Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021506.1 Corchorus olitorius cultivar O-4 contig21539, 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: 11291
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2108 original size:454 final size:456
Alignment explanation
Indices: 1197--2111 Score: 1755
Period size: 456 Copynumber: 2.0 Consensus size: 456
1187 ATTATTATAA
1197 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
1 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
1262 AAAAGTTAAAAAGTTGCCATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTGT
66 AAAAGTTAAAAAGTTGCCATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTGT
1327 TCCATTTGATTGGTATTAAAGTCATTATTATAAATTCATAACGGTTAATTTTTTTTTTGTAAGAA
131 TCCATTTGATTGGTATTAAAGTCATTATTATAAATTCATAACGGTTAATTTTTTTTTTGTAAGAA
1392 TTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATGT
196 TTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATGT
1457 TTCTGTTTTTTGTTGGAATAATCAATTTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACA
261 TTCTGTTTTTTGTTGGAATAATCAATTTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACA
1522 ACTTCTTAGCTTCTACGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATGAGGCGA
326 ACTTCTTAGCTTCTACGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATGAGGCGA
1587 AAAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTTA
391 AAAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTTA
1652 C
456 C
1653 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
1 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
1718 AAAAGTTAAAAAGTTGCCATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTGT
66 AAAAGTTAAAAAGTTGCCATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTGT
*
1783 TCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAA-TTTTTTTTTG-AAGAA
131 TCCATTTGATTGGTATTAAAGTCATTATTATAAATTCATAACGGTTAATTTTTTTTTTGTAAGAA
1846 TTTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATG
196 -TTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATG
1911 TTTCTGTTTTTTGTTGGAATAATCAA-TTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGAC
260 TTTCTGTTTTTTGTTGGAATAATCAATTTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGAC
** **
1975 AACTTCTTAGCTTCTGTGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATTTGGCG
325 AACTTCTTAGCTTCTACGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATGAGGCG
2040 AAAAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTT
390 AAAAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTT
2105 AC
455 AC
2107 ATAAA
1 ATAAA
2112 TTGTACTTAA
Statistics
Matches: 453, Mismatches: 5, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
454 176 0.39
455 100 0.22
456 177 0.39
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (456 bp):
ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
AAAAGTTAAAAAGTTGCCATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTGT
TCCATTTGATTGGTATTAAAGTCATTATTATAAATTCATAACGGTTAATTTTTTTTTTGTAAGAA
TTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATGT
TTCTGTTTTTTGTTGGAATAATCAATTTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACA
ACTTCTTAGCTTCTACGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATGAGGCGA
AAAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTTA
C
Found at i:6219 original size:53 final size:53
Alignment explanation
Indices: 6156--6256 Score: 202
Period size: 53 Copynumber: 1.9 Consensus size: 53
6146 GAATACTACT
6156 TATCTTTAAAACAGGAGGACTACTAATTTTGGCCAAAGAAAACTTAAAATTAC
1 TATCTTTAAAACAGGAGGACTACTAATTTTGGCCAAAGAAAACTTAAAATTAC
6209 TATCTTTAAAACAGGAGGACTACTAATTTTGGCCAAAGAAAACTTAAA
1 TATCTTTAAAACAGGAGGACTACTAATTTTGGCCAAAGAAAACTTAAA
6257 TTTCCCAAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.28
Consensus pattern (53 bp):
TATCTTTAAAACAGGAGGACTACTAATTTTGGCCAAAGAAAACTTAAAATTAC
Found at i:9719 original size:2 final size:2
Alignment explanation
Indices: 9712--9737 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9702 AGGTAAATTA
9712 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
9738 GCACAATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10784 original size:16 final size:16
Alignment explanation
Indices: 10742--10830 Score: 103
Period size: 16 Copynumber: 5.6 Consensus size: 16
10732 CTCGGGCGGG
10742 TTCGGGTTCGGGT-TCT
1 TTCGGGTTCGGGTAT-T
10758 TT-GGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
10773 TTCGGATTCGGGTATT
1 TTCGGGTTCGGGTATT
* *
10789 TTCGGGCTCGGGT-TAA
1 TTCGGGTTCGGGTAT-T
*
10805 GTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
10821 TTCGGGTTCG
1 TTCGGGTTCG
10831 AGCTCGGGTA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
15 14 0.23
16 46 0.75
17 1 0.02
ACGTcount: A:0.07, C:0.15, G:0.38, T:0.40
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:10850 original size:23 final size:23
Alignment explanation
Indices: 10821--10872 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
10811 TTCGGGTATT
*
10821 TTCGGGTTCGAGCTCGGGTAGGG
1 TTCGGGTTCGAGCCCGGGTAGGG
* * *
10844 TTCGGGTTTGGGCCCGGGTCGGG
1 TTCGGGTTCGAGCCCGGGTAGGG
10867 TTCGGG
1 TTCGGG
10873 CTCGGGTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.04, C:0.19, G:0.50, T:0.27
Consensus pattern (23 bp):
TTCGGGTTCGAGCCCGGGTAGGG
Found at i:10865 original size:17 final size:17
Alignment explanation
Indices: 10845--10879 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
10835 CGGGTAGGGT
*
10845 TCGGGTTTGGGCCCGGG
1 TCGGGTTCGGGCCCGGG
*
10862 TCGGGTTCGGGCTCGGG
1 TCGGGTTCGGGCCCGGG
10879 T
1 T
10880 TTGATTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.51, T:0.26
Consensus pattern (17 bp):
TCGGGTTCGGGCCCGGG
Found at i:11025 original size:8 final size:8
Alignment explanation
Indices: 11005--11038 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
10995 AAGTTTATTG
11005 ATAATAT-
1 ATAATATA
11012 ATAATATA
1 ATAATATA
11020 ATAATATA
1 ATAATATA
11028 ATAATATA
1 ATAATATA
11036 ATA
1 ATA
11039 TAACATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAATATA
Found at i:11028 original size:13 final size:13
Alignment explanation
Indices: 11005--11041 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
10995 AAGTTTATTG
11005 ATAAT-ATATAAT
1 ATAATAATATAAT
11017 ATAATAATATAAT
1 ATAATAATATAAT
11030 A-ATATAATATAA
1 ATA-ATAATATAA
11042 CATTATTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATAATATAAT
Done.