Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012914.1 Corchorus olitorius cultivar O-4 contig12947, 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: 24260
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:8151 original size:45 final size:45
Alignment explanation
Indices: 8073--8169 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 45
8063 AGCAACAATT
* * *** * *
8073 AATATTAACTTTATTTTGATGAATTATTTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTAATGAATTACCCAGAGACGGAAGAGTAG
*
8118 AATATTAGCTTTATTTTAATGAATTACCCAGAGACGGAATAGTAG
1 AATATTAGCTTTATTTTAATGAATTACCCAGAGACGGAAGAGTAG
8163 AAT-TTAG
1 AATATTAG
8170 GTAATTAATG
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 4 0.09
45 40 0.91
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (45 bp):
AATATTAGCTTTATTTTAATGAATTACCCAGAGACGGAAGAGTAG
Found at i:10060 original size:2 final size:2
Alignment explanation
Indices: 10055--10083 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10045 ATATACACAC
10055 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10084 CGATGATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10588 original size:144 final size:144
Alignment explanation
Indices: 10328--10617 Score: 571
Period size: 144 Copynumber: 2.0 Consensus size: 144
10318 ATTTATATGG
*
10328 AACGTTTACAATAAGGACAAAGATATACATATTAGTGTGCGGGAGATGCACATATGTATTGATGT
1 AACGTTTACAATAAGAACAAAGATATACATATTAGTGTGCGGGAGATGCACATATGTATTGATGT
10393 CCGGGTGAAGGACACAGACATTATGTTGTGCGGGAGATGCACATGGTTATTATCATGATGGTGTG
66 CCGGGTGAAGGACACAGACATTATGTTGTGCGGGAGATGCACATGGTTATTATCATGATGGTGTG
10458 CAGGAGGTGCACAC
131 CAGGAGGTGCACAC
10472 AACGTTTACAATAAGAACAAAGATATACATATTAGTGTGCGGGAGATGCACATATGTATTGATGT
1 AACGTTTACAATAAGAACAAAGATATACATATTAGTGTGCGGGAGATGCACATATGTATTGATGT
10537 CCGGGTGAAGGACACAGACATTATGTTGTGCGGGAGATGCACATGGTTATTATCATGATGGTGTG
66 CCGGGTGAAGGACACAGACATTATGTTGTGCGGGAGATGCACATGGTTATTATCATGATGGTGTG
10602 CAGGAGGTGCACAC
131 CAGGAGGTGCACAC
10616 AA
1 AA
10618 TTATTATTAT
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 145 1.00
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (144 bp):
AACGTTTACAATAAGAACAAAGATATACATATTAGTGTGCGGGAGATGCACATATGTATTGATGT
CCGGGTGAAGGACACAGACATTATGTTGTGCGGGAGATGCACATGGTTATTATCATGATGGTGTG
CAGGAGGTGCACAC
Found at i:10625 original size:3 final size:3
Alignment explanation
Indices: 10617--10650 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
10607 GGTGCACACA
10617 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
10651 GATGCACACG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:14978 original size:25 final size:24
Alignment explanation
Indices: 14944--15014 Score: 106
Period size: 25 Copynumber: 2.9 Consensus size: 24
14934 TTGCTGTAGG
*
14944 AAGTGGCGCAGTGCCTGAGAGAAGA
1 AAGTGGCGCAGGGCCTGAGAGAA-A
14969 AAGTGGCGCAGGGCCTGAGAGAAA
1 AAGTGGCGCAGGGCCTGAGAGAAA
*
14993 AACGGGGCGCAGGGCCTGAGAG
1 AA-GTGGCGCAGGGCCTGAGAG
15015 GAAATAAGCA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 3 0.07
25 40 0.93
ACGTcount: A:0.30, C:0.18, G:0.44, T:0.08
Consensus pattern (24 bp):
AAGTGGCGCAGGGCCTGAGAGAAA
Found at i:17363 original size:54 final size:51
Alignment explanation
Indices: 17254--17363 Score: 130
Period size: 54 Copynumber: 2.1 Consensus size: 51
17244 TTATAAACTA
* * * **
17254 AAATTATCTTTTATTCAATAAAATTGACATTGTTATAATTTTACTTATTCT
1 AAATTATCATTTATTCAATAAAATTGACATTATTATAATTTTACCTATAAT
* *
17305 AAATTATCATTTATTCAATACAATTTGTATTATTATTATAATTTTACCTATAAT
1 AAATTATCATTTATTCAATA-AAATTG-A-CATTATTATAATTTTACCTATAAT
17359 AAATT
1 AAATT
17364 GTGATTGAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
51 19 0.39
52 5 0.10
53 1 0.02
54 24 0.49
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (51 bp):
AAATTATCATTTATTCAATAAAATTGACATTATTATAATTTTACCTATAAT
Found at i:21579 original size:24 final size:24
Alignment explanation
Indices: 21552--21597 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
21542 AAATCTGGTT
21552 GAAAATGTAGAA-GAAAATGTTGTG
1 GAAAATGTA-AATGAAAATGTTGTG
21576 GAAAATGTAAATGAAAATGTTG
1 GAAAATGTAAATGAAAATGTTG
21598 AAAAGGTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (24 bp):
GAAAATGTAAATGAAAATGTTGTG
Found at i:23109 original size:13 final size:13
Alignment explanation
Indices: 23087--23117 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
23077 TCTTTTAATT
*
23087 ATTTTTGTAAATG
1 ATTTTAGTAAATG
23100 ATTTTAGTAAATG
1 ATTTTAGTAAATG
23113 ATTTT
1 ATTTT
23118 GCTTGTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
ATTTTAGTAAATG
Done.