Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021809.1 Corchorus olitorius cultivar O-4 contig21842, 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: 30000
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:5293 original size:57 final size:57
Alignment explanation
Indices: 5229--5337 Score: 182
Period size: 57 Copynumber: 1.9 Consensus size: 57
5219 AACTTGTACT
* * * *
5229 AAAAAGGATAAAATGAACCTCGAACTTGTATCAAAATGATGATGTAGACTCTGAACC
1 AAAAAGGACAAAATAAACCTCGAACTTGTATCAAAATGATAATATAGACTCTGAACC
5286 AAAAAGGACAAAATAAACCTCGAACTTGTATCAAAATGATAATATAGACTCT
1 AAAAAGGACAAAATAAACCTCGAACTTGTATCAAAATGATAATATAGACTCT
5338 AAACATAGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.23
Consensus pattern (57 bp):
AAAAAGGACAAAATAAACCTCGAACTTGTATCAAAATGATAATATAGACTCTGAACC
Found at i:8967 original size:28 final size:24
Alignment explanation
Indices: 8934--9000 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 24
8924 AAGTATAATC
*
8934 AATATTTAATTTCTTTATTCACTAGAAA
1 AATATTTAATTTCTTCATT---TA-AAA
8962 AATATTTAATTTCTTCATTTAAAA
1 AATATTTAATTTCTTCATTTAAAA
*
8986 AATATTCAATTTCTT
1 AATATTTAATTTCTT
9001 AAATCAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 17 0.46
25 2 0.05
28 18 0.49
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49
Consensus pattern (24 bp):
AATATTTAATTTCTTCATTTAAAA
Found at i:8978 original size:24 final size:24
Alignment explanation
Indices: 8951--9000 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
8941 AATTTCTTTA
*
8951 TTCA-CTAGAAAAATATTTAATTTC
1 TTCATCTA-AAAAATATTCAATTTC
*
8975 TTCATTTAAAAAATATTCAATTTC
1 TTCATCTAAAAAATATTCAATTTC
8999 TT
1 TT
9001 AAATCAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (24 bp):
TTCATCTAAAAAATATTCAATTTC
Found at i:10033 original size:80 final size:80
Alignment explanation
Indices: 9917--10072 Score: 287
Period size: 80 Copynumber: 1.9 Consensus size: 80
9907 TAGTTTTACA
9917 CAACTAAAAACTATATTTTTATTTAATTAAATCTAATAT-CTTTATAACTATTTTATTTTACCAT
1 CAACTAAAAACTATATTTTTATTTAATTAAATCTAATATAC-TTATAACTATTTTATTTTACCAT
9981 TTTACTATTTTATATT
65 TTTACTATTTTATATT
*
9997 CAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATACTTATAACTATTTTATTTTACCATT
1 CAACTAAAAACTATATTTTTATTTAATTAAATCTAATATACTTATAACTATTTTATTTTACCATT
10062 TTACTATTTTA
66 TTACTATTTTA
10073 ATCAAAAAAC
Statistics
Matches: 74, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
80 73 0.99
81 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (80 bp):
CAACTAAAAACTATATTTTTATTTAATTAAATCTAATATACTTATAACTATTTTATTTTACCATT
TTACTATTTTATATT
Found at i:10996 original size:17 final size:17
Alignment explanation
Indices: 10970--11008 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
10960 GTTCTTTCAT
10970 TAAATCAATTAA-AATTA
1 TAAATCAATTAATAA-TA
*
10987 TAAATGAATTAATAATA
1 TAAATCAATTAATAATA
11004 TAAAT
1 TAAAT
11009 ATTCATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
TAAATCAATTAATAATA
Found at i:19106 original size:28 final size:28
Alignment explanation
Indices: 19066--19121 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
19056 ATGCTGAAAA
19066 ATGCGGTTGCACTTGAGCGGATGATTCT
1 ATGCGGTTGCACTTGAGCGGATGATTCT
19094 ATGCGGTTGCACTTGAGCGGATGATTCT
1 ATGCGGTTGCACTTGAGCGGATGATTCT
19122 TGACACCACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (28 bp):
ATGCGGTTGCACTTGAGCGGATGATTCT
Found at i:20684 original size:72 final size:71
Alignment explanation
Indices: 20542--20685 Score: 254
Period size: 72 Copynumber: 2.0 Consensus size: 71
20532 ATATGAAACT
*
20542 TTGATTTTTAGGCGAGCTGGTCCATAGCACCAGTTCTTACTCTTTTCTCTCAAGTTGAAATAAAC
1 TTGATTTTTAGACGAGCTGGTCCATAGCACCAGTTCTTACTC-TTTCTCTCAAGTTGAAATAAAC
20607 ATGTGTG
65 ATGTGTG
*
20614 TTGATTTTTTGACGAGCTGGTCCATAGCACCAGTTCTTACTC-TTCTCTCAAGTTGAAATAAACA
1 TTGATTTTTAGACGAGCTGGTCCATAGCACCAGTTCTTACTCTTTCTCTCAAGTTGAAATAAACA
20678 TGTGTG
66 TGTGTG
20684 TT
1 TT
20686 CATGTCAGCT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
70 30 0.43
72 40 0.57
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (71 bp):
TTGATTTTTAGACGAGCTGGTCCATAGCACCAGTTCTTACTCTTTCTCTCAAGTTGAAATAAACA
TGTGTG
Found at i:27559 original size:36 final size:36
Alignment explanation
Indices: 27512--27581 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
27502 TTCAATAACC
* *
27512 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
27548 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
27582 CCAAAATCTC
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:28453 original size:204 final size:201
Alignment explanation
Indices: 28069--28478 Score: 730
Period size: 204 Copynumber: 2.0 Consensus size: 201
28059 GCTTAAAAAC
28069 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
28134 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
* * *
28199 ATTTATTAAATTAAATTAGATCAATGTCAAAGAAAATTTCAAATTTATAAAAGATTTTAAAGATC
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATC
28264 CGATTTA
195 CGATTTA
28271 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
28336 GATACAACACATTACTATTATATATATAGAACTATACCAAAAACAATTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAAGTAGTTGAACATTAGTGGT
28401 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
129 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
*
28466 CCGGTTTA
194 CCGATTTA
28474 TTTAT
1 TTTAT
28479 TATTAAGGAA
Statistics
Matches: 199, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
202 90 0.45
203 18 0.09
204 91 0.46
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.37
Consensus pattern (201 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCC
GATTTA
Found at i:28586 original size:25 final size:24
Alignment explanation
Indices: 28552--28598 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
28542 ATGTTTGCAC
*
28552 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAAAATTT-AATTAAAA
28577 AAATACCTAAAAATTTAATTAA
1 AAATACCTAAAAATTTAATTAA
28599 TGTAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (24 bp):
AAATACCTAAAAATTTAATTAAAA
Found at i:28643 original size:39 final size:40
Alignment explanation
Indices: 28589--28669 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
28579 ATACCTAAAA
*
28589 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
28628 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
28668 AT
1 AT
28670 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:29973 original size:2 final size:2
Alignment explanation
Indices: 29966--29999 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
29956 AGCAGTTTAG
29966 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30000 G
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.