Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016662.1 Corchorus olitorius cultivar O-4 contig16695, 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: 37951
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7858 original size:49 final size:49
Alignment explanation
Indices: 7787--7880 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
7777 CTTTTGTGTT
* *
7787 TTTTTTTTCATAAAATTAAAATTTTTTGTGCGACTATTGAAATAAAACG
1 TTTTCTTTCATAAAATTAAAATTCTTTGTGCGACTATTGAAATAAAACG
* *
7836 TTTTCTTTCTTAAAATTAAAATTCTTTGTGCGACTATTTAAATAA
1 TTTTCTTTCATAAAATTAAAATTCTTTGTGCGACTATTGAAATAA
7881 TAAAAAAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.47
Consensus pattern (49 bp):
TTTTCTTTCATAAAATTAAAATTCTTTGTGCGACTATTGAAATAAAACG
Found at i:10834 original size:42 final size:40
Alignment explanation
Indices: 10736--10841 Score: 151
Period size: 40 Copynumber: 2.6 Consensus size: 40
10726 TAAAATGAGG
*
10736 GTGGACCTGATCTCTCCCTATTCTTACTTAATTAGCCATGAT
1 GTGGACCTGATCTCT--CTATTCTTACTTAAGTAGCCATGAT
* *
10778 GTGGACCTGATCTCTCTATTCTTACTTAGGTATCCAT-AGT
1 GTGGACCTGATCTCTCTATTCTTACTTAAGTAGCCATGA-T
10818 GTGGACCTGATCTCTCTATTCTTA
1 GTGGACCTGATCTCTCTATTCTTA
10842 TTTGATAATA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
39 1 0.02
40 44 0.73
42 15 0.25
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.40
Consensus pattern (40 bp):
GTGGACCTGATCTCTCTATTCTTACTTAAGTAGCCATGAT
Found at i:14476 original size:11 final size:11
Alignment explanation
Indices: 14452--14486 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
14442 TTGACAGCAC
14452 AACAAAAACAA
1 AACAAAAACAA
* *
14463 AACGAAAACGA
1 AACAAAAACAA
14474 AACAAAAACAA
1 AACAAAAACAA
14485 AA
1 AA
14487 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:14478 original size:16 final size:16
Alignment explanation
Indices: 14457--14515 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
14447 AGCACAACAA
14457 AAACAAAACGAAAACG
1 AAACAAAACGAAAACG
*
14473 AAACAAAAACAAAAAAC-
1 AAAC-AAAAC-GAAAACG
*
14490 AGA-AAAACGAAAACG
1 AAACAAAACGAAAACG
* *
14505 ATACCAAACGA
1 AAACAAAACGA
14516 CCCCTTAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 10 0.29
17 7 0.21
18 5 0.15
ACGTcount: A:0.69, C:0.19, G:0.10, T:0.02
Consensus pattern (16 bp):
AAACAAAACGAAAACG
Found at i:18686 original size:88 final size:88
Alignment explanation
Indices: 18511--18691 Score: 301
Period size: 88 Copynumber: 2.1 Consensus size: 88
18501 GCCCTGATTT
*
18511 GGAGATCATATTTAGAATCCAATCACTTCTTTTTAGTTAATGGTTTTTTTTGGGTAAAAAGTTAA
1 GGAGATCATATTTAGAATCCAATCACTTCTTTTTAGTTAATAGTTTTTTTTGGGTAAAAAGTTAA
18576 TGACTTATTGCCAAAAGAAAAAA
66 TGACTTATTGCCAAAAGAAAAAA
* * *
18599 GGAGATCATATTTAGAATCCAATTACTTTTTTTTAGTTAATAATTTTTTTTTGGGTAAAAAGTTA
1 GGAGATCATATTTAGAATCCAATCACTTCTTTTTAGTTAAT-AGTTTTTTTTGGGTAAAAAGTTA
*
18664 ATGGCTTATTGCCAAAAG-AAAAA
65 ATGACTTATTGCCAAAAGAAAAAA
18687 GGAGA
1 GGAGA
18692 AATAGGATTT
