Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014481.1 Corchorus capsularis cultivar CVL-1 contig14502, 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: 55724
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1771 original size:22 final size:22
Alignment explanation
Indices: 1713--1777 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
1703 GAAGATCTCA
*
1713 ATATGAAATTTTGATAACCAAC
1 ATATGAAATATTGATAACCAAC
* * **
1735 ACTATGAGATGTTGATAACCTCC
1 A-TATGAAATATTGATAACCAAC
*
1758 ATATGATATATTGATAACCA
1 ATATGAAATATTGATAACCA
1778 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (22 bp):
ATATGAAATATTGATAACCAAC
Found at i:1834 original size:44 final size:43
Alignment explanation
Indices: 1713--1907 Score: 131
Period size: 44 Copynumber: 4.4 Consensus size: 43
1703 GAAGATCTCA
* * * * * *
1713 ATATGAAATTTTGATAACCAACACTATGAGATGTTGATAACCTCC
1 ATATGAAATTTTGATAATC-ACACTATAAAAT-TTAAAAACATCC
* * * **
1758 ATATGATATATTGATAACCACGTTATGAAAATTTAAAAACATCC
1 ATATGAAATTTTGATAATCACACTAT-AAAATTTAAAAACATCC
* * * *
1802 ATATGAAATTTTGATAATCACACTCGTGAAATTTTAATA-ATCAC
1 ATATGAAATTTTGATAATCACACT-ATAAAATTTAAAAACATC-C
* * * *
1846 ACTATGAAATTGTGATAATCTCGCTATAAAATTTGATAAACATCC
1 A-TATGAAATTTTGATAATCACACTATAAAATTT-AAAAACATCC
* *
1891 CTATAAAATTTTGATAA
1 ATATGAAATTTTGATAA
1908 CTTTCTTATG
Statistics
Matches: 115, Mismatches: 29, Indels: 13
0.73 0.18 0.08
Matches are distributed among these distances:
43 3 0.03
44 65 0.57
45 44 0.38
46 3 0.03
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (43 bp):
ATATGAAATTTTGATAATCACACTATAAAATTTAAAAACATCC
Found at i:1864 original size:22 final size:22
Alignment explanation
Indices: 1670--2076 Score: 119
Period size: 22 Copynumber: 18.7 Consensus size: 22
1660 TTTTTAACCT
* *
1670 TATGAAATTTTGTTAACCTAC-C
1 TATGAAATTTTGATAATC-ACAC
* * * *
1692 TAAGGAATTTTGA-AGATCTCAA
1 TATGAAATTTTGATA-ATCACAC
*
1714 TATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAATC-ACAC
* *
1737 TATGAGATGTTGATAACCTC-CA-
1 TATGAAATTTTGATAA--TCACAC
* * * **
1759 TATGATATATTGATAACCACGT
1 TATGAAATTTTGATAATCACAC
* * *
1781 TATGAAAATTT-AAAAACATC-C
1 TATGAAATTTTGATAATCA-CAC
1802 ATATGAAATTTTGATAATCACAC
1 -TATGAAATTTTGATAATCACAC
* *
1825 TCGTGAAATTTTAATAATCACAC
1 T-ATGAAATTTTGATAATCACAC
* * *
1848 TATGAAATTGTGATAATCTCGC
1 TATGAAATTTTGATAATCACAC
* * *
1870 TAT-AAAATTTGATAAACATCCC
1 TATGAAATTTTGATAATCA-CAC
* ** *
1892 TATAAAATTTTGATAACTTTC-T
1 TATGAAATTTTGATAA-TCACAC
*
1914 TATGAAATCTTG---AT-A-AC
1 TATGAAATTTTGATAATCACAC
* * * *
1931 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAATCACAC
* ** * * * *
1952 AATGATTTTTTCATAACCTCAT
1 TATGAAATTTTGATAATCACAC
* * *
1974 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAATCACAC
* * *
1996 TATAAAATTTTGAT-CTGCATAC
1 TATGAAATTTTGATAAT-CACAC
* *
2018 TATGAAATTTTGATAA-CCCTC
1 TATGAAATTTTGATAATCACAC
* *
2039 TTATGAAATTTTGA-AAACTAAAC
1 -TATGAAATTTTGATAATC-ACAC
2062 TATGAAATTTTGATA
1 TATGAAATTTTGATA
2077 TCCTCCCTGA
Statistics
Matches: 274, Mismatches: 82, Indels: 57
0.66 0.20 0.14
Matches are distributed among these distances:
16 7 0.03
17 2 0.01
18 1 0.00
19 2 0.01
20 1 0.00
21 26 0.09
22 175 0.64
23 59 0.22
25 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAC
Found at i:2276 original size:22 final size:22
Alignment explanation
Indices: 2181--2526 Score: 91
Period size: 22 Copynumber: 16.0 Consensus size: 22
2171 GAAATACCAC
*
2181 TATGAAATTTTTG-TAATCACAT
1 TATGAAA-TTTTGATAACCACAT
* * * *
2203 TTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCACAT
* *
2225 TATGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAACCACAT
** * *
2247 TACAAAATTTTGTTAACCACAC
1 TATGAAATTTTGATAACCACAT
* **
2269 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCACAT
* * *
2291 TATGACATTTTGATAATCTC-T
