Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024329.1 Corchorus olitorius cultivar O-4 contig24362, 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: 11264
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Found at i:741 original size:35 final size:35
Alignment explanation
Indices: 593--1139 Score: 358
Period size: 35 Copynumber: 15.6 Consensus size: 35
583 CATAGGTTGC
* * * *
593 AGAAAGACCACCCTGGGTCTACTGAAATAAATTCA
1 AGAAAGACCACCCTGGGTCAACTAAAATAAACTGA
* * * * *
628 AGAAAGATCACCCCGGGTTAACAAAAACAAACTGA
1 AGAAAGACCACCCTGGGTCAACTAAAATAAACTGA
* *** * ** * * *
663 AGAACGACCACCCTCAATCATTCCGACA-CAATTGA
1 AGAAAGACCACCCTGGGTCA-ACTAAAATAAACTGA
* * *
698 AGAGAGACCACCCTGGGTCAACTAAAATAAATTCA
1 AGAAAGACCACCCTGGGTCAACTAAAATAAACTGA
* * *
733 AGAAAGACCACCTTGGGTTAAC-AGAAACAAACTGA
1 AGAAAGACCACCCTGGGTCAACTA-AAATAAACTGA
* * ** ** * *
768 AGAACGACCACCCTTGACCAATCCGACA-CAACTGA
1 AGAAAGACCACCCTGGGTCAA-CTAAAATAAACTGA
* *
803 AGAAAGACCACCCTAGGTCAACTAAAATAAATTGA
1 AGAAAGACCACCCTGGGTCAACTAAAATAAACTGA
*
838 AGAAAGACCACCCTGGGTCAAC-AGATATAAACTGA
1 AGAAAGACCACCCTGGGTCAACTA-AAATAAACTGA
* * * * * ** * *
873 AGAACGACCCCCCTCGATCATTCCGACA-CAACTGA
1 AGAAAGACCACCCTGGGTCA-ACTAAAATAAACTGA
* * * *
908 A-AAGAGACCACCCTAGGTAAACTAGAATAAATTGA
1 AGAA-AGACCACCCTGGGTCAACTAAAATAAACTGA
*
943 AGAAAGACCACACTGGGTCAAC-AGAAATAAACTGA
1 AGAAAGACCACCCTGGGTCAACTA-AAATAAACTGA
* * * * * ** * *
978 AGAACGACCCCCCTCGATCATTCCGACA-CAACTGA
1 AGAAAGACCACCCTGGGTCA-ACTAAAATAAACTGA
* *
1013 A-AAGAGACCACCCTGGGTCAACTAAGATAAATTGA
1 AGAA-AGACCACCCTGGGTCAACTAAAATAAACTGA
1048 AGAAAGACCACCCTGGGTCAAC-AGAAATAAACTGA
1 AGAAAGACCACCCTGGGTCAACTA-AAATAAACTGA
* *
1083 AGAACGACCACCCTGGGTCAACTAAAATAAATTGA
1 AGAAAGACCACCCTGGGTCAACTAAAATAAACTGA
*
1118 AGAAAGACCACCCTAGGTCAAC
1 AGAAAGACCACCCTGGGTCAAC
1140 AGAAACAACT
Statistics
Matches: 382, Mismatches: 110, Indels: 40
0.72 0.21 0.08
Matches are distributed among these distances:
34 19 0.05
35 346 0.91
36 17 0.04
ACGTcount: A:0.42, C:0.26, G:0.17, T:0.15
Consensus pattern (35 bp):
AGAAAGACCACCCTGGGTCAACTAAAATAAACTGA
Found at i:779 original size:105 final size:105
Alignment explanation
Indices: 597--1096 Score: 741
Period size: 105 Copynumber: 4.8 Consensus size: 105
587 GGTTGCAGAA
* * * * * * * *
597 AGACCACCCTGGGTCTACTGAAATAAATTCAAGAAAGATCACCCCGGGTTAACAAAAACAAACTG
1 AGACCACCCTGGGTCAACTAAAATAAATTGAAGAAAGACCACCCTGGGTCAACAGAAATAAACTG
* * *
662 AAGAACGACCACCCTCAATCATTCCGACACAATTGAAGAG
66 AAGAACGACCACCCTCGATCATTCCGACACAACTGAAAAG
* * * *
702 AGACCACCCTGGGTCAACTAAAATAAATTCAAGAAAGACCACCTTGGGTTAACAGAAACAAACTG
1 AGACCACCCTGGGTCAACTAAAATAAATTGAAGAAAGACCACCCTGGGTCAACAGAAATAAACTG
* * *
767 AAGAACGACCACCCTTGACCAATCCGACACAACTGAAGAA-
66 AAGAACGACCACCCTCGATCATTCCGACACAACTGAA-AAG
* *
807 AGACCACCCTAGGTCAACTAAAATAAATTGAAGAAAGACCACCCTGGGTCAACAGATATAAACTG
1 AGACCACCCTGGGTCAACTAAAATAAATTGAAGAAAGACCACCCTGGGTCAACAGAAATAAACTG
*
872 AAGAACGACCCCCCTCGATCATTCCGACACAACTGAAAAG
66 AAGAACGACCACCCTCGATCATTCCGACACAACTGAAAAG
* * * *
912 AGACCACCCTAGGTAAACTAGAATAAATTGAAGAAAGACCACACTGGGTCAACAGAAATAAACTG
1 AGACCACCCTGGGTCAACTAAAATAAATTGAAGAAAGACCACCCTGGGTCAACAGAAATAAACTG
