Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018257.1 Corchorus olitorius cultivar O-4 contig18290, 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: 29708
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1700 original size:100 final size:100
Alignment explanation
Indices: 1527--1947 Score: 743
Period size: 100 Copynumber: 4.2 Consensus size: 100
1517 TTTTATCTTC
* * * *
1527 GACCTTAGAATTCGATCCGGACTCCCCGTCAGAACATCGAATCTAAGTTGGCCAAACGTAAAGCC
1 GACCTTAGATTTCGATACGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAGCC
* * *
1592 CCGGACTCTTTGTGAGAACGGCAACGTTCGTAATT
66 CTGGACTCTTTGGGAGAACGACAACGTTCGTAATT
* *
1627 GACCTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAGCC
1 GACCTTAGATTTCGATACGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAGCC
1692 CTGGACTCTTTGGGAGAACGACAACGTTCGTAATT
66 CTGGACTCTTTGGGAGAACGACAACGTTCGTAATT
*
1727 GACCTTAGATTTCGATACGGACTCCCCGTGAGAACATCGAAACTAAGTTGGCCGAACGTAAAGCC
1 GACCTTAGATTTCGATACGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAGCC
*
1792 CTGGACTCTTTGGGAGAACGGCAACGTTCGTAATT
66 CTGGACTCTTTGGGAGAACGACAACGTTCGTAATT
1827 GACCTTAGATTTCGATACGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAGCC
1 GACCTTAGATTTCGATACGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAGCC
1892 CTGGACTCTTTGGGAGAACGACAACGTTCGTAATT
66 CTGGACTCTTTGGGAGAACGACAACGTTCGTAATT
1927 GACCTTAGATTTCGATACGGA
1 GACCTTAGATTTCGATACGGA
1948 ATTGACCTTA
Statistics
Matches: 310, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 310 1.00
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (100 bp):
GACCTTAGATTTCGATACGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAGCC
CTGGACTCTTTGGGAGAACGACAACGTTCGTAATT
Found at i:1955 original size:24 final size:24
Alignment explanation
Indices: 1923--1971 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1913 CAACGTTCGT
1923 AATTGACCTTAGATTTCGATACGG
1 AATTGACCTTAGATTTCGATACGG
1947 AATTGACCTTAGATTTCGATACGG
1 AATTGACCTTAGATTTCGATACGG
1971 A
1 A
1972 CTCCTCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (24 bp):
AATTGACCTTAGATTTCGATACGG
Found at i:8509 original size:22 final size:22
Alignment explanation
Indices: 8481--8526 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
8471 TTTGTTTTTC
8481 TTAGTTTGCAATAGATTGAGAA
1 TTAGTTTGCAATAGATTGAGAA
8503 TTAGTTTGCAATAGATTGAGAA
1 TTAGTTTGCAATAGATTGAGAA
8525 TT
1 TT
8527 GATAGACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (22 bp):
TTAGTTTGCAATAGATTGAGAA
Found at i:9302 original size:108 final size:109
Alignment explanation
Indices: 9112--9331 Score: 354
Period size: 108 Copynumber: 2.0 Consensus size: 109
9102 TCGAATTTGC
* *
9112 TAACCACCTACTCACATATATGATAAGAATCGAGAGGGAAAAAAAAACTCTATAACTAAAATGAT
1 TAACCACCTACTCACATATATGATAAGAATCGAGA--GAAAAAAAAACTCTAAAACTAAAATAAT
* *
9177 TTGCTAGCCACATATCAAGAATGCTCG-ACGTGCCAGCGCGAGCCGA
