Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015651.1 Corchorus olitorius cultivar O-4 contig15684, 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: 33907
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:1123 original size:20 final size:20
Alignment explanation
Indices: 1098--1137 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1088 AATTACAAAC
1098 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
1118 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
1138 TTGAACCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAACTCACATTCCGTGAGAG
Found at i:1553 original size:14 final size:13
Alignment explanation
Indices: 1520--1604 Score: 62
Period size: 12 Copynumber: 7.2 Consensus size: 13
1510 AACCGTTTAA
1520 TAATTATATATAT
1 TAATTATATATAT
*
1533 T-ATTATATAT-G
1 TAATTATATATAT
1544 TAATTATATATAT
1 TAATTATATATAT
1557 CTAA-TAT-TAT-T
1 -TAATTATATATAT
*
1568 TTA-TATATATA-
1 TAATTATATATAT
1579 TAA-TATATAT-T
1 TAATTATATATAT
* *
1590 TAATAATAAATAT
1 TAATTATATATAT
1603 TA
1 TA
1605 TTAAACGGTC
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
10 5 0.09
11 17 0.29
12 26 0.45
13 7 0.12
14 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (13 bp):
TAATTATATATAT
Found at i:1571 original size:21 final size:22
Alignment explanation
Indices: 1523--1590 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 22
1513 CGTTTAATAA
*
1523 TTATATATAT-TATTATATATGT
1 TTATATATATATAATATATAT-T
*
1545 AATTATATATATCTAATAT-TATT
1 --TTATATATATATAATATATATT
1568 TTATATATATATAATATATATT
1 TTATATATATATAATATATATT
1590 T
1 T
1591 AATAATAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
21 16 0.40
22 5 0.12
23 1 0.03
24 13 0.32
25 5 0.12
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (22 bp):
TTATATATATATAATATATATT
Found at i:1591 original size:21 final size:20
Alignment explanation
Indices: 1523--1606 Score: 75
Period size: 21 Copynumber: 4.0 Consensus size: 20
1513 CGTTTAATAA
*
1523 TTATATATATTATTATATATGTAA
1 TTATATATA-TA-TA-ATAT-TAT
*
1547 TTATATATATCTAATATTATT
1 TTATATATATATAATATTA-T
1568 TTATATATATATAATATATAT
1 TTATATATATATAATAT-TAT
1589 TTA-ATA-ATA-AATATTAT
1 TTATATATATATAATATTAT
1606 T
1 T
1607 AAACGGTCGG
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
17 4 0.07
18 5 0.09
19 3 0.05
20 5 0.09
21 24 0.44
22 4 0.07
23 1 0.02
24 9 0.16
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (20 bp):
TTATATATATATAATATTAT
Found at i:14997 original size:282 final size:277
Alignment explanation
Indices: 14498--15022 Score: 888
Period size: 282 Copynumber: 1.9 Consensus size: 277
14488 TGTAGATCAG
* *
14498 AAAAGGGGATCCTAATTTCTACACTGCGTCGTCGACTATCTCAATCCCTACGCTATATACGTGCT
1 AAAAGGGGATCCTAATTTCTACACTGCATCATCGACTATCTCAATCCCTACGCTATATACGTGCT
*
14563 CGGTGGCGGCTGATGTTACCACTGCTACGACTCAACCACCATTCTGAGTGTTGTTCTGCCTTTGT
66 CGGTGGCGGCTGATGTTACCACTGCTACGACTCAACCACCATTCTGAGTGTTGTTCTGCATTTGT
