Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014878.1 Corchorus olitorius cultivar O-4 contig14911, 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: 28886
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:5999 original size:20 final size:20
Alignment explanation
Indices: 5971--6034 Score: 119
Period size: 20 Copynumber: 3.2 Consensus size: 20
5961 TTGGTTGGAA
*
5971 TGATCTTTGATCACCTGTGG
1 TGATTTTTGATCACCTGTGG
5991 TGATTTTTGATCACCTGTGG
1 TGATTTTTGATCACCTGTGG
6011 TGATTTTTGATCACCTGTGG
1 TGATTTTTGATCACCTGTGG
6031 TGAT
1 TGAT
6035 CTTGGTAGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.44
Consensus pattern (20 bp):
TGATTTTTGATCACCTGTGG
Found at i:14870 original size:5 final size:5
Alignment explanation
Indices: 14847--14898 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
14837 TTTGTCTTTA
* *
14847 ATTAT CTTAT CTTACT ATTAT ATTAT ATTAT A-TAT A-TAT ATATAT ATTAT
1 ATTAT ATTAT ATTA-T ATTAT ATTAT ATTAT ATTAT ATTAT AT-TAT ATTAT
14897 AT
1 AT
14899 AAAATGACGA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 8 0.19
5 25 0.60
6 9 0.21
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (5 bp):
ATTAT
Found at i:14872 original size:16 final size:15
Alignment explanation
Indices: 14847--14898 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
14837 TTTGTCTTTA
* *
14847 ATTATCTTATCTTACT
1 ATTATATTATATTA-T
14863 ATTATATTATATTAT
1 ATTATATTATATTAT
14878 A-TATA-TATATATAT
1 ATTATATTATAT-TAT
14892 ATTATAT
1 ATTATAT
14899 AAAATGACGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 8 0.26
15 6 0.19
16 12 0.39
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTATATTATATTAT
Found at i:15059 original size:26 final size:27
Alignment explanation
Indices: 15027--15079 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
15017 TTAGAAAGAT
15027 ATTAATAATCTATTAT-T-ATAATTATA
1 ATTAATAATCTATT-TCTCATAATTATA
*
15053 ATTAATAATTTATTTCTCATAATTATA
1 ATTAATAATCTATTTCTCATAATTATA
15080 TATATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 1 0.04
26 14 0.58
27 9 0.38
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTAATAATCTATTTCTCATAATTATA
Found at i:16822 original size:59 final size:59
Alignment explanation
Indices: 16750--16869 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
16740 CTCTATCGGA
16750 ATTCCAAAGGATTGGTGCTTTAAATGTATCTACCCGAGTTCATTAATTTAACAATTGCT
1 ATTCCAAAGGATTGGTGCTTTAAATGTATCTACCCGAGTTCATTAATTTAACAATTGCT
16809 ATTCCAAAGGATTGGTGCTTTAAATGTATCTACCCGAGTTCATTAATTTAACAATTGCT
1 ATTCCAAAGGATTGGTGCTTTAAATGTATCTACCCGAGTTCATTAATTTAACAATTGCT
16868 AT
1 AT
16870 GGAAATTATC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (59 bp):
ATTCCAAAGGATTGGTGCTTTAAATGTATCTACCCGAGTTCATTAATTTAACAATTGCT
Found at i:17290 original size:45 final size:45
Alignment explanation
Indices: 17241--17329 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
17231 AGCAACAATT
* *
17241 AATATTAGTTTTATTTTGATGAATTATCTAGAGATGGAGGAGAAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGAAG
* *
17286 AATATTAGCTTTATTTTGATGAATTACCTATAGATGGAGTAGAA
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGAA
17330 TTTAGGTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.38
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGAAG
Found at i:19520 original size:45 final size:45
Alignment explanation
Indices: 19456--19584 Score: 240
Period size: 45 Copynumber: 2.9 Consensus size: 45
19446 AGCAACAATT
19456 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
* *
19501 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAAGAGTAT
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
19546 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAG
19585 TAGAATTTAG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 81 1.00
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
Found at i:22650 original size:18 final size:18
Alignment explanation
Indices: 22627--22676 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
22617 TCAAAATCGC
*
22627 TTCAATTAAGGGCATATA
1 TTCAATTAAGGCCATATA
*
22645 TTCAATTTAGGCCATATA
1 TTCAATTAAGGCCATATA
*
22663 TTCAATTTAGGCCA
1 TTCAATTAAGGCCA
22677 AAACCTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (18 bp):
TTCAATTAAGGCCATATA
Found at i:22953 original size:24 final size:23
Alignment explanation
Indices: 22922--22972 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
22912 ATAGTTAAGA
*
22922 AAAATAAAATAATATACAAAAAGT
1 AAAATAAAATAAAATACAAAAA-T
* *
22946 AAAATAAACTAAAATAGAAAAAT
1 AAAATAAAATAAAATACAAAAAT
22969 AAAA
1 AAAA
22973 AGTGAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (23 bp):
AAAATAAAATAAAATACAAAAAT
Found at i:23679 original size:16 final size:16
Alignment explanation
Indices: 23651--23683 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
23641 CACACTTTTC
23651 AACATTAATAATAATA
1 AACATTAATAATAATA
23667 AACA-TAATAAATAATA
1 AACATTAAT-AATAATA
23683 A
1 A
23684 GGACTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (16 bp):
AACATTAATAATAATA
Found at i:28285 original size:15 final size:15
Alignment explanation
Indices: 28265--28295 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28255 TTTCTTTTCT
28265 TCAATTCAGGAGAAG
1 TCAATTCAGGAGAAG
28280 TCAATTCAGGAGAAG
1 TCAATTCAGGAGAAG
28295 T
1 T
28296 ATATCATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.23
Consensus pattern (15 bp):
TCAATTCAGGAGAAG
Done.