Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022911.1 Corchorus olitorius cultivar O-4 contig22944, 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: 9992
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:5278 original size:27 final size:27
Alignment explanation
Indices: 5227--5279 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
5217 AGAGAAAATG
* *
5227 GATAAGTTCAGATTGAAAGCCTACAAA
1 GATAAGCTCAGATTGAAAGACTACAAA
*
5254 GATAAGCTCAGATTGAAAGAGTACAA
1 GATAAGCTCAGATTGAAAGACTACAA
5280 TCAGTGGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (27 bp):
GATAAGCTCAGATTGAAAGACTACAAA
Found at i:6205 original size:109 final size:107
Alignment explanation
Indices: 5984--6267 Score: 288
Period size: 109 Copynumber: 2.6 Consensus size: 107
5974 TCAGTTCATT
* * *
5984 TCAGTTGACCCAGGGCGATCCTTCTTCAATTTATTTCAATTGACCTAGGGCGGTCTTTCTTCAAT
1 TCAGTTGATCCAGGGCGACCCTTCTTCAATTTATTTCAATTGACCCAGGGCGGTCTTTCTTCAAT
* * * *
6049 TCATTTCAGTTTGATCTAGGATGATCTTTTCTTCATTTTACC
66 TCATGTCAGTTTGATCCAGGATGATCTTCTCCTCATTTTACC
* *
6091 TCAGTTGATCCAGGGCGACCCATTCTTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTTCATT
1 TCAGTTGATCCAGGGCGACCC-TTCTTCAATTTATTTCAA-TTGACCCAGGGCGGTC-TTTC-TT
* * * *
6156 CAGTTTATGTCAG-TTGATCCGGGGTGATC-TCTCCTCAATTTT--C
62 CAATTCATGTCAGTTTGATCCAGGATGATCTTCTCCTC-ATTTTACC
** * * * * *
6199 TCCAGTTGATCCAGGGCGATCTTTTATTCAATTTATTTCAGTCGATCCAGGGCGATCTTTCCTTC
1 T-CAGTTGATCCAGGGCGA-CCCTTCTTCAATTTATTTCAATTGACCCAGGGCGGTCTTT-CTTC
6264 AATT
63 AATT
6268 TATTTTAGCT
Statistics
Matches: 146, Mismatches: 23, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
107 28 0.19
108 32 0.22
109 51 0.35
110 23 0.16
111 12 0.08
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (107 bp):
TCAGTTGATCCAGGGCGACCCTTCTTCAATTTATTTCAATTGACCCAGGGCGGTCTTTCTTCAAT
TCATGTCAGTTTGATCCAGGATGATCTTCTCCTCATTTTACC
Found at i:6246 original size:36 final size:36
Alignment explanation
Indices: 5972--6519 Score: 395
Period size: 35 Copynumber: 15.5 Consensus size: 36
5962 ATTTCAGATG
* * * *
5972 CTTCAGTTCATTTCAGTTGACCCAGGGCGATC-CTT
1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTT
* *
6007 CTTCAATTTATTTCAATTGA-CCTAGGGCGGTC-TTT
1 CTTCAATTTATTTCAGTTGATCC-AGGGCGATCTTTT
* * **
6042 CTTCAATTCATTTCAGTTTGATCTAGGATGATCTTTT
1 CTTCAATTTATTTCAG-TTGATCCAGGGCGATCTTTT
* ** * **
6079 CTTCATTTTACCTCAGTTGATCCAGGGCGACCCATT
1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * *
6115 CTTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTT
1 CTTCAATTTATTTC-AGTTGATCCAGGGCGATCTTTT
* * * * *
6152 CATTCAGTTTATGTCAGTTGATCCGGGGTGATC-TCT
1 C-TTCAATTTATTTCAGTTGATCCAGGGCGATCTTTT
* *
6188 CCTCAATTT-TCTCCAGTTGATCCAGGGCGATCTTTT
1 CTTCAATTTAT-TTCAGTTGATCCAGGGCGATCTTTT
* * *
6224 ATTCAATTTATTTCAGTCGATCCAGGGCGATCTTTC
1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * *
6260 CTTCAATTTATTTTAGCTGACCCAGGGCGGTC-ATT
1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTT
* * *
6295 CTTCAAGTTATTTCAGTTGACCCAGGGCGGTC-TTT
1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * *
6330 CTTCAATTCATTTCAATTGATCCAGGGTGATC-CTA
1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * *
6365 CTTCAAGTCATTTTAGTTGATCGAGGGAGATCTTTT
1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTT
** *
6401 CTTCGGTTTA--T---TTGATCCAGGGCGATATTTT
1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTT
* * *
6432 CTTCAGTTCATTTCAATTGATCCAGGGCGATCTTTT
1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * * *
6468 CTTCAGTTT-CTTCAATTTATCCATGGTGATCTTTT
1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTT
* *
6503 CTGCAGTTTATTTCAGT
1 CTTCAATTTATTTCAGT
6520 AAACCGCAAA
Statistics