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
88 49 0.56
89 38 0.44
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (88 bp):
GGAGATCATATTTAGAATCCAATCACTTCTTTTTAGTTAATAGTTTTTTTTGGGTAAAAAGTTAA
TGACTTATTGCCAAAAGAAAAAA
Found at i:19065 original size:483 final size:482
Alignment explanation
Indices: 18115--19085 Score: 1667
Period size: 483 Copynumber: 2.0 Consensus size: 482
18105 GCTCTTATTT
* * *
18115 GGAGATCATATTTAGAATCCAATTACTTCTTTTTAGTTAATGATTTTTTTTTTTGGTAAAATGTT
1 GGAGATCATATTTAGAATCCAATTACTTCTTTTTAGTTAATGAATTTTTTTTTGGGTAAAAAGTT
18180 AATGACTTATTGCCAAAAGAAAAAGGAGAAATAGAATTTGCTCATTATTTCATTTTACCAATTAG
66 AATGACTTATTGCCAAAAGAAAAAGGAGAAATAGAATTTGCTCATTATTTCATTTTACCAATTAG
* *
18245 TTCTTTTTGGACACCTAAAGATACAGGAAGGTTGTCATCTTTATCAGATTCCGAATCCACAAAGG
131 TTCTTTTTGGACAACTAAAGATACAGGAAGGTTGTCATCCTTATCAGATTCCGAATCCACAAAGG
*
18310 TAATTTTTTTTTTTAAATGGTTGTGAAACAATGTTACAGTACTATAAGAAAAATACAGATGAAGA
196 TAA-TTTTTTTTTTAAATGGTTGTGAAACAATGTTACAGTACTATAAGAAAAATACAGACGAAGA
* * *
18375 ATATTCGTCACAGATCGCCACGAAAATTGCCAAAATATTCTTTTTGCAAGTGTGAGCCAAATAGC
260 ATATTCATCACAAATCGCCACGAAAATTGCCAAAATATTCTTTTTGCAAGTGTGAGCCAAAGAGC
*
18440 AGCCAATGAGAGTTTAAAGAAGAGAAGTAGAGGAAGAAAGAGAATAAAGATAACATCAAATGCCC
325 AGCCAATGAGAGTTTAAAGAAGAGAAGTAGAGGAAGAAAGAGAATAAAGATAACATCAAAGGCCC
** *
18505 TGATTTGGAGATCATATTTAGAATCCAATCACTTCTTTTTAGTTAATGGTTTTTTTTGGGTAAAA
390 TGATTTGGAGATCATATTTAGAATCCAATCACTTCTTTTTAGTTAATAATTTTTTTGGGGTAAAA
18570 AGTTAATGACTTATTGCCAAAAGAAAAAA
455 AGTTAATGACTTATTGCCAAAAG-AAAAA
*
18599 GGAGATCATATTTAGAATCCAATTACTTTTTTTTAGTTAAT-AATTTTTTTTTGGGTAAAAAGTT
1 GGAGATCATATTTAGAATCCAATTACTTCTTTTTAGTTAATGAATTTTTTTTTGGGTAAAAAGTT
* *
18663 AATGGCTTATTGCCAAAAGAAAAAGGAGAAATAGGATTTGCTCATTATTTCATTTTACCAATTAG
66 AATGACTTATTGCCAAAAGAAAAAGGAGAAATAGAATTTGCTCATTATTTCATTTTACCAATTAG
*
18728 TTCTTTTTGGACAACTAAAGATACAGGAAGGTTGTCATCCTTATCAGATTCTGAATCCACAAAGG
131 TTCTTTTTGGACAACTAAAGATACAGGAAGGTTGTCATCCTTATCAGATTCCGAATCCACAAAGG
* *
18793 TGA-TTTTTTTTTAAATGGTTGTGATCAACAATGTTACAGTACTATAAGAAAAATGCAGACGAAG
196 TAATTTTTTTTTTAAATGGTTGTGA--AACAATGTTACAGTACTATAAGAAAAATACAGACGAAG
* * *
18857 AATATTCATCGCAAATCGCCATGGAAATTGCCAAAATATTCTTTTTGCAAGTGTGAGCCAAAGAG
259 AATATTCATCACAAATCGCCACGAAAATTGCCAAAATATTCTTTTTGCAAGTGTGAGCCAAAGAG
*
18922 CAGCCAATGAGAGTTTAAATAAGAGAAGTAGAGGAAGAAAGAGAATAAAGATAACATCAAAGGCC
324 CAGCCAATGAGAGTTTAAAGAAGAGAAGTAGAGGAAGAAAGAGAATAAAGATAACATCAAAGGCC
* *
18987 CTTATTTGGAGATCATATTTAGAATCCAATTACTTCTTTTTAGTTAATAATTTTTTTGGGGTAAA
389 CTGATTTGGAGATCATATTTAGAATCCAATCACTTCTTTTTAGTTAATAATTTTTTTGGGGTAAA
19052 AAGTTAATGACTTATTGCCAAAAGAAAAA
454 AAGTTAATGACTTATTGCCAAAAGAAAAA
19081 GGAGA
1 GGAGA
19086 AGTAGGATTT
Statistics
Matches: 460, Mismatches: 25, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
481 21 0.05
482 10 0.02
483 389 0.85
484 40 0.09
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (482 bp):
GGAGATCATATTTAGAATCCAATTACTTCTTTTTAGTTAATGAATTTTTTTTTGGGTAAAAAGTT
