Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024283.1 Corchorus olitorius cultivar O-4 contig24316, 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: 23430
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:1392 original size:21 final size:21
Alignment explanation
Indices: 1368--1484 Score: 182
Period size: 21 Copynumber: 5.6 Consensus size: 21
1358 CTTAGGCAAT
* *
1368 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
1389 TCCAATGATCTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
1410 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
1431 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
1452 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAACTTGGAACCTT-C
1473 TCCAATGAACTT
1 TCCAATGAACTT
1485 CTAGCATCTT
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
20 3 0.03
21 87 0.97
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30
Consensus pattern (21 bp):
TCCAATGAACTTGGAACCTTC
Found at i:2161 original size:5 final size:6
Alignment explanation
Indices: 2146--2175 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
2136 TTGTGAATTA
2146 TTTTTC TTTTTC TTTTTC TTTTTC TATTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC T-TTTT
2176 AATTTGCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:4720 original size:49 final size:48
Alignment explanation
Indices: 4659--4784 Score: 150
Period size: 49 Copynumber: 2.6 Consensus size: 48
4649 CTTTTTACTA
** *
4659 CACTTTTTCTCAATTTTTACTACAAAATTGAACTTTT-ATTTTTACTTG
1 CACTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCA-TTG
* **
4707 CCCATTTTTCTCAATTTTTAAGACAAAATTGATTTTTTAATTTTCATTG
1 CAC-TTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCATTG
*
4756 CACTTTTTATCAATTTTT--GACAAAATTGA
1 CACTTTTTCTCAATTTTTAAGACAAAATTGA
4785 TTGGCACCTT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
46 11 0.16
48 16 0.24
49 35 0.51
50 6 0.09
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (48 bp):
CACTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCATTG
Found at i:11125 original size:44 final size:44
Alignment explanation
Indices: 11062--11148 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
11052 CCCGGTCTTT
11062 CCAATGTGTTACTACTGTAAATCTAACACGAATCTAATTGCAAA
1 CCAATGTGTTACTACTGTAAATCTAACACGAATCTAATTGCAAA
11106 CCAATGTGTTACTACTGTAAATCTAACACGAATCTAATTGCAA
1 CCAATGTGTTACTACTGTAAATCTAACACGAATCTAATTGCAA
11149 TTTGGTTTGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (44 bp):
CCAATGTGTTACTACTGTAAATCTAACACGAATCTAATTGCAAA
Found at i:14083 original size:16 final size:15
Alignment explanation
Indices: 14046--14135 Score: 74
Period size: 16 Copynumber: 5.7 Consensus size: 15
14036 AGAAAAAGTA
14046 AATGACCCGAACCCG
1 AATGACCCGAACCCG
***
14061 CCCGACCCGAGACCCG
1 AATGACCCGA-ACCCG
14077 AATGACCCGTAACCC-
1 AATGACCCG-AACCCG
14092 AGATGACCCGTAACCCG
1 A-ATGACCCG-AACCCG
* *
14109 AGTGACCCGAGACCTG
1 AATGACCCGA-ACCCG
*
14125 TATGACCCGAA
1 AATGACCCGAA
14136 ATCCGAATAA
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
15 10 0.17
16 48 0.80
17 2 0.03
ACGTcount: A:0.29, C:0.39, G:0.22, T:0.10
Consensus pattern (15 bp):
AATGACCCGAACCCG
Found at i:17681 original size:21 final size:21
Alignment explanation
Indices: 17655--17696 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
17645 TCTTTTGGTG
* *
17655 ATGATCTCTAATGGGCTTCAA
1 ATGATCTCCAATGGCCTTCAA
17676 ATGATCTCCAATGGCCTTCAA
1 ATGATCTCCAATGGCCTTCAA
17697 CTCTTCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (21 bp):
ATGATCTCCAATGGCCTTCAA
Found at i:17836 original size:21 final size:21
Alignment explanation
Indices: 17812--17882 Score: 124
Period size: 21 Copynumber: 3.4 Consensus size: 21
17802 CTTAGGCAAT
17812 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
17833 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
**
17854 TCCAATGAGCTTAAAACTTGC
1 TCCAATGAGCTTGGAACTTGC
17875 TCCAATGA
1 TCCAATGA
17883 ACTCCTAGCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:19765 original size:33 final size:33
Alignment explanation
Indices: 19680--19817 Score: 127
Period size: 33 Copynumber: 4.2 Consensus size: 33
19670 ATGATCAACC
* ** * *
19680 AAAACAGATTT-GTTTTCATCACAAGTAGCATCC
1 AAAACAGATTTAG-TATCATCACAAACAACATCT
* * *
19713 AAAATAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTATCATCACAAACAACATCT
* *
19746 AAAACAGATTTAGTGTCATCACAAACAACATTT
1 AAAACAGATTTAGTATCATCACAAACAACATCT
** *
19779 AAATTAGATTTAGTATCATCACTAACAACATCT
1 AAAACAGATTTAGTATCATCACAAACAACATCT
19812 AAAACA
1 AAAACA
19818 CTCTTTGCAA
Statistics
Matches: 86, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
32 4 0.05
33 77 0.90
34 5 0.06
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCACAAACAACATCT
Found at i:23181 original size:21 final size:21
Alignment explanation
Indices: 23155--23288 Score: 191
Period size: 21 Copynumber: 6.4 Consensus size: 21
23145 TGCTAGAAGT
23155 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
23176 TCATTGGAGCAA-GTTTCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
23197 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
23218 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
23239 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
*
23260 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
23281 TCATTGGA
1 TCATTGGA
23289 ATTGCCTGAT
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
20 2 0.02
21 104 0.98
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.