Matches: 405, Mismatches: 92, Indels: 31
0.77 0.17 0.06
Matches are distributed among these distances:
31 25 0.06
33 1 0.00
34 4 0.01
35 180 0.44
36 134 0.33
37 49 0.12
38 12 0.03
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (36 bp):
CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTT
Found at i:6246 original size:71 final size:73
Alignment explanation
Indices: 5985--6337 Score: 194
Period size: 71 Copynumber: 4.9 Consensus size: 73
5975 CAGTTCATTT
* * * * * *
5985 CAGTTGACCCAGGGCGATC-CTTC-TTCAATTTATTTCAATTGA-CCTAGGGCGGTCT-TTCTTC
1 CAGTTGACCCAGGGCGATCTTTTCATTCAATTTATGTCAGTCGATCC-AGGGCGATCTCTCCTTC
6046 AATTCATT-T-
65 AATT--TTCTC
* * ** * ** * * *
6055 CAGTTTGATCTAGGATGATCTTTTC-TTCATTTTACCTCAGTTGATCCAGGGCGA-CCCATTCTT
1 CAG-TTGACCCAGGGCGATCTTTTCATTCAATTTATGTCAGTCGATCCAGGGCGATCTC-TCCTT
* *
6118 CAGTTTATTTC
64 CAATTT-TCTC
* * * * * * *
6129 AAGTTGACCCAGGGTGGTCTTTTCATTCAGTTTATGTCAGTTGATCCGGGGTGATCTCTCC-TCA
1 CAGTTGACCCAGGGCGATCTTTTCATTCAATTTATGTCAGTCGATCCAGGGCGATCTCTCCTTCA
6193 ATTTTCTC
66 ATTTTCTC
* * *
6201 CAGTTGATCCAGGGCGATCTTTT-ATTCAATTTATTTCAGTCGATCCAGGGCGATCTTTCCTTCA
1 CAGTTGACCCAGGGCGATCTTTTCATTCAATTTATGTCAGTCGATCCAGGGCGATCTCTCCTTCA
*
6265 ATTTAT-TT
66 ATTT-TCTC
* * * * * * * * * *
6273 TAGCTGACCCAGGGCGGTC-ATTC-TTCAAGTTATTTCAGTTGACCCAGGGCGGTCT-TTCTTCA
1 CAGTTGACCCAGGGCGATCTTTTCATTCAATTTATGTCAGTCGATCCAGGGCGATCTCTCCTTCA
6335 ATT
66 ATT
6338 CATTTCAATT
Statistics
Matches: 223, Mismatches: 47, Indels: 26
0.75 0.16 0.09
Matches are distributed among these distances:
70 12 0.05
71 75 0.34
72 70 0.31
73 36 0.16
74 28 0.13
75 2 0.01
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (73 bp):
CAGTTGACCCAGGGCGATCTTTTCATTCAATTTATGTCAGTCGATCCAGGGCGATCTCTCCTTCA
ATTTTCTC
Found at i:6432 original size:31 final size:31
Alignment explanation
Indices: 6376--6476 Score: 94
Period size: 31 Copynumber: 3.1 Consensus size: 31
6366 TTCAAGTCAT
* * *
6376 TTTAGTTGATCGAGGGAGATCTTTTCTTCGG
1 TTTAATTGATCCAGGGCGATCTTTTCTTCGG
* * *
6407 TTTATTTGATCCAGGGCGATATTTTCTTCAGTTCA
1 TTTAATTGATCCAGGGCGATCTTTTCTTC-G---G
*
6442 TTTCAATTGATCCAGGGCGATCTTTTCTTCAG
1 TTT-AATTGATCCAGGGCGATCTTTTCTTCGG
6474 TTT
1 TTT
6477 CTTCAATTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
31 25 0.45
32 4 0.07
35 3 0.05
36 24 0.43
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.45
Consensus pattern (31 bp):
TTTAATTGATCCAGGGCGATCTTTTCTTCGG
Found at i:6499 original size:102 final size:101
Alignment explanation
Indices: 6327--6515 Score: 229
Period size: 102 Copynumber: 1.9 Consensus size: 101
6317 CAGGGCGGTC
* * *
6327 TTTCTTCAATTCATTTCAATTGATCCAGGGTGATCCTACTTCAAGTCATTTTAGTTGATCGAGGG
1 TTTCTTCAATTCATTTCAATTGATCCAGGGCGATCCTACTTCAAGT-ATTTTAATTGATCCAGGG
* *
6392 AGATCTTTTCTTCGGTTTATTTGATCCAGGGCGATAT
65 AGATCTTTTCTGCAGTTTATTTGATCCAGGGCGATAT
* * * * *
6429 TTTCTTCAGTTCATTTCAATTGATCCAGGGCGATCTTTTCTTC-AGT-TTCTTCAATTTATCCAT
1 TTTCTTCAATTCATTTCAATTGATCCAGGGCGATC-CTACTTCAAGTATT-TT-AATTGATCCAG
*
6492 GGTGATCTTTTCTGCAGTTTATTT
63 GGAGATCTTTTCTGCAGTTTATTT
6516 CAGTAAACCG
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
100 2 0.03
101 2 0.03
102 64 0.88
103 5 0.07
ACGTcount: A:0.20, C:0.19, G:0.17, T:0.45
Consensus pattern (101 bp):
TTTCTTCAATTCATTTCAATTGATCCAGGGCGATCCTACTTCAAGTATTTTAATTGATCCAGGGA
GATCTTTTCTGCAGTTTATTTGATCCAGGGCGATAT
Found at i:6807 original size:30 final size:30
Alignment explanation
Indices: 6773--7739 Score: 1303
Period size: 30 Copynumber: 32.2 Consensus size: 30
6763 TGCTTTATCA
6773 GCTTTATTTTAATCCTGGTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
*
6803 GCTTTATTTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
