Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014496.1 Corchorus olitorius cultivar O-4 contig14529, 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: 1708
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Found at i:68 original size:13 final size:13
Alignment explanation
Indices: 50--75 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40 AATCTCATAT
50 CTCTAATATATAA
1 CTCTAATATATAA
63 CTCTAATATATAA
1 CTCTAATATATAA
76 AGGTGTGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
CTCTAATATATAA
Found at i:631 original size:2 final size:2
Alignment explanation
Indices: 626--656 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
616 ACACACACAC
626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
657 AGTATGGTTT
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1026 original size:133 final size:131
Alignment explanation
Indices: 777--1126 Score: 373
Period size: 133 Copynumber: 2.6 Consensus size: 131
767 TTAGGGTTTA
* ** ** * * *
777 ACTATCAAAATTTGTTGTTTGACCATGCATATGCAATTAAATGTTTTGTGTGGTTTGACAATCG-
1 ACTATTAAAATTTGGGGTTTGACCATGCATATATAATAAAATGTTTTATGTGGTTTGACTATCGA
* * * *
841 GACTTTGGAGTTTAACCATCATCCTTTGGAATTTGATCATGTATGTATAATGATGTTTTTTGAGA
66 G-CTTTGGA-TTTAACCATCATCCTTTGGAATTTGACCATGCATATACAATGATG-TTTTTGAGA
906 TTCG
128 TTCG
* * * *
910 ACTATTAAAATTTGGGGTTTAATCATGCATATATAATGAAATGCTTTATGTGGTTTGACTATCGA
1 ACTATTAAAATTTGGGGTTTGACCATGCATATATAATAAAATGTTTTATGTGGTTTGACTATCGA
* * ** * *
975 GCTTTGTGATTTAACTATCATCTTTTGGGGTTT-AGCCATGCATATACAATGATGTTTTTGGGGT
66 GCTTTG-GATTTAACCATCATCCTTTGGAATTTGA-CCATGCATATACAATGATGTTTTTGAGAT
*
1039 TTG
129 TCG
*
1042 ACTATTAAAATTTGGGGTTTGACCATGCATATACT-ATAAAATGTTTTTTTGTGGTTTGACTATC
1 ACTATTAAAATTTGGGGTTTGACCATGCATATA-TAATAAAATG-TTTTATGTGGTTTGACTATC
* *
1106 GAACTTTGGGGTTTAACCATC
64 GAGCTTT-GGATTTAACCATC
1127 CATGCACAAT
Statistics
Matches: 181, Mismatches: 30, Indels: 12
0.81 0.13 0.05
Matches are distributed among these distances:
132 49 0.27
133 128 0.71
134 4 0.02
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (131 bp):
ACTATTAAAATTTGGGGTTTGACCATGCATATATAATAAAATGTTTTATGTGGTTTGACTATCGA
GCTTTGGATTTAACCATCATCCTTTGGAATTTGACCATGCATATACAATGATGTTTTTGAGATTC
G
Found at i:1070 original size:54 final size:54
Alignment explanation
Indices: 998--1157 Score: 178
Period size: 58 Copynumber: 2.9 Consensus size: 54
988 ACTATCATCT
*
998 TTTGGGGTTTAGCCATGCATATACAATGATG-TTTTTGGGGTTTGACTATTAAAA
1 TTTGGGGTTTA-CCATGCATATACAATGATGTTTTTTGGGGTTTGACTATCAAAA
** * * *
1052 TTTGGGGTTTGACCATGCATATACTATAAAATGTTTTTTTGTGGTTTGACTATCGAAC
1 TTTGGGGTTT-ACCATGCATATAC-A-ATGATG-TTTTTTGGGGTTTGACTATCAAAA
* **
1110 TTTGGGGTTTAACCATCCATGCACAATGATGTTTTTTGGGGTTTGACT
1 TTTGGGGTTT-ACCATGCATATACAATGATGTTTTTTGGGGTTTGACT
1158 GTGCATATAC
Statistics
Matches: 88, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
54 22 0.25
55 18 0.20
56 8 0.09
57 1 0.01
58 39 0.44
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (54 bp):
TTTGGGGTTTACCATGCATATACAATGATGTTTTTTGGGGTTTGACTATCAAAA
Found at i:1209 original size:56 final size:56
Alignment explanation
Indices: 1143--1320 Score: 167
Period size: 56 Copynumber: 3.2 Consensus size: 56
1133 CAATGATGTT
* *
1143 TTTTGGGGTTTGACTGTGCATATACAATGAAAATTTTTTGTGGTTTGACTATTGAA
1 TTTTGAGGTTTGACTATGCATATACAATGAAAATTTTTTGTGGTTTGACTATTGAA
* * *
1199 TTTTGAGGTTTGA-TCATGCATATGCAATG---ATGTTTTTG-GG--GGACTATTAAAA
1 TTTTGAGGTTTGACT-ATGCATATACAATGAAAAT-TTTTTGTGGTTTGACTATT-GAA
* * *
1251 TATTG-GGTTTGACCATGCATATACAATGAAATGTTTTTTGTGGTTTGACTATTGAA
1 TTTTGAGGTTTGACTATGCATATACAATGAAA-ATTTTTTGTGGTTTGACTATTGAA
*
1307 GTTT-AGGATTTGAC
1 TTTTGAGG-TTTGAC
1321 CATCATTCTT
Statistics
Matches: 96, Mismatches: 13, Indels: 25
0.72 0.10 0.19
Matches are distributed among these distances:
51 27 0.28
52 6 0.06
53 4 0.04
54 12 0.12
55 4 0.04
56 30 0.31
57 13 0.14
ACGTcount: A:0.26, C:0.08, G:0.24, T:0.43
Consensus pattern (56 bp):
TTTTGAGGTTTGACTATGCATATACAATGAAAATTTTTTGTGGTTTGACTATTGAA
Found at i:1230 original size:90 final size:90
Alignment explanation
Indices: 1052--1240 Score: 227
Period size: 90 Copynumber: 2.1 Consensus size: 90
1042 ACTATTAAAA
* *
1052 TTTGGGGTTTGACCATGCATATACTATAAAATGTTTTTTTGTGGTTTGACTATCGAACTTTGGGG
1 TTTGGGGTTTGACCATGCATATACAATAAAA--TTTTTTTGTGGTTTGACTATCGAACTTTGAGG
*
1117 TTTAACCATCCATGCACAATGATGTTT
64 TTTAACCATCCATACACAATGATGTTT
** * *
1144 TTTGGGGTTTGACTGTGCATATACAATGAAAA-TTTTTTGTGGTTTGACTATTGAATTTTGAGGT
1 TTTGGGGTTTGACCATGCATATACAAT-AAAATTTTTTTGTGGTTTGACTATCGAACTTTGAGGT
* * * **
1208 TTGATCATGCATATGCAATGATGTTT
65 TTAACCATCCATACACAATGATGTTT
*
1234 TTGGGGG
1 TTTGGGG
1241 ACTATTAAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
90 55 0.66
92 24 0.29
93 4 0.05
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.42
Consensus pattern (90 bp):
TTTGGGGTTTGACCATGCATATACAATAAAATTTTTTTGTGGTTTGACTATCGAACTTTGAGGTT
TAACCATCCATACACAATGATGTTT
Done.