*
977 AAGAACGACCCCCCTCGATCATTCCGACACAACTGAAAAG
66 AAGAACGACCACCCTCGATCATTCCGACACAACTGAAAAG
*
1017 AGACCACCCTGGGTCAACTAAGATAAATTGAAGAAAGACCACCCTGGGTCAACAGAAATAAACTG
1 AGACCACCCTGGGTCAACTAAAATAAATTGAAGAAAGACCACCCTGGGTCAACAGAAATAAACTG
1082 AAGAACGACCACCCT
66 AAGAACGACCACCCT
1097 GGGTCAACTA
Statistics
Matches: 361, Mismatches: 32, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
104 2 0.01
105 358 0.99
106 1 0.00
ACGTcount: A:0.42, C:0.27, G:0.17, T:0.15
Consensus pattern (105 bp):
AGACCACCCTGGGTCAACTAAAATAAATTGAAGAAAGACCACCCTGGGTCAACAGAAATAAACTG
AAGAACGACCACCCTCGATCATTCCGACACAACTGAAAAG
Found at i:1188 original size:210 final size:208
Alignment explanation
Indices: 593--1201 Score: 701
Period size: 210 Copynumber: 2.9 Consensus size: 208
583 CATAGGTTGC
* * * * * * *
593 AGAAAGACCACCCTGGGTCTACTGAAATAAATTCAAGAAAGATCACCCCGGGTTAACAAAAACAA
1 AGAAAGACCACCCTGGGTCAACT-AAATAAATTGAAGAAAGACCACCCTGGGTCAACAGAAATAA
* * * *
658 ACTGAAGAACGACCACCCTCAATCATTCCGACACAATTGAAGAGAGACCACCCTGGGTCAACTAA
65 ACTGAAGAACGACCACCCTCGATCATTCCGACACAATTGAAGAAAGACCACCCTAGGTCAACTAG
* * * *
723 AATAAATTCAAGAAAGACCA-CCTTGGGTTAACAGAAACAAACTGAAGAACGACCACCCTTGACC
130 AA-AAATTAAAGAAAGACCACCCTTGGGTCAACAG-AATAAACTGAAGAACGACCACCCTCGACC
787 AATCCGACACAACTGA
193 AATCCGACACAACTGA
* *
803 AGAAAGACCACCCTAGGTCAACTAAAATAAATTGAAGAAAGACCACCCTGGGTCAACAGATATAA
1 AGAAAGACCACCCTGGGTCAACT-AAATAAATTGAAGAAAGACCACCCTGGGTCAACAGAAATAA
* * *
868 ACTGAAGAACGACCCCCCTCGATCATTCCGACACAACTGAA-AAGAGACCACCCTAGGTAAACTA
65 ACTGAAGAACGACCACCCTCGATCATTCCGACACAATTGAAGAA-AGACCACCCTAGGTCAACTA
* * * *
932 GAATAAATTGAAGAAAGACCACAC-TGGGTCAACAGAAATAAACTGAAGAACGACCCCCCTCGAT
129 GAA-AAATTAAAGAAAGACCACCCTTGGGTCAACAG-AATAAACTGAAGAACGACCACCCTCGAC
*
996 CATTCCGACACAACTGA
192 CAATCCGACACAACTGA
1013 A-AAGAGACCACCCTGGGTCAACTAAGATAAATTGAAGAAAGACCACCCTGGGTCAACAGAAATA
1 AGAA-AGACCACCCTGGGTCAACTAA-ATAAATTGAAGAAAGACCACCCTGGGTCAACAGAAATA
* * * ** * *
1077 AACTGAAGAACGACCACCCTGGGTCA-ACTAAAATAAATTGAAGAAAGACCACCCTAGGTCAAC-
64 AACTGAAGAACGACCACCCTCGATCATTCCGACA-CAATTGAAGAAAGACCACCCTAGGTCAACT
* * * * * * *
1140 AGAAACAACTAAATAAAGGCCACCCTTGGATCAATCATG-ATTAACTGAAGAATGATCACCCT
128 AGAAA-AATTAAAGAAAGACCACCCTTGGGTCAA-CA-GAATAAACTGAAGAACGACCACCCT
1202 GGATCAAACT
Statistics
Matches: 342, Mismatches: 47, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
208 1 0.00
209 26 0.08
210 309 0.90
211 5 0.01
212 1 0.00
ACGTcount: A:0.42, C:0.26, G:0.17, T:0.15
Consensus pattern (208 bp):
AGAAAGACCACCCTGGGTCAACTAAATAAATTGAAGAAAGACCACCCTGGGTCAACAGAAATAAA
CTGAAGAACGACCACCCTCGATCATTCCGACACAATTGAAGAAAGACCACCCTAGGTCAACTAGA
AAAATTAAAGAAAGACCACCCTTGGGTCAACAGAATAAACTGAAGAACGACCACCCTCGACCAAT
CCGACACAACTGA
Found at i:1268 original size:34 final size:35
Alignment explanation
Indices: 1225--1309 Score: 113
Period size: 35 Copynumber: 2.5 Consensus size: 35
1215 TTGAATGACA
1225 ACCGCCCTGGATCAATTGAAA-TTA-TCGAA-GAGAG
1 ACCGCCCTGGATCAATTGAAATTTACT-GAATG-GAG
*
1259 ACCGCCCTGGATCGATTGAAATTTACTGAATGGAG
1 ACCGCCCTGGATCAATTGAAATTTACTGAATGGAG
*
1294 ACCGCCCTGGGTCAAT
1 ACCGCCCTGGATCAAT