AATGACTTATTGCCAAAAGAAAAAGGAGAAATAGAATTTGCTCATTATTTCATTTTACCAATTAG
TTCTTTTTGGACAACTAAAGATACAGGAAGGTTGTCATCCTTATCAGATTCCGAATCCACAAAGG
TAATTTTTTTTTTAAATGGTTGTGAAACAATGTTACAGTACTATAAGAAAAATACAGACGAAGAA
TATTCATCACAAATCGCCACGAAAATTGCCAAAATATTCTTTTTGCAAGTGTGAGCCAAAGAGCA
GCCAATGAGAGTTTAAAGAAGAGAAGTAGAGGAAGAAAGAGAATAAAGATAACATCAAAGGCCCT
GATTTGGAGATCATATTTAGAATCCAATCACTTCTTTTTAGTTAATAATTTTTTTGGGGTAAAAA
GTTAATGACTTATTGCCAAAAGAAAAA
Found at i:21935 original size:45 final size:45
Alignment explanation
Indices: 21851--21936 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
21841 TATGTTTTTT
** **
21851 TTTTCATAAAATTAAAATTTTTTATGTGATTATTGAAATAAAACG
1 TTTTCATAAAATTAAAATTTTTTATACGACAATTGAAATAAAACG
* *
21896 TTTTCTTAAAATTAAAATTCTTTT-TACGACAATTTAAATAA
1 TTTTCATAAAATTAAAATT-TTTTATACGACAATTGAAATAA
21937 TAAAAAGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
45 30 0.88
46 4 0.12
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (45 bp):
TTTTCATAAAATTAAAATTTTTTATACGACAATTGAAATAAAACG
Found at i:24822 original size:42 final size:39
Alignment explanation
Indices: 24775--24878 Score: 147
Period size: 38 Copynumber: 2.6 Consensus size: 39
24765 TAAAATGAGG
* *
24775 GTGGACCTGATCTCACACTATTCTTACTTAGTTATCCATGAT
1 GTGGACCTGATCT--C-CTATTCTTACTTAGGTATCCATAAT
24817 GTGGACCTGATCT-CTATTCTTACTTAGGTATCCATAAT
1 GTGGACCTGATCTCCTATTCTTACTTAGGTATCCATAAT
24855 GTGGACCTGATCTCTCTATTCTTA
1 GTGGACCTGATCTC-CTATTCTTA
24879 TTTGATAATG
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
38 36 0.62
40 9 0.16
42 13 0.22
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.39
Consensus pattern (39 bp):
GTGGACCTGATCTCCTATTCTTACTTAGGTATCCATAAT
Found at i:30489 original size:18 final size:18
Alignment explanation
Indices: 30466--30517 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
30456 GTTCCCACTA
30466 ATATTATGCCTCAGAATG
1 ATATTATGCCTCAGAATG
*
30484 ATATTAGTG-C-C--ACTG
1 ATATTA-TGCCTCAGAATG
30499 ATATTATGCCTCAGAATG
1 ATATTATGCCTCAGAATG
30517 A
1 A
30518 GATTGCTCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
14 2 0.07
15 10 0.37
16 1 0.04
17 1 0.04
18 11 0.41
19 2 0.07
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (18 bp):
ATATTATGCCTCAGAATG
Found at i:30503 original size:33 final size:33
Alignment explanation
Indices: 30453--30578 Score: 164
Period size: 33 Copynumber: 3.8 Consensus size: 33
30443 TTCGAATTCT
* *
30453 ATTGTTCCCACTAATATTATGCCTCAGAATGAT
1 ATTGCTCCCACTAATATTATGCCTCAGAATGAG
* *
30486 ATTAG-TGCCACTGATATTATGCCTCAGAATGAG
1 ATT-GCTCCCACTAATATTATGCCTCAGAATGAG
* * *
30519 ATTGCTCCCACTAATATTGTGTCTTAGAATGAG
1 ATTGCTCCCACTAATATTATGCCTCAGAATGAG
*
30552 ATTGCTCCCACTAATATTGTGCCTCAG
1 ATTGCTCCCACTAATATTATGCCTCAG
30579 CGAACACACC
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
32 1 0.01
33 79 0.98
34 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (33 bp):
ATTGCTCCCACTAATATTATGCCTCAGAATGAG
Done.