Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024565.1 Corchorus olitorius cultivar O-4 contig24598, 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: 25804
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:1820 original size:40 final size:40
Alignment explanation
Indices: 1765--1844 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
1755 GGGTGATTCA
1765 AGGTACTATGAAAGGCAAAAGGAATTGTAAATAAAAGATG
1 AGGTACTATGAAAGGCAAAAGGAATTGTAAATAAAAGATG
*
1805 AGGTACTATGCAAGGCAAAAGGAATTGTAAATAAAAGATG
1 AGGTACTATGAAAGGCAAAAGGAATTGTAAATAAAAGATG
1845 GGCTAATACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.49, C:0.06, G:0.25, T:0.20
Consensus pattern (40 bp):
AGGTACTATGAAAGGCAAAAGGAATTGTAAATAAAAGATG
Found at i:2418 original size:27 final size:27
Alignment explanation
Indices: 2376--2449 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 27
2366 AAGTGGACTT
* * *
2376 AAAATGACCAACATGCCCCTGAATATG
1 AAAATGACTAAAATGCCCCTGAATATA
* * * *
2403 CAAATGACTAAAATG-CCCTTAGTGTA
1 AAAATGACTAAAATGCCCCTGAATATA
2429 AAAATGACTAAAATGCCCCTG
1 AAAATGACTAAAATGCCCCTG
2450 GGTGACCCTA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 21 0.57
27 16 0.43
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.22
Consensus pattern (27 bp):
AAAATGACTAAAATGCCCCTGAATATA
Found at i:2792 original size:2 final size:2
Alignment explanation
Indices: 2785--2811 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2775 CTACTACTTG
2785 TA 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 TA T
2812 TAATATAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6582 original size:21 final size:21
Alignment explanation
Indices: 6558--6603 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
6548 AGCACCATTC
6558 TCTTCATCTTTCTTTTCAGTT
1 TCTTCATCTTTCTTTTCAGTT
6579 TCTTCATCTTTCTTTTCAGTT
1 TCTTCATCTTTCTTTTCAGTT
6600 TCTT
1 TCTT
6604 TCAATCTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.09, C:0.24, G:0.04, T:0.63
Consensus pattern (21 bp):
TCTTCATCTTTCTTTTCAGTT
Found at i:9546 original size:27 final size:27
Alignment explanation
Indices: 9489--9556 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 27
9479 AGGGTTATCC
* * *
9489 AGGGCCATTTTGGTCGTTTGCACGTCT
1 AGGGGCATTTTGGTCATTTGCACATCT
* *
9516 -GGGGCATTTTGGTCATTTGTACATTT
1 AGGGGCATTTTGGTCATTTGCACATCT
*
9542 AGGGGTATTTTGGTC
1 AGGGGCATTTTGGTC
9557 CCTTTCTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 21 0.62
27 13 0.38
ACGTcount: A:0.13, C:0.15, G:0.31, T:0.41
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCACATCT
Found at i:14108 original size:27 final size:27
Alignment explanation
Indices: 14078--14152 Score: 132
Period size: 27 Copynumber: 2.8 Consensus size: 27
14068 TTAGGGTCAC
*
14078 CCAGGGGCATTTTGGTCATTTGCACAT
1 CCAGGGGCATTTTGGTCATTTACACAT
*
14105 CCAGGGGCATTTTGGTCATTTACACGT
1 CCAGGGGCATTTTGGTCATTTACACAT
14132 CCAGGGGCATTTTGGTCATTT
1 CCAGGGGCATTTTGGTCATTT
14153 CAAGTGCACT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (27 bp):
CCAGGGGCATTTTGGTCATTTACACAT
Found at i:19246 original size:166 final size:164
Alignment explanation
Indices: 18972--19301 Score: 606
Period size: 166 Copynumber: 2.0 Consensus size: 164
18962 GATTCTCAGC
* * *
18972 TACTTGTTCATATTTGTCTTCAGTTACTGACTACTCTTTGTTTTTGTTTTCAGGCTTAGACGTAC
1 TACTTGTTCATATTTGTCTTCAGTTACTGACTACTCTTTGTTTTCGTTTTCAGGCTCAGACATAC
19037 CTGCATAACTCTTCTGTTTTGCAGGTTGCATTGTGCATCCCCATGCATTTCACATCTTCAAAAGC
66 CTGCATAACTCTTCTGTTTTGCAGGTTGCATTGTGCATCCCCATGCATTTCACATCTTCAAAAGC