14628 AGTTTACCATCAACTAAACCACGGGTACGCACAACAATTCTCCAATATTTTCAAACCCGAACCGG
131 AGTTTACCATCAACTAAACCACGGGTACGCACAACAATTCTCCAATATTTTCAAACCCGAACCGG
* * *
14693 ACCGACCGGTCCGATCGGGACCCGGAGGCCTATCCGGCCGGAGGGGGTGCGATCCGACCGGTTCA
196 ACCGACCGGTCCAACCGGGACCCGGAAGCCTATCCGGCCGGAGGGGGTGCGATCCGACCGGTTCA
14758 ACCGGGACCCGGAGGCA
261 ACCGGGACCCGGAGGCA
* * *
14775 AAAAGGGGATCCTAATTTCTGCACTGCATCATCGACTATCTCAATCTCTACGTTATATACGTGCT
1 AAAAGGGGATCCTAATTTCTACACTGCATCATCGACTATCTCAATCCCTACGCTATATACGTGCT
*
14840 CGGTGGCGGCTGGTGTTACCACTGCTACGACTCAAGTCAACCACCATTCTGAGTGTTGTTCTGCA
66 CGGTGGCGGCTGATGTTACCACTGCTACGA--C---TCAACCACCATTCTGAGTGTTGTTCTGCA
*
14905 TTTGTAGTTTACCATCAACTAAACCACGGGTACGCACAACAATTCTCCAATATTTTCAAACTCGA
126 TTTGTAGTTTACCATCAACTAAACCACGGGTACGCACAACAATTCTCCAATATTTTCAAACCCGA
* *
14970 GCCGGACCGACCGGTTCAACCGGGACCCGGAAGCCTATCCGGCCGGAGGGGGT
191 ACCGGACCGACCGGTCCAACCGGGACCCGGAAGCCTATCCGGCCGGAGGGGGT
15023 TAACCGGGAG
Statistics
Matches: 230, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
277 89 0.39
279 1 0.00
282 140 0.61
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (277 bp):
AAAAGGGGATCCTAATTTCTACACTGCATCATCGACTATCTCAATCCCTACGCTATATACGTGCT
CGGTGGCGGCTGATGTTACCACTGCTACGACTCAACCACCATTCTGAGTGTTGTTCTGCATTTGT
AGTTTACCATCAACTAAACCACGGGTACGCACAACAATTCTCCAATATTTTCAAACCCGAACCGG
ACCGACCGGTCCAACCGGGACCCGGAAGCCTATCCGGCCGGAGGGGGTGCGATCCGACCGGTTCA
ACCGGGACCCGGAGGCA
Found at i:27057 original size:2 final size:2
Alignment explanation
Indices: 27050--27076 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27040 GTGAGTTCAA
27050 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 A
27077 AAAGGAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32994 original size:32 final size:32
Alignment explanation
Indices: 32949--33010 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
32939 TTTGAATCAC
*
32949 CTATTATATCCTTATTTTTCAAATATATTTGT
1 CTATTATACCCTTATTTTTCAAATATATTTGT
*
32981 CTATTATACCCTTATTTTTCGAATATATTT
1 CTATTATACCCTTATTTTTCAAATATATTT
33011 CTTAAATGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.27, C:0.15, G:0.03, T:0.55
Consensus pattern (32 bp):
CTATTATACCCTTATTTTTCAAATATATTTGT
Found at i:33202 original size:14 final size:15
Alignment explanation
Indices: 33169--33202 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
33159 AAACTCTATT
33169 TTTTATTTATACCTA
1 TTTTATTTATACCTA
*
33184 TTTTATTTTTACC-A
1 TTTTATTTATACCTA
33198 TTTTA
1 TTTTA
33203 CTAATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTATTTATACCTA
Found at i:33826 original size:15 final size:16
Alignment explanation
Indices: 33790--33832 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
33780 AATTTTCTCG
33790 GGTCATTTGGGTTTCA
1 GGTCATTTGGGTTTCA
* *
33806 GCTCATTTTGG-TTCA
1 GGTCATTTGGGTTTCA
*
33821 GGTCATTCGGGT
1 GGTCATTTGGGT
33833 CTCGGGTTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.12, C:0.16, G:0.30, T:0.42
Consensus pattern (16 bp):
GGTCATTTGGGTTTCA
Done.