Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009626.1 Corchorus olitorius cultivar O-4 contig09658, 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: 10936
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:19 original size:10 final size:10
Alignment explanation
Indices: 5--112 Score: 62
Period size: 10 Copynumber: 10.3 Consensus size: 10
1 CAAA
5 AAATAAAAAT
1 AAATAAAAAT
15 AAAT-AAAAT
1 AAATAAAAAT
*
24 ATAATATAATAT
1 A-AATA-AAAAT
36 AAAATAAACAAT
1 -AAATAAA-AAT
* *
48 ATATAAATAT
1 AAATAAAAAT
58 ATAATAATAAAT
1 A-AATAA-AAAT
70 AAAATATAAAAT
1 -AAATA-AAAAT
82 -AATAAAAA-
1 AAATAAAAAT
*
90 AGAATAAAAAG
1 A-AATAAAAAT
*
101 AAA-AAGAAT
1 AAATAAAAAT
110 AAA
1 AAA
113 GGAAAGAAGT
Statistics
Matches: 78, Mismatches: 8, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
9 17 0.22
10 24 0.31
11 13 0.17
12 21 0.27
13 3 0.04
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:60 original size:29 final size:26
Alignment explanation
Indices: 7--86 Score: 94
Period size: 25 Copynumber: 3.2 Consensus size: 26
1 CAAAAA
* *
7 ATAAAAATAAATAAAATATAATATAAT
1 ATAATAATAAATAAAATATAAAAT-AT
* *
34 ATAA-AATAAACAATATAT-AAATAT
1 ATAATAATAAATAAAATATAAAATAT
58 ATAATAATAAATAAAATATAAAATA-
1 ATAATAATAAATAAAATATAAAATAT
83 ATAA
1 ATAA
87 AAAAGAATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
24 6 0.13
25 19 0.41
26 17 0.37
27 4 0.09
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (26 bp):
ATAATAATAAATAAAATATAAAATAT
Found at i:99 original size:19 final size:19
Alignment explanation
Indices: 2--99 Score: 64
Period size: 19 Copynumber: 5.2 Consensus size: 19
1 C
*
2 AAAA-AATAAAAATAA-AT
1 AAAATAATAAAAAAAATAT
* *
19 AAAAT-AT-AATATAATAT
1 AAAATAATAAAAAAAATAT
36 AAAATAA-ACAATATATAAATAT
1 AAAATAATA-AA-A-A-AAATAT
* *
58 ATAATAATAAATAAAATAT
1 AAAATAATAAAAAAAATAT
77 AAAATAATAAAAAAGAATA-
1 AAAATAATAAAAAA-AATAT
96 AAAA
1 AAAA
100 GAAAAAGAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
16 6 0.09
17 13 0.20
18 1 0.02
19 24 0.38
20 5 0.08
21 1 0.02
22 13 0.20
23 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (19 bp):
AAAATAATAAAAAAAATAT
Found at i:788 original size:94 final size:97
Alignment explanation
Indices: 647--830 Score: 232
Period size: 94 Copynumber: 1.9 Consensus size: 97
637 ATGATCTACG
** *
647 ACTTTCATGAAGGACCCGAAAGCTAAAATTGAATTACGAGTTCCATGAAGGGTTCAAAA-G-GTT
1 ACTTTCATGAAGGACCCGAAAGCTAAAATTGAATTACGAGTTCCATGAAAAGTCCAAAAGGAGTT
710 TTATGTTTCAAAATCTCCATCAATAAACATTT
66 TTATGTTTCAAAATCTCCATCAATAAACATTT
* * * *
742 ACTTTCATGAAGGA-CTGAAAGCTAAATTTG-ATCTACTAGTTTCATGAAAAGTCCAAAAGGGAA
1 ACTTTCATGAAGGACCCGAAAGCTAAAATTGAAT-TACGAGTTCCATGAAAAGTCCAAAA-GG-A
* *
805 GTTTTATGTTTCAAGATTTCCATCAA
63 GTTTTATGTTTCAAAATCTCCATCAA
831 CAAGTATTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
93 2 0.03
94 34 0.45
95 14 0.19
96 1 0.01
98 24 0.32
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (97 bp):
ACTTTCATGAAGGACCCGAAAGCTAAAATTGAATTACGAGTTCCATGAAAAGTCCAAAAGGAGTT
TTATGTTTCAAAATCTCCATCAATAAACATTT
Found at i:1398 original size:20 final size:20
Alignment explanation
Indices: 1373--1414 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1363 GAAGTTGAAA