19102 ATAATTGATCAAGCATGCTCATGCATCTGCTCACCA
131 ATAATTGATCAAGCATGCTCATG--TCTGCTCACCA
19138 TACTTGTTCATATTTGTCTTCAGTTACTGACTACTCTTTGTTTTCGTTTTCAGGCTCAGACATAC
1 TACTTGTTCATATTTGTCTTCAGTTACTGACTACTCTTTGTTTTCGTTTTCAGGCTCAGACATAC
*
19203 CTGCATAACTCTTCTGTTTTGCAGGTTGCATTGTGCATCCCCATGCATTTCACATCTTCAAGAGC
66 CTGCATAACTCTTCTGTTTTGCAGGTTGCATTGTGCATCCCCATGCATTTCACATCTTCAAAAGC
19268 ATAATTGATCAAGCATGCTCATGTCTGCTCACCA
131 ATAATTGATCAAGCATGCTCATGTCTGCTCACCA
19302 ATATAGTTTG
Statistics
Matches: 160, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
164 11 0.07
166 149 0.93
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.39
Consensus pattern (164 bp):
TACTTGTTCATATTTGTCTTCAGTTACTGACTACTCTTTGTTTTCGTTTTCAGGCTCAGACATAC
CTGCATAACTCTTCTGTTTTGCAGGTTGCATTGTGCATCCCCATGCATTTCACATCTTCAAAAGC
ATAATTGATCAAGCATGCTCATGTCTGCTCACCA
Found at i:21181 original size:12 final size:11
Alignment explanation
Indices: 21154--21201 Score: 78
Period size: 12 Copynumber: 4.2 Consensus size: 11
21144 TTCGTTAAGT
21154 AATTCAAATCA
1 AATTCAAATCA
21165 AATTCAAATCGA
1 AATTCAAATC-A
21177 AATTCAAATCA
1 AATTCAAATCA
21188 AAGTTCAAATCA
1 AA-TTCAAATCA
21200 AA
1 AA
21202 AGCGAATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.37
12 22 0.63
ACGTcount: A:0.54, C:0.17, G:0.04, T:0.25
Consensus pattern (11 bp):
AATTCAAATCA
Found at i:21184 original size:23 final size:24
Alignment explanation
Indices: 21154--21198 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
21144 TTCGTTAAGT
21154 AATTCAAATCAAA-TTCAAATCGA
1 AATTCAAATCAAAGTTCAAATCGA
21177 AATTCAAATCAAAGTTCAAATC
1 AATTCAAATCAAAGTTCAAATC
21199 AAAAGCGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (24 bp):
AATTCAAATCAAAGTTCAAATCGA
Found at i:23435 original size:50 final size:50
Alignment explanation
Indices: 23360--23503 Score: 229
Period size: 50 Copynumber: 2.9 Consensus size: 50
23350 CGAATGTTTT
*
23360 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
* *
23410 GGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCGTTTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
* *
23460 GGCTTTTCCACAAGCCGAACTCATTTCCATACGAGTC-ATT-TCAA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAA
23504 ACCTTGGTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
48 4 0.05
49 2 0.02
50 81 0.93
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
Found at i:23825 original size:50 final size:50
Alignment explanation
Indices: 23556--23814 Score: 383
Period size: 50 Copynumber: 5.1 Consensus size: 50
23546 TTACCTTTTT
* * *
23556 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAACGGAAGACGGTCT
1 TTTTAAAATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
**
23606 TTTTATAGAATTGAATTGGTAGACAGTTCAAAGGATAAGCAAAAGACGGTCC
1 TTTTA-A-AATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
23658 TTTTAAAAATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGATTC
1 TTTT-AAAATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* * *
23709 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGAAAGACAGTCC
1 TTTTAAAATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
23759 TTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAAATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
23809 TTTTAA
1 TTTTAA
23815 TATTAGATTG
Statistics
Matches: 188, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
50 98 0.52
51 45 0.24
52 44 0.23
53 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.27
Consensus pattern (50 bp):
TTTTAAAATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Done.