Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006979.1 Corchorus capsularis cultivar CVL-1 contig07000, 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: 55906
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1236 original size:11 final size:11
Alignment explanation
Indices: 1202--1237 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1192 ACCAAAAGCC
1202 AATAATAATCA
1 AATAATAATCA
1213 AATCAATAATCA
1 AAT-AATAATCA
*
1225 AATAAAAATCA
1 AATAATAATCA
1236 AA
1 AA
1238 CCATAAGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (11 bp):
AATAATAATCA
Found at i:1798 original size:7 final size:7
Alignment explanation
Indices: 1788--1835 Score: 64
Period size: 7 Copynumber: 7.0 Consensus size: 7
1778 AAAATCAGAT
1788 ATATATA
1 ATATATA
1795 ATATATA
1 ATATATA
1802 TATATATA
1 -ATATATA
1810 ATATA-A
1 ATATATA
1816 A-ATATA
1 ATATATA
*
1822 AAATATA
1 ATATATA
1829 ATATATA
1 ATATATA
1836 TTAATATTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
5 3 0.08
6 4 0.11
7 23 0.62
8 7 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATATATA
Found at i:19472 original size:108 final size:109
Alignment explanation
Indices: 19236--19530 Score: 432
Period size: 108 Copynumber: 2.7 Consensus size: 109
19226 ACTATTATAG
* * * *
19236 TTTTATTCTACTAGAAACTATATTTTTATTCAATTAAATTAAATCTAACATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
19301 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
19350 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
19415 TTACCAAAAAA-TTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* **
19458 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTTTATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATA-TCTTTATAA-TTACTTTA
19522 TTTTTACCA
63 TTTTTACCA
19531 TTTTAATTTA
Statistics
Matches: 170, Mismatches: 8, Indels: 10
0.90 0.04 0.05
Matches are distributed among these distances:
107 1 0.01
108 74 0.44
109 55 0.32
110 18 0.11
111 2 0.01
114 20 0.12
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:20804 original size:19 final size:19
Alignment explanation
Indices: 20772--20816 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
20762 ATAGTGGGAC
*
20772 AACTCGGCTTGAACAAGGTT
1 AACT-GGCTCGAACAAGGTT
*
20792 AACTGGCTCGAACAAGTTT
1 AACTGGCTCGAACAAGGTT
20811 AACTGG
1 AACTGG
20817 TAAATATACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (19 bp):
AACTGGCTCGAACAAGGTT
Found at i:27738 original size:23 final size:23
Alignment explanation
Indices: 27712--27759 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
27702 AGTACATTTT
27712 AACCGTATCACAAAGTTTAAGAA
1 AACCGTATCACAAAGTTTAAGAA
27735 AACCGTATCACAAAGTTTAAGAA
1 AACCGTATCACAAAGTTTAAGAA
27758 AA
1 AA
27760 GTAGTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (23 bp):
AACCGTATCACAAAGTTTAAGAA
Found at i:31840 original size:29 final size:27
Alignment explanation
Indices: 31796--31851 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 27
31786 CAAAGTGCAA
31796 AGTAGAGGGACTAAATTGATCATTTTTTT
1 AGTAGAGGGACTAAATTGAT--TTTTTTT
31825 AGTAGAGGGA-TGAAATTGATTTTTTTT
1 AGTAGAGGGACT-AAATTGATTTTTTTT
31852 GTGAAAGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 7 0.27
28 1 0.04
29 18 0.69
ACGTcount: A:0.30, C:0.04, G:0.23, T:0.43
Consensus pattern (27 bp):
AGTAGAGGGACTAAATTGATTTTTTTT
Found at i:33579 original size:30 final size:29
Alignment explanation
Indices: 33500--33584 Score: 118
Period size: 29 Copynumber: 2.9 Consensus size: 29
33490 ACATGGCACA
*
33500 TGGCATTTTTG-ACACGTGGCGTGCCATG
1 TGGCATTTTTGTACACGTGGCATGCCATG
* * *
33528 TGTCCTTTTTGTACACATGGCATGCCATG
1 TGGCATTTTTGTACACGTGGCATGCCATG
33557 TGGCATTTTTGGTACACGTGGCATGCCA
