAACCTCGCTTTGAAATTTTAATAAACTC
T
Found at i:2265 original size:20 final size:21
Alignment explanation
Indices: 2219--2265 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
2209 ATCTTTATGA
* *
2219 AAATTCGATAACCACTCTATG
1 AAATTTGATAACCACTCTATC
* *
2240 AGATTTGATAACC-TTCTATC
1 AAATTTGATAACCACTCTATC
2260 AAATTT
1 AAATTT
2266 TAGTACTCCT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (21 bp):
AAATTTGATAACCACTCTATC
Found at i:3695 original size:540 final size:538
Alignment explanation
Indices: 2618--3698 Score: 1699
Period size: 540 Copynumber: 2.0 Consensus size: 538
2608 TAGGCTCGTT
2618 TGAGTCCACGAAATCCAAATAGTCGTCAGATGTTTTGAAGTCTAAATCTGATATTCTTAGACCCA
1 TGAGTCCACGAAATCCAAATAGTCGTCAGATGTTTTGAAGTCTAAATCTGATATTCTTAGACCCA
* * *
2683 ATTCGTTAATATGGAAGCCAAAAGAATGAATCCAAGTCCAATCAGTAATTATGATGAAATAATGA
66 ATTCGTTAATATGAAAGCCAAAAGAAGGAATCCAAATCCAATCAGTAATTATGATGAAATAATGA
2748 TTCAGTCCTGATGCAGCATTGTTAAATCCTATTTAAAGAAGGACTTCACAAGAGCAGCTCTGGAA
131 TTCAGTCCTGATGCAGCATTGTTAAATCCTATTTAAAGAAGGACTTCACAAGAGCAGCTCTGGAA
* * * *
2813 GAAATTTCATAACTTTTAAATTCAGAGCTCAGAAAAATGCAAATGAGGTACCGTTAGAAAGAGGA
196 GAAAATTCATAACTTTTAAATCCAGAACTCAAAAAAATGCAAATGAGGTACCGTTAGAAAGAGGA
* ** *
2878 TTCCAAGATCTACAGCTTTTATGTTTATCTCGAGATTTAATTCTACCATTTCGGTGGACGATTTT
261 TTCCAAGATCTACAACTTTTATGTTTATCTCGAGACCTAATTATACCATTTCGGTGGACGATTTT
* * *
2943 ACCCTTGAAATTTCTGGACAGAATTGATCTTCTCCTAAACCGACTTTGAGAATGTTTTAGACGAA
326 ACCCTTAAAATTTCTGGACAGAATTGATCTTCTCCTAAACCGACTTGGAGAATATTTTAGACGAA
*
3008 AAATTCAGATGCTAAAAATGATGTGGGGCATCTCTATTGGCCACGTTGGATTCTAATTAATGAGG
391 AAATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGGCCACGTTGGATTCTAATTAATGAGG
3073 ATAATCTAAATTGCCATTATTTTAATAGTGGAATAATTAAAATATTATTTAATAATGGCAATTTA
456 ATAATCTAAATTGCCATTATTTTAATAGTGGAATAATTAAAATATTATTTAATAATGGCAATTTA
3138 GAAATATATTTAAAAAAA
521 GAAATATATTTAAAAAAA
* * *
3156 TGAGTCCATGAAGTCCAAATTGTCAAGTCAGAT-TTATTGAAGTCTAAATCTGATATTCTTAGAC
1 TGAGTCCACGAAATCCAAATAGTC--GTCAGATGTT-TTGAAGTCTAAATCTGATATTCTTAGAC
* * * *
3220 CCAATTCGTTAATATGAAAGCCCAAAGAAGGAGTCCAAATCCAATCAGTAATTATGATGCAGTAA
63 CCAATTCGTTAATATGAAAGCCAAAAGAAGGAATCCAAATCCAATCAGTAATTATGATGAAATAA
* * *
3285 TGATTCAG-CACTGATGCAGCATTGTTAAATCCTATTTAAA-ATATGACTTCACAAGAGCAGTTT
128 TGATTCAGTC-CTGATGCAGCATTGTTAAATCCTATTTAAAGA-AGGACTTCACAAGAGCAGCTC
* *
3348 TGGAAGAAAATTCATAACTTTT-GATCCAGAACTCAAAAAAATGCAAATGAGGTACCGTTTGAAA
191 TGGAAGAAAATTCATAACTTTTAAATCCAGAACTCAAAAAAATGCAAATGAGGTACCGTTAGAAA
* *
3412 GAGGATTCCGAA-ATCTACAACTTTTATGTTTATCTCGAGACCTAATTATGCCGTTTCGGTGGAC
256 GAGGATTCC-AAGATCTACAACTTTTATGTTTATCTCGAGACCTAATTATACCATTTCGGTGGAC
*
3476 GATTTTGCCCTTAAAATTTCTGGACAGAATTGATCTTCTCCTAAACCGACTTGGAGAATATTTT-
320 GATTTTACCCTTAAAATTTCTGGACAGAATTGATCTTCTCCTAAACCGACTTGGAGAATATTTTA