1 TATGAAATTTTGATAACCACAT
*
2312 T-TGATAACCTCTCT-ATAA--A-AT
1 TATGA-AA--T-TTTGATAACCACAT
* *
2333 TGTGAAA--AT--TAACCACCA-
1 TATGAAATTTTGATAACCA-CAT
** *
2351 TATGAAATTTCAATAACCA-ACC
1 TATGAAATTTTGATAACCACA-T
* * **
2373 TAAGAAATTTTAATAACCTGAT
1 TATGAAATTTTGATAACCACAT
* *
2395 CCTATGAAATTTTGGTAACCACAC
1 --TATGAAATTTTGATAACCACAT
2419 TATGAAATTTTGAT-ACTTC-CA-
1 TATGAAATTTTGATAAC--CACAT
** *
2440 TAT-AAATTTTGGCAACCACAC
1 TATGAAATTTTGATAACCACAT
* * *
2461 TATGGAATTTTGATAACCTCCT
1 TATGAAATTTTGATAACCACAT
* * *
2483 CATGAAATTATAATAACCATC-T
1 TATGAAATTTTGATAACCA-CAT
*
2505 TAAGAAATTTTGATAACCACAT
1 TATGAAATTTTGATAACCACAT
2527 AGAGACAAGA
Statistics
Matches: 238, Mismatches: 56, Indels: 60
0.67 0.16 0.17
Matches are distributed among these distances:
15 3 0.01
16 1 0.00
17 1 0.00
18 6 0.03
19 2 0.01
20 14 0.06
21 23 0.10
22 160 0.67
23 10 0.04
24 18 0.08
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAT
Found at i:2720 original size:19 final size:20
Alignment explanation
Indices: 2689--2726 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2679 TATTGACATT
2689 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
2708 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
2727 ACTAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:7971 original size:2 final size:2
Alignment explanation
Indices: 7952--7991 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
7942 CCTAGTACAC
*
7952 TA TA CA TA TA TA -A T- TA TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7991 T
1 T
7992 TAATTTTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:10857 original size:104 final size:103
Alignment explanation
Indices: 10668--10963 Score: 434
Period size: 104 Copynumber: 2.9 Consensus size: 103
10658 TTTTGTTTTA
*
10668 TAAAATCCTAGAAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTTTTATATAATTT
1 TAAAACCCTAG-AATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTTTTATATAATTT
*
10733 GGGACTAAACCTAAATGATTTGGGGCTCAACTAAAATTC
65 GGGGCTAAACCTAAATGATTTGGGGCTCAACTAAAATTC
* *
10772 TAAAACCCTAGAATAAATATTTTAAATTCAAGGCATACCCTTAAAATATTTTTTTTATAGAATTT
1 TAAAACCCTAGAATAAATATTTTAAATTCAAGACATACCCTTAAAATA-TTTTTTTATATAATTT
* * * * *
10837 GGGGCTAAATCTTAGTGATTTGAGACTCAACTAAAATTC
65 GGGGCTAAACCTAAATGATTTGGGGCTCAACTAAAATTC
* * *
10876 TAAAACCCTATAAATAAATATTTTAAATTCAAGACATACCATTAAAATA-TATTTTATATAATTT
1 TAAAACCCTA-GAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTTTTATATAATTT
*
10940 -GGGCTAAACCTAACTGATTTGGGG
65 GGGGCTAAACCTAAATGATTTGGGG
10964 TTAAACTTAG
Statistics
Matches: 171, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
102 19 0.11
103 49 0.29
104 68 0.40
105 35 0.20
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (103 bp):
TAAAACCCTAGAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTTTTATATAATTTG
GGGCTAAACCTAAATGATTTGGGGCTCAACTAAAATTC
Found at i:16342 original size:14 final size:14
Alignment explanation
Indices: 16322--16355 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
16312 CAAAAAAATC
16322 ATATATTACTATTAT
1 ATATATTA-TATTAT
16337 -TATATTATATTAT
1 ATATATTATATTAT
16350 ATATAT
1 ATATAT
16356 GTAATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATATTATATTAT
Found at i:16770 original size:2 final size:2
Alignment explanation
Indices: 16763--16802 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
16753 TAGCTATACC
*
16763 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16803 ATAATATCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:16803 original size:10 final size:11
Alignment explanation
Indices: 16763--16809 Score: 57
Period size: 10 Copynumber: 4.6 Consensus size: 11
16753 TAGCTATACC
16763 TATATATAT-A
1 TATATATATAA
16773 TATATATAT-A
1 TATATATATAA
*
16783 TATATAAATAA
1 TATATATATAA
16794 TATA-ATATAA
1 TATATATATAA
16804 TA-ATAT