1310 AAACCTTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
34 20 0.44
35 23 0.51
36 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (35 bp):
ACCGCCCTGGATCAATTGAAATTTACTGAATGGAG
Found at i:1302 original size:35 final size:34
Alignment explanation
Indices: 1225--1309 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 34
1215 TTGAATGACA
1225 ACCGCCCTGGATCAATTGAAATTATCGAAGAGAG
1 ACCGCCCTGGATCAATTGAAATTATCGAAGAGAG
*
1259 ACCGCCCTGGATCGATTGAAATT-TACTGAATG-GAG
1 ACCGCCCTGGATCAATTGAAATTAT-C-GAA-GAGAG
*
1294 ACCGCCCTGGGTCAAT
1 ACCGCCCTGGATCAAT
1310 AAACCTTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
33 1 0.02
34 23 0.51
35 20 0.44
36 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (34 bp):
ACCGCCCTGGATCAATTGAAATTATCGAAGAGAG
Found at i:3581 original size:2 final size:2
Alignment explanation
Indices: 3574--3610 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3564 GAATAGTAGA
*
3574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3611 CTAAAGGCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:7972 original size:12 final size:12
Alignment explanation
Indices: 7955--7980 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
7945 TTCGTCGGCC
7955 TTAGACCCCCAA
1 TTAGACCCCCAA
7967 TTAGACCCCCAA
1 TTAGACCCCCAA
7979 TT
1 TT
7981 GAACACCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.38, G:0.08, T:0.23
Consensus pattern (12 bp):
TTAGACCCCCAA
Found at i:8353 original size:22 final size:22
Alignment explanation
Indices: 8311--8353 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
8301 TTTTCCGCAA
* *
8311 CAAGTCCTGGGCAAGAGTTGTC
1 CAAGTCCTGGACAAGACTTGTC
*
8333 CAAGTCCTGGACAGGACTTGT
1 CAAGTCCTGGACAAGACTTGT
8354 TCTGAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (22 bp):
CAAGTCCTGGACAAGACTTGTC
Found at i:8445 original size:69 final size:70
Alignment explanation
Indices: 8311--8502 Score: 230
Period size: 69 Copynumber: 2.7 Consensus size: 70
8301 TTTTCCGCAA
* * *
8311 CAAGTCCTGGGCAAGAGTTGTCCAAGTCCTGGACAGGACTTGTTCTGAATTTTCTTCCGGTTTTC
1 CAAGTCCTGGGCAGGAGTTGT-CAAGT-CTGGGCAGGACTTGTTCTGATTTTTCTTCCGGTTTTC
8376 AACAGAC
64 AACAGAC
* *
8383 CAAGTCCTGGGCAGGAGTTGTCAAAT-TGGGCAGGAGTTGTTCTGATTTTTCTTCC-GTCTTTCA
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCTGGGCAGGACTTGTTCTGATTTTTCTTCCGGT-TTTCA
8446 ACAGAC
65 ACAGAC
** * *
8452 C-AGCTTTTGGGCAGTAGTTGTCAAGTCCTGGGCAGGACTTGTCCTG-TTTTT
1 CAAG-TCCTGGGCAGGAGTTGTCAAGT-CTGGGCAGGACTTGTTCTGATTTTT
8503 AGGCTTCAAT
Statistics
Matches: 105, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
68 4 0.04
69 56 0.53
70 5 0.05
71 20 0.19
72 20 0.19
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.33
Consensus pattern (70 bp):
CAAGTCCTGGGCAGGAGTTGTCAAGTCTGGGCAGGACTTGTTCTGATTTTTCTTCCGGTTTTCAA
CAGAC
Found at i:11137 original size:15 final size:15
Alignment explanation
Indices: 11113--11143 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11103 CTAAGTGGAG
11113 CTTGTCGATTTTGAA
1 CTTGTCGATTTTGAA
*
11128 CTTGTTGATTTTGAA
1 CTTGTCGATTTTGAA
11143 C
1 C
11144 CCCCAAGGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (15 bp):
CTTGTCGATTTTGAA
Done.