1 TGGCATTTTT-GTACACGTGGCATGCCA
33585 CGTCGGATGC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 9 0.19
29 23 0.48
30 16 0.33
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.34
Consensus pattern (29 bp):
TGGCATTTTTGTACACGTGGCATGCCATG
Found at i:36968 original size:12 final size:13
Alignment explanation
Indices: 36951--36988 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
36941 GGCTGGAGTA
36951 GCAGTTGCA-GTT
1 GCAGTTGCAGGTT
36963 GCAGTTGCAGGTT
1 GCAGTTGCAGGTT
*
36976 GCA-TTTCAGGTT
1 GCAGTTGCAGGTT
36988 G
1 G
36989 ATTCTTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 18 0.75
13 6 0.25
ACGTcount: A:0.16, C:0.16, G:0.34, T:0.34
Consensus pattern (13 bp):
GCAGTTGCAGGTT
Found at i:40512 original size:184 final size:184
Alignment explanation
Indices: 40196--40543 Score: 474
Period size: 184 Copynumber: 1.9 Consensus size: 184
40186 AATAAAGATA
* ** *
40196 GCTTGGATGATAATCATGATCAAGATGAGCATAGTGAAAGTTCTGAATCCCATGAAGCAGTTGAT
1 GCTTGGATGATAATCATGATCAAGACGAGCATAGTGAAAGGACTCAATCCCATGAAGCAGTTGAT
* *
40261 GAGAGTAATTCATCTGAAGATGAGGTCAGACTGCTGTTTACTATTTTCAAAAACAAGATTTCTTT
66 GAGAGTAATTCATCTGAAGATGAGGTCAGACTGCTGTTTACTATTTACAAAAACAAGATTCCTTT
*
40326 TGGATTCTTACATTTCTATTTTGGCTTAACAGGTTGATGGAGGCAGTGTTGATG
131 TGGATTCTTACATCTCTATTTTGGCTTAACAGGTTGATGGAGGCAGTGTTGATG
* *
40380 GCTTGGATGATAATCATGATGAATACGAGCATAGTGAAAGCGAC-CAATCCCATGAAGCAGTTGA
1 GCTTGGATGATAATCATGATCAAGACGAGCATAGTGAAAG-GACTCAATCCCATGAAGCAGTTGA
* * *
40444 TGAGAGTGATTCATCTGAAGATGAGGTCAGGCATGCCT-TTTAGC-A-TTAGAAAGTAA-AAG-T
65 TGAGAGTAATTCATCTGAAGATGAGGTCAGAC-TG-CTGTTTA-CTATTTACAAA--AACAAGAT
* *
40504 TCCTTTTGGGTTCTTACATCTCTCTTTTGGCTTAACAGGT
125 TCCTTTTGGATTCTTACATCTCTATTTTGGCTTAACAGGT
40544 GGCTCCTCGA
Statistics
Matches: 144, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
184 128 0.89
185 11 0.08
186 5 0.03
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (184 bp):
GCTTGGATGATAATCATGATCAAGACGAGCATAGTGAAAGGACTCAATCCCATGAAGCAGTTGAT
GAGAGTAATTCATCTGAAGATGAGGTCAGACTGCTGTTTACTATTTACAAAAACAAGATTCCTTT
TGGATTCTTACATCTCTATTTTGGCTTAACAGGTTGATGGAGGCAGTGTTGATG
Found at i:53816 original size:1 final size:1
Alignment explanation
Indices: 53810--53840 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
53800 GTGTAGAGTT
*
53810 GGGGGGGGGGGGGGGGGGGGGTGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
53841 CATTATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.03
Consensus pattern (1 bp):
G
Found at i:54534 original size:38 final size:39
Alignment explanation
Indices: 54455--54535 Score: 98
Period size: 38 Copynumber: 2.1 Consensus size: 39
54445 TTGTTCCAGT
* *
54455 TTAA-ATAGAAATAGATAGATAATCACATTGGAATCTGA
1 TTAATATAGAAATAGATAGATAATCACACTGAAATCTGA
54493 TTAATATAGATAATA-ATA-ATAATCACACTGAAATCCT-A
1 TTAATATAGA-AATAGATAGATAATCACACTGAAAT-CTGA
54531 TTAAT
1 TTAAT
54536 TTAGTATGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
38 24 0.63
39 10 0.26
40 4 0.11
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (39 bp):
TTAATATAGAAATAGATAGATAATCACACTGAAATCTGA
Found at i:54886 original size:2 final size:2
Alignment explanation
Indices: 54879--54909 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54869 CCCACAATTA
54879 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
54910 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:54914 original size:2 final size:2
Alignment explanation
Indices: 54909--54950 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
54899 ACACACACAC
* *
54909 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54951 CCAACAAAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Done.