1 TATATAT
16810 CAAAGCATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 1 0.03
10 27 0.82
11 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TATATATATAA
Found at i:26374 original size:91 final size:92
Alignment explanation
Indices: 26227--26510 Score: 435
Period size: 91 Copynumber: 3.0 Consensus size: 92
26217 AAAAAAAAAA
*
26227 CACAAACTTTCTATTCCAAAAAGATCAATAAGATCAAAATCATCCTTTTATCATGAACTCAACAT
1 CACAAACTTTCTATTCCAAAAAGATCAATAAGATCAAAATCACCCTTTTATCATGAACTCAACAT
*
26292 GAACACATGAA-CCTAACCAAAAAATT
66 GAACACATGAACCCTAACCCAAAAATT
26318 CACAAACTTTCTATTCCAAAAAGATCAATAAGATCAAAATCACCCTTTTATCATGAACTCAACAT
1 CACAAACTTTCTATTCCAAAAAGATCAATAAGATCAAAATCACCCTTTTATCATGAACTCAACAT
26383 GAACACATGAACCCTAACCCAAAAATT
66 GAACACATGAACCCTAACCCAAAAATT
26410 CACAAACTTTCTATTCCAAAAAGATCAATAAGATCAATAAGATCAAAATCACCCTTTTATCATGA
1 CACAAACTTTCTATTCC------A--AA-AAGATCAATAAGATCAAAATCACCCTTTTATCATGA
***
26475 AAAAAACATGAACACATGAACCCTAACCCAAAAATT
57 ACTCAACATGAACACATGAACCCTAACCCAAAAATT
26511 TCTAGTTCCG
Statistics
Matches: 178, Mismatches: 5, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
91 75 0.42
92 31 0.17
98 1 0.01
100 2 0.01
101 69 0.39
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (92 bp):
CACAAACTTTCTATTCCAAAAAGATCAATAAGATCAAAATCACCCTTTTATCATGAACTCAACAT
GAACACATGAACCCTAACCCAAAAATT
Found at i:26444 original size:9 final size:9
Alignment explanation
Indices: 26430--26455 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
26420 CTATTCCAAA
26430 AAGATCAAT
1 AAGATCAAT
26439 AAGATCAAT
1 AAGATCAAT
26448 AAGATCAA
1 AAGATCAA
26456 AATCACCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (9 bp):
AAGATCAAT
Found at i:52126 original size:38 final size:38
Alignment explanation
Indices: 52084--52274 Score: 301
Period size: 38 Copynumber: 5.0 Consensus size: 38
52074 GGCTGTGCAT
52084 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
* * *
52122 AGTGGACCCGCACCTCAGCGGGTTAAACTGCTGGTAAG
1 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
*
52160 AGTGGACCCGCACCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
* *
52198 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
* * *
52236 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGCAAG
1 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
52274 A
1 A
52275 TTGTGGTTGT
Statistics
Matches: 144, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 144 1.00
ACGTcount: A:0.24, C:0.21, G:0.35, T:0.20
Consensus pattern (38 bp):
AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
Found at i:54758 original size:2 final size:2
Alignment explanation
Indices: 54751--54785 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
54741 TATAGTACAT
*
54751 TA TA TA TA TA TA TA TA TA TA TC TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
54786 AAAGTACGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:55073 original size:109 final size:109
Alignment explanation
Indices: 54877--55172 Score: 432
Period size: 109 Copynumber: 2.7 Consensus size: 109
54867 ACTATTATAG
* * * *
54877 TTTTATTCTACTAGAAACTATATTTTTATTCAATTAAATTAAATCTAACATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
*
54942 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAAATTGGATATACTAAAATTTTTTCTAATATACAA
54991 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
55056 TTACCAAAAAAATTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAAATTGGATATACTAAAATTTTTTCTAATATACAA
* **
55100 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAA-TTACTTTA
55164 TTTTTACCA
63 TTTTTACCA
55173 TTTTAATTTA
Statistics
Matches: 170, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
108 1 0.01
109 124 0.73
110 8 0.05
111 17 0.10
114 20 0.12
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAAATTGGATATACTAAAATTTTTTCTAATATACAA
Done.