64 TTGCTAGCCACAAATCAAGAATGCT-GAACGCGCCAGCGCGAGCCGA
9223 TAACCACCTACTCACATATATGATAAGAATCGAGA-AAAAAAAAACTCTAAAACTAAAATAATTT
1 TAACCACCTACTCACATATATGATAAGAATCGAGAGAAAAAAAAACTCTAAAACTAAAATAATTT
*
9287 GCTAGCCACAAATCAAGAATGCTGAACGCGCCAGCGTGAGCCGA
66 GCTAGCCACAAATCAAGAATGCTGAACGCGCCAGCGCGAGCCGA
9331 T
1 T
9332 CAACTTGTTA
Statistics
Matches: 103, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
107 1 0.01
108 67 0.65
111 35 0.34
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (109 bp):
TAACCACCTACTCACATATATGATAAGAATCGAGAGAAAAAAAAACTCTAAAACTAAAATAATTT
GCTAGCCACAAATCAAGAATGCTGAACGCGCCAGCGCGAGCCGA
Found at i:12977 original size:23 final size:20
Alignment explanation
Indices: 12925--12963 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12915 TTAAAAAAAA
*
12925 TTAATAATTAGTTATTATTT
1 TTAAAAATTAGTTATTATTT
12945 TTAAAAATTAGTTATTATT
1 TTAAAAATTAGTTATTATT
12964 ATTTTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTAAAAATTAGTTATTATTT
Found at i:13451 original size:16 final size:16
Alignment explanation
Indices: 13430--13466 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
13420 ATGTGACTTC
13430 ATTTCCCTTCCTTCCT
1 ATTTCCCTTCCTTCCT
*
13446 ATTTCCTTTCCTTCCT
1 ATTTCCCTTCCTTCCT
13462 ATTTC
1 ATTTC
13467 TTTCCTCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.08, C:0.38, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTCCCTTCCTTCCT
Found at i:16683 original size:129 final size:129
Alignment explanation
Indices: 16479--16720 Score: 348
Period size: 129 Copynumber: 1.9 Consensus size: 129
16469 ATTGTTTAAT
* * *
16479 TTTTATAGTTTTACTCAACAAGAAATTCTACTTTTATTTAATTAAATCTAATATCCTTATAATTA
1 TTTTATAATTTTACTCAACAAGAAACTCTACTTTTATTTAATTAAATCTAATATCCTTATAACTA
* *
16544 TTTTATTTTTATCATTTTACTATTTTAA-TAAAAACTTATATATATTACAAAATTTAAATATAC
66 TTTTATTTTTAACATTTTACTAATTTAATTAAAAACTTATATATATTACAAAATTTAAATATAC
**
16607 TTTTATAATTTTACTCATTTAA-AAACTCTA-TTTT-TTTAATTAAATCTAATAATTTCCTTATA
1 TTTTATAATTTTACTCA-ACAAGAAACTCTACTTTTATTTAATTAAATCTAAT-A--TCCTTATA
*
16669 CCTATTTTATTTTTAACATTTTACTAATTTAATTAAAAACTTATATATATTA
62 ACTATTTTATTTTTAACATTTTACTAATTTAATTAAAAACTTATATATATTA
16721 GAATTTTTAA
Statistics
Matches: 101, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
126 16 0.16
127 5 0.05
128 23 0.23
129 38 0.38
130 19 0.19
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51
Consensus pattern (129 bp):
TTTTATAATTTTACTCAACAAGAAACTCTACTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTAACATTTTACTAATTTAATTAAAAACTTATATATATTACAAAATTTAAATATAC
Found at i:17101 original size:76 final size:78
Alignment explanation
Indices: 17000--17163 Score: 271
Period size: 79 Copynumber: 2.1 Consensus size: 78
16990 TAAGAAATCA
* *
17000 AAATATTCAATTAAACAAATATTTAAATAATAAT-AA-A-TATTAATTAGAAGTGAAAGCTTAGT
1 AAATATTTAATTAAACAAATATTTAAATAATAATGAATATTATTAATTAGAAGCGAAAGCTTAGT
17062 ATATTATCAAAAC
66 ATATTATCAAAAC