1373 ATTTAACTTGACACGAACAT
1 ATTTAACTTGACACGAACAT
1393 ATTTAACTTGACACGAACAT
1 ATTTAACTTGACACGAACAT
1413 AT
1 AT
1415 GGATTCATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (20 bp):
ATTTAACTTGACACGAACAT
Found at i:5311 original size:19 final size:20
Alignment explanation
Indices: 5275--5313 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
5265 GTATACTTTT
*
5275 ATTTATTTTATTCCAAAAAA
1 ATTTATTTTATTCAAAAAAA
*
5295 ATTT-TTTTTTTCAAAAAAA
1 ATTTATTTTATTCAAAAAAA
5314 TCTCCAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTATTTTATTCAAAAAAA
Found at i:6045 original size:30 final size:30
Alignment explanation
Indices: 6011--6084 Score: 148
Period size: 30 Copynumber: 2.5 Consensus size: 30
6001 ATATGGAAAA
6011 TTAGTACAAGTAATAATTAATGGTAAGAAC
1 TTAGTACAAGTAATAATTAATGGTAAGAAC
6041 TTAGTACAAGTAATAATTAATGGTAAGAAC
1 TTAGTACAAGTAATAATTAATGGTAAGAAC
6071 TTAGTACAAGTAAT
1 TTAGTACAAGTAAT
6085 CATCGCTGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.31
Consensus pattern (30 bp):
TTAGTACAAGTAATAATTAATGGTAAGAAC
Found at i:6670 original size:16 final size:17
Alignment explanation
Indices: 6639--6671 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6629 TCAATTAAAC
6639 TAATTATATTAATAATT
1 TAATTATATTAATAATT
*
6656 TAATTA-ATTAGTAATT
1 TAATTATATTAATAATT
6672 AACTAACAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TAATTATATTAATAATT
Found at i:7306 original size:245 final size:247
Alignment explanation
Indices: 6872--7351 Score: 766
Period size: 245 Copynumber: 1.9 Consensus size: 247
6862 AAAAAATTAT
* * *
6872 CAGTAGAGTTTACCATACTACATATGTGGGGTTTAAGGGGTTGACATGTGTCTTTTAGGTAATAG
1 CAGTAGAGTTTACCAGACAACACATGTGGGGTTTAAGGGGTTGACATGTGTCTTTTAGGTAATAG
*
6937 TTTTGAAATTTAAAAACAAAATTAAATTAGAAAATTGGTATGTGTCAACTCCTTACTAGACCTGT
66 TTTTGAAATTTAAAAACAAAATTAAATCAGAAAATTGGTATGTGTCAACTCCTTACTAGACCTGT
*** * *
7002 TCAAGGGCCCGGGTACCCGTCCAGACCCGAAAGTCCGCCCAAAAAATGGGAGGATTTGGG-TAGT
131 TCAAGGGCCCAACTACCCGTCCAGACCCGAAAGCCCGCCCAAAAAATGGGAGAATTTGGGATAGT
* *
7066 TTAAGGCTCGAAGGTCAGACTTTGGACAAAGAAAGAGACATTTGGGGTTTAC
196 TTAAGCCCCGAAGGTCAGACTTTGGACAAAGAAAGAGACATTTGGGGTTTAC
*
7118 CAGTAGAGTTTACCGGACAACACATGTGGGGTTTAA-GGGTTGACATGTGTCTTTTAGGTAATAG
1 CAGTAGAGTTTACCAGACAACACATGTGGGGTTTAAGGGGTTGACATGTGTCTTTTAGGTAATAG
*
7182 TTTTGAATTTTAAAAACAAAATTAAATCAGAAAATTGGTATGTGTCAACTCCTTACTAGACCTGT
66 TTTTGAAATTTAAAAACAAAATTAAATCAGAAAATTGGTATGTGTCAACTCCTTACTAGACCTGT
* * *
7247 TCAAGGGCCCAACTACCCGTCCAGACTCGAAAGCCCGCCCGATAAATGGGAGAATTTGGGCAATA
131 TCAAGGGCCCAACTACCCGTCCAGACCCGAAAGCCCGCCCAAAAAATGGGAGAATTTGGG--ATA
* *
7312 GTTTAAGCCCCGCAGGTCGGACTTTGGACAAAGAAAGAGA
194 GTTTAAGCCCCGAAGGTCAGACTTTGGACAAAGAAAGAGA
7352 TACATTTGTA
Statistics
Matches: 213, Mismatches: 18, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
245 143 0.67
246 32 0.15
248 38 0.18
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (247 bp):
CAGTAGAGTTTACCAGACAACACATGTGGGGTTTAAGGGGTTGACATGTGTCTTTTAGGTAATAG
TTTTGAAATTTAAAAACAAAATTAAATCAGAAAATTGGTATGTGTCAACTCCTTACTAGACCTGT
TCAAGGGCCCAACTACCCGTCCAGACCCGAAAGCCCGCCCAAAAAATGGGAGAATTTGGGATAGT
TTAAGCCCCGAAGGTCAGACTTTGGACAAAGAAAGAGACATTTGGGGTTTAC
Done.