*
6833 GCTTTATTTTAATCCTGTTTGAGGATC-TT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
* * *
6862 AGCTTTGTTTTAATACTGGTTGAGGATCGTT
1 -GCTTTATTTTAATCCTGGTTGAGGATCATT
* * *
6893 GCTTTATCTTAATCCTGTTTGAGGATCGTT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
*
6923 GCTTTATTTTTAATCCTGTTTGAGGATCATT
1 GCTTTA-TTTTAATCCTGGTTGAGGATCATT
*
6954 GCTTTATTTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
* * *
6984 GTTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
* * *
7014 ACTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
* *
7044 GCTTTATTGTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
*
7074 GCTTTATTTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
*
7104 GCTTTTATTTTAATCCTGTTTGAGGATCATT
1 GC-TTTATTTTAATCCTGGTTGAGGATCATT
* *
7135 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
* *
7165 GCTTTATTGTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
* *
7195 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
* *
7225 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
* *
7255 GTTTTATTCTAATCCTGGTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
* * *
7285 GCTTCATGTTAATCCTGGTTGAGAATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
*
7315 GCTTTATTTTAATCCTGGTTTAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
*
7345 GCTTTATTTTAATCCTGGTTTAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
*
7375 GCTTTATTTTAATCCTGGTTTAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
7405 GCTTTATTTTAATCCTGGTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
*
7435 GCTTTATTTTAATCCTGGTTTAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
*
7465 GCTTTATTTTAATCCTGGTTTAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
7495 GCTTTATTTTAATCCTGGTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
*
7525 GCTTTATTTTAATCCTGGTTAAGGATCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
* *
7555 GCTTCATTTTAATCCTGATTGAGGAT-ATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
** *
7584 CGCTCCATTTTTATCCTGGTTGAGGAT-ATTT
1 -GCTTTATTTTAATCCTGGTTGAGGATCA-TT
* * * * **
7615 GCATCATTTTAATCATGGTGGAGGATTGTT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
* * *
7645 GCTTTATTTTAATCATGGTTGAAGACCATT
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
* * *
7675 ACTTTGTTTTAATCCTGGTTGAGGATCATC
1 GCTTTATTTTAATCCTGGTTGAGGATCATT
* * * *
7705 G-TTATATTTTTATCCTGATTTAGGATTATT
1 GCTT-TATTTTAATCCTGGTTGAGGATCATT
*
7735 ACTTT
1 GCTTT
7740 GGTTTATTTG
Statistics
Matches: 855, Mismatches: 73, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
29 7 0.01
30 784 0.92
31 64 0.07
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.48
Consensus pattern (30 bp):
GCTTTATTTTAATCCTGGTTGAGGATCATT
Found at i:8204 original size:28 final size:29
Alignment explanation
Indices: 8172--8248 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
8162 AGGGTCATCT
* *
8172 AGGGGCATTTCGGTCATTTTCG-ATATTC
1 AGGGGCATTTTGGTCATTTTCGCACATTC
*
8200 AGGGGCATTTTGGTCATTTTTGCACATTC
1 AGGGGCATTTTGGTCATTTTCGCACATTC
*
8229 AGGGGTATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
8249 AAGTTCACAT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 20 0.45
29 24 0.55
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTCGCACATTC
Found at i:8580 original size:11 final size:10
Alignment explanation
Indices: 8548--8573 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
8538 AAAGAATAAT
8548 AATACAGAAA
1 AATACAGAAA
8558 AATACAGAAA
1 AATACAGAAA
8568 AATACA
1 AATACA
8574 TTAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.12, G:0.08, T:0.12
Consensus pattern (10 bp):
AATACAGAAA
Done.