Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012647.1 Corchorus olitorius cultivar O-4 contig12680, 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: 44356
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:6972 original size:60 final size:59
Alignment explanation
Indices: 6873--7011 Score: 206
Period size: 60 Copynumber: 2.3 Consensus size: 59
6863 CTTACGTCAT
* * *
6873 GCCCTTATTTGAGCATTTTGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGG
1 GCCCTTATTTGAGCATTTTGATAACATTAGGCCCTTATTTAGCCAAATTAAAAGATCAG
*
6932 GCCCTTATTTGAGCATTTTCGATAATATTAGGCCCTTATTTAGCCAAATTAAAAGATCAG
1 GCCCTTATTTGAGCATTTT-GATAACATTAGGCCCTTATTTAGCCAAATTAAAAGATCAG
* * *
6992 TCCCTCATTTGAGTATTTTG
1 GCCCTTATTTGAGCATTTTG
7012 GCTTTGAAAC
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 20 0.28
60 52 0.72
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (59 bp):
GCCCTTATTTGAGCATTTTGATAACATTAGGCCCTTATTTAGCCAAATTAAAAGATCAG
Found at i:20127 original size:21 final size:21
Alignment explanation
Indices: 20086--20131 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
20076 AAGCAACGTG
*
20086 CTTCTTCATTATCACCATCGT
1 CTTCTTCATTATCAACATCGT
*
20107 CTTCTTCATCT-TCAACTTCGT
1 CTTCTTCAT-TATCAACATCGT
20128 CTTC
1 CTTC
20132 GTCGAGTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.15, C:0.35, G:0.04, T:0.46
Consensus pattern (21 bp):
CTTCTTCATTATCAACATCGT
Found at i:27600 original size:54 final size:55
Alignment explanation
Indices: 27509--27618 Score: 179
Period size: 54 Copynumber: 2.0 Consensus size: 55
27499 TTTATTTTGT
* *
27509 AGAATTATTAAGTAGATATATGGGGATAGTATTTATTATAACATTTATTGTGTGA
1 AGAATAATTAAGTAGAGATATGGGGATAGTATTTATTATAACATTTATTGTGTGA
27564 AGAATAATTAAGTAGAGATA-GGGGATA-TGATTTATTATAACATTTATTGTGTGA
1 AGAATAATTAAGTAGAGATATGGGGATAGT-ATTTATTATAACATTTATTGTGTGA
27618 A
1 A
27619 AGGAAACGAA
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
53 1 0.02
54 33 0.63
55 18 0.35
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.39
Consensus pattern (55 bp):
AGAATAATTAAGTAGAGATATGGGGATAGTATTTATTATAACATTTATTGTGTGA
Found at i:30966 original size:58 final size:58
Alignment explanation
Indices: 30870--30979 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
30860 ATTAATCAAA
*
30870 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT
* * *
30928 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACC
30980 GAGGCATGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
58 32 0.68
59 15 0.32
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT
Found at i:32297 original size:36 final size:36
Alignment explanation
Indices: 32250--32319 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
32240 TTCAATAACC
* *
32250 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
32286 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
32320 CTAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:33178 original size:202 final size:203
Alignment explanation
Indices: 32832--33241 Score: 695
Period size: 202 Copynumber: 2.0 Consensus size: 203
32822 GCTTAATAAC
32832 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
32897 AATACAGCACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
66 AATACAACACATTATAATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
*
32962 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTTAAAATTATAAAAGA-TATTAAAGAT
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATTATT-AAGAT
33026 CC-AATTTA
195 CCGAATTTA
*
33034 TTTATCAATGGTGAATGTTATTAA-TTTTTAAGTTTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
33098 GATACAACACATTACTAATTATATATATAGAACTATACC-AAAAAAATTAGTTGAACATTAGT-G
66 AATACAACACATTA-TAATTATATATA-A-AACTATACCAAAAAAAAGTAGTTGAACATTAGTGG
33161 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATTATTAAG
128 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATTATTAAG
33226 ATCCGAATTTA
193 ATCCGAATTTA
33237 TTTAT
1 TTTAT
33242 TATAAGAAAA
Statistics
Matches: 197, Mismatches: 6, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
201 51 0.26
202 99 0.50
203 38 0.19
204 9 0.05
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (203 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
AATACAACACATTATAATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATTATTAAGATC
CGAATTTA
Found at i:33349 original size:25 final size:24
Alignment explanation
Indices: 33311--33357 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
33301 ACGTTTGCAC
* *
33311 AAATGCCTACGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
33336 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
33358 TGTAAGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:34784 original size:21 final size:20
Alignment explanation
Indices: 34754--34793 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
34744 CATATTGTAA
34754 TTTTAACTTTATTTAAGTTG
1 TTTTAACTTTATTTAAGTTG
34774 TTTTAAACTTTATTTAAGTT
1 TTTT-AACTTTATTTAAGTT
34794 TTAATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTTAACTTTATTTAAGTTG
Found at i:38237 original size:10 final size:10
Alignment explanation
Indices: 38211--38251 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
38201 AGCAAAAGAA
38211 AAAGAAAAAG
1 AAAGAAAAAG
*
38221 AAAAGAAAAGG
1 -AAAGAAAAAG
*
38232 AGAGAAAAAG
1 AAAGAAAAAG
38242 AAAGAAAAAG
1 AAAGAAAAAG
38252 CTCCTCTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:42291 original size:21 final size:21
Alignment explanation
Indices: 42265--42307 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
42255 ATATACATCT
42265 GATAATCCATGGTTGAGGGTG
1 GATAATCCATGGTTGAGGGTG
42286 GATAATCCATGGTTGAGGGTG
1 GATAATCCATGGTTGAGGGTG
42307 G
1 G
42308 TATAGACTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.40, T:0.28
Consensus pattern (21 bp):
GATAATCCATGGTTGAGGGTG
Done.