Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000652.1 Corchorus olitorius cultivar O-4 contig00652, 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: 11175
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Found at i:3127 original size:21 final size:21
Alignment explanation
Indices: 3103--3155 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3093 AATAAAAACG
3103 TAATTATAATA-TAACTAATAA
1 TAATTATAATACT-ACTAATAA
* *
3124 TAATTTTAGTACTACTAATAA
1 TAATTATAATACTACTAATAA
*
3145 TTATTATAATA
1 TAATTATAATA
3156 ATAAGAAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (21 bp):
TAATTATAATACTACTAATAA
Found at i:3137 original size:18 final size:18
Alignment explanation
Indices: 3116--3159 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3106 TTATAATATA
3116 ACTAATAATAATT-TTAGT
1 ACTAATAATAATTATTA-T
*
3134 ACTACTAATAATTATTAT
1 ACTAATAATAATTATTAT
*
3152 AATAATAA
1 ACTAATAA
3160 GAAGTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (18 bp):
ACTAATAATAATTATTAT
Found at i:3174 original size:24 final size:24
Alignment explanation
Indices: 3142--3191 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
3132 GTACTACTAA
*
3142 TAATTATTATAATAATAAGAAGTT
1 TAATAATTATAATAATAAGAAGTT
*
3166 TAATAATTATAATAATAAGATGTT
1 TAATAATTATAATAATAAGAAGTT
3190 TA
1 TA
3192 GCGTAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (24 bp):
TAATAATTATAATAATAAGAAGTT
Found at i:3283 original size:56 final size:57
Alignment explanation
Indices: 3221--3334 Score: 203
Period size: 56 Copynumber: 2.0 Consensus size: 57
3211 AGAAGTCGTT
3221 TATGTAAAAGTAATTGTTATCATCTTAG-ACTTTTTTTTAATTATAGAAATAAAATC
1 TATGTAAAAGTAATTGTTATCATCTTAGAACTTTTTTTTAATTATAGAAATAAAATC
* *
3277 TATGTAAAAGTAATTGTTATCATCTTAGAATTTTTTTTTAATTATGGAAATAAAATC
1 TATGTAAAAGTAATTGTTATCATCTTAGAACTTTTTTTTAATTATAGAAATAAAATC
3334 T
1 T
3335 GGTTGGATTA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 28 0.51
57 27 0.49
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.46
Consensus pattern (57 bp):
TATGTAAAAGTAATTGTTATCATCTTAGAACTTTTTTTTAATTATAGAAATAAAATC
Found at i:3483 original size:2 final size:2
Alignment explanation
Indices: 3460--3506 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
3450 AATTTAAACT
* * *
3460 TA TA TA -A TA TA AA GA TA AA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3501 TA TA TA
1 TA TA TA
3507 AACATATAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:3513 original size:12 final size:12
Alignment explanation
Indices: 3460--3514 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
3450 AATTTAAACT
3460 TATATAATATAAA
1 TATAT-ATATAAA
* * *
3473 GATAAATATATA
1 TATATATATAAA
*
3485 TATATATATATA
1 TATATATATAAA
3497 TATATATATAAA
1 TATATATATAAA
*
3509 CATATA
1 TATATA
3515 ATATGGATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
12 32 0.91
13 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (12 bp):
TATATATATAAA
Found at i:5973 original size:77 final size:79
Alignment explanation
Indices: 5871--6016 Score: 251
Period size: 78 Copynumber: 1.9 Consensus size: 79
5861 AAATGTTAAA
* *
5871 AAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATATAG-TTTTTAGTAGAGTAAAATTAT
1 AAATAGTTATAAAAATATTAGATTTAATCAAATAAAAATATAGTTTTTTAGTAGAGTAAAAATAT
5935 AATAGAGTTTTTAT
66 AATAGAGTTTTTAT
*
5949 AAATAGTTA-GAAAATATTAGATTTAATCAAATAAAAATATAGTTTTTTAGTAGAGTAAAAATAT
1 AAATAGTTATAAAAATATTAGATTTAATCAAATAAAAATATAGTTTTTTAGTAGAGTAAAAATAT
6013 AATA
66 AATA
6017 ATTTAAAAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
77 31 0.48
78 33 0.52
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (79 bp):
AAATAGTTATAAAAATATTAGATTTAATCAAATAAAAATATAGTTTTTTAGTAGAGTAAAAATAT
AATAGAGTTTTTAT
Found at i:9228 original size:2 final size:2
Alignment explanation
Indices: 9216--9248 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
9206 ATATTTAGTC
9216 TA TA T- TA TA TA TA TA TA TA TA TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9249 GCTTGAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9242 original size:17 final size:17
Alignment explanation
Indices: 9216--9248 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9206 ATATTTAGTC
*
9216 TATATTATATATATATA
1 TATATAATATATATATA
9233 TATATAATATATATAT
1 TATATAATATATATAT
9249 GCTTGAATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATAATATATATATA
Found at i:10085 original size:22 final size:23
Alignment explanation
Indices: 10034--10085 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
10024 AAGAAAAAAA
10034 AAAATCAAGACTACTAAAACTTTTT
1 AAAATCAAGACTACTAAAAC--TTT
*
10059 GAAATCAAGACTACTAAAAC-TT
1 AAAATCAAGACTACTAAAACTTT
10081 AAAAT
1 AAAAT
10086 TTAAAAGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.24
25 19 0.76
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (23 bp):
AAAATCAAGACTACTAAAACTTT
Found at i:10126 original size:2 final size:2
Alignment explanation
Indices: 10119--10143 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10109 TGATTTCTCT
10119 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
10144 TATTTGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.