* * *
3540 GCACG-AAAATTCAGATGTTAAAGATGATGTGGGGCATCCCTATTGGCCATGTTGGATTCTAATT
385 G-ACGAAAAATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGGCCACGTTGGATTCTAATT
* ** *
3604 AATGAGGATAATCTAAATTTCCATTATTTTAATCTTGGAGTAATTAAAATATTATTTAATAATGG
449 AATGAGGATAATCTAAATTGCCATTATTTTAATAGTGGAATAATTAAAATATTATTTAATAATGG
3669 CAATTTAGAAATATATTTGGAAAAAAA
514 CAATTTAGAAATATATTT--AAAAAAA
3696 TGA
1 TGA
3699 TACAATTGGA
Statistics
Matches: 497, Mismatches: 37, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
538 156 0.31
539 159 0.32
540 182 0.37
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (538 bp):
TGAGTCCACGAAATCCAAATAGTCGTCAGATGTTTTGAAGTCTAAATCTGATATTCTTAGACCCA
ATTCGTTAATATGAAAGCCAAAAGAAGGAATCCAAATCCAATCAGTAATTATGATGAAATAATGA
TTCAGTCCTGATGCAGCATTGTTAAATCCTATTTAAAGAAGGACTTCACAAGAGCAGCTCTGGAA
GAAAATTCATAACTTTTAAATCCAGAACTCAAAAAAATGCAAATGAGGTACCGTTAGAAAGAGGA
TTCCAAGATCTACAACTTTTATGTTTATCTCGAGACCTAATTATACCATTTCGGTGGACGATTTT
ACCCTTAAAATTTCTGGACAGAATTGATCTTCTCCTAAACCGACTTGGAGAATATTTTAGACGAA
AAATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGGCCACGTTGGATTCTAATTAATGAGG
ATAATCTAAATTGCCATTATTTTAATAGTGGAATAATTAAAATATTATTTAATAATGGCAATTTA
GAAATATATTTAAAAAAA
Found at i:3828 original size:121 final size:122
Alignment explanation
Indices: 3614--3856 Score: 407
Period size: 121 Copynumber: 2.0 Consensus size: 122
3604 AATGAGGATA
* * *
3614 ATCTAAATTTCCATTATTTTAATCTTGGAGTAATTAAAATATTATTTAATAATGGCAATTTAGAA
1 ATCTAAATTTCCATTATTTTAATATTGGAATAATTAAAATATTATTTAATAATGACAATTTAGAA
* *
3679 ATATATTTGGAAAAAAATGATACAATTGGAAAACATAAAGTTT-CCCTTCTTCGTAC
66 ATATATTTGGAAAAAAATGATACAATTGGAAAACATAAAATTTCCCCTTATTCGTAC
* *
3735 ATCTAAATTTCCATTATTTTAATATTTGAATAATTAAAATATTATTTAATAATGATAATTTAGAA
1 ATCTAAATTTCCATTATTTTAATATTGGAATAATTAAAATATTATTTAATAATGACAATTTAGAA
*
3800 ATATATTTGGAAAAAAATGGTACAATTGGAAAACATAAAATTTCCCCTTATTCGTAC
66 ATATATTTGGAAAAAAATGATACAATTGGAAAACATAAAATTTCCCCTTATTCGTAC
3857 TTTTATATAT
Statistics
Matches: 113, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
121 101 0.89
122 12 0.11
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (122 bp):
ATCTAAATTTCCATTATTTTAATATTGGAATAATTAAAATATTATTTAATAATGACAATTTAGAA
ATATATTTGGAAAAAAATGATACAATTGGAAAACATAAAATTTCCCCTTATTCGTAC
Found at i:4478 original size:25 final size:24
Alignment explanation
Indices: 4450--4511 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
4440 GTGGATTGTA
*
4450 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
4475 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
*
4499 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
4512 CTGACCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 9 0.26
24 8 0.24
25 17 0.50
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Done.