17075 AAATATTTAATTAAAACAAATATTTAAATAATAATGAATATTATTAATTAGAAGCGAAAGCTTAG
1 AAATATTTAATT-AAACAAATATTTAAATAATAATGAATATTATTAATTAGAAGCGAAAGCTTAG
*
17140 TATATTATCCAAAC
65 TATATTATCAAAAC
17154 AAATATTTAA
1 AAATATTTAA
17164 ATAACAATGA
Statistics
Matches: 82, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
75 11 0.13
76 22 0.27
77 2 0.02
78 1 0.01
79 46 0.56
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (78 bp):
AAATATTTAATTAAACAAATATTTAAATAATAATGAATATTATTAATTAGAAGCGAAAGCTTAGT
ATATTATCAAAAC
Found at i:17196 original size:59 final size:62
Alignment explanation
Indices: 17088--17207 Score: 192
Period size: 59 Copynumber: 2.0 Consensus size: 62
17078 TATTTAATTA
*
17088 AAACAAATATTTAAATAATAATGAATATTATTAATTAGAAGCGAAAGCTTAGTATATTATCC
1 AAACAAATATTTAAATAACAATGAATATTATTAATTAGAAGCGAAAGCTTAGTATATTATCC
**
17150 AAACAAATATTTAAATAACAATG-A-A-TATTAATTAGAAGTTAAAGCTTAGTATATTATC
1 AAACAAATATTTAAATAACAATGAATATTATTAATTAGAAGCGAAAGCTTAGTATATTATC
17208 AAAATACATT
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
59 31 0.56
60 1 0.02
61 1 0.02
62 22 0.40
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.34
Consensus pattern (62 bp):
AAACAAATATTTAAATAACAATGAATATTATTAATTAGAAGCGAAAGCTTAGTATATTATCC
Found at i:17377 original size:63 final size:64
Alignment explanation
Indices: 17271--17415 Score: 247
Period size: 63 Copynumber: 2.2 Consensus size: 64
17261 CTGAGAAGCA
*
17271 GCACCAAGCTATGTTGTTCGGTAAAAAGTATAGCTTGGTTCGGTAGAAGAGCTGTAGAGGTTTC
1 GCACGAAGCTATGTTGTTCGGTAAAAAGTATAGCTTGGTTCGGTAGAAGAGCTGTAGAGGTTTC
17335 GCACGAAGCTATGTTGTTCGGT-AAAAGTATAGCTTGGTTCGGTAGAAGAGCTGTAGAGGTTTC
1 GCACGAAGCTATGTTGTTCGGTAAAAAGTATAGCTTGGTTCGGTAGAAGAGCTGTAGAGGTTTC
*
17398 ACACGAAAGACTATGTTG
1 GCACG-AAG-CTATGTTG
17416 AGGGTCCCCA
Statistics
Matches: 77, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
63 45 0.58
64 24 0.31
65 8 0.10
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.29
Consensus pattern (64 bp):
GCACGAAGCTATGTTGTTCGGTAAAAAGTATAGCTTGGTTCGGTAGAAGAGCTGTAGAGGTTTC
Found at i:20417 original size:45 final size:45
Alignment explanation
Indices: 20353--20442 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
20343 AAAAGGGAAG
20353 GATAATTTCTAAGCAAAAATCAGTATAAAGTTGAATAATATTACC
1 GATAATTTCTAAGCAAAAATCAGTATAAAGTTGAATAATATTACC
20398 GATAATTTCTAAGCAAAAATCAGTATAAAGTTGAATAATATTACC
1 GATAATTTCTAAGCAAAAATCAGTATAAAGTTGAATAATATTACC
20443 AATTTTAAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (45 bp):
GATAATTTCTAAGCAAAAATCAGTATAAAGTTGAATAATATTACC
Found at i:26152 original size:17 final size:17
Alignment explanation
Indices: 26130--26166 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
26120 GCTTGCTTGG
26130 TAAGTGAGTTGTTGTTT
1 TAAGTGAGTTGTTGTTT
26147 TAAGTGAGTTGTTGTTT
1 TAAGTGAGTTGTTGTTT
26164 TAA
1 TAA
26167 TTGTGGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (17 bp):
TAAGTGAGTTGTTGTTT
Done.