Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015032.1 Corchorus olitorius cultivar O-4 contig15065, 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: 31451
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:2923 original size:145 final size:141
Alignment explanation
Indices: 2763--3270 Score: 537
Period size: 145 Copynumber: 3.7 Consensus size: 141
2753 TTGGCCACTA
*
2763 AAAAAAATAACTTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTT
1 AAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTT
*
2828 GTCAATCAAAGTTATAATTGATAGATGGTGATTTGATCATTTTGCTATAAATAAAAGAATCAATT
66 GTCAATCAAAGTTATAACTGATAGAT-GT-ATTTGA-CATTTTGC-ATAAATAAAAGAATCAATT
*
2893 AGAAATTATGTTAGC
127 AGTAATTATGTTAGC
* * * * *
2908 AAAAAAATAAATTGATTGAACATACTAAATAAATAAATAAATCAAATTAGTCGTTAATTAACTTT
1 AAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTT
* * * * * *
2973 GCCAATCAAAGTTATAACTAATTGATG-ATTATTAAATTTTGCCATAAATAAATGAATCAATTAG
66 GTCAATCAAAGTTATAACTGATAGATGTATT-TGACATTTTG-CATAAATAAAAGAATCAATTAG
3037 TAATTATGTTAGC
129 TAATTATGTTAGC
* * * *
3050 --AAAAATAAACTGATTCAACATGCTAAATAAACAAATGAACCAAGTTAGTCC-TAAGTCAACTT
1 AAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAA-TCAACTT
* *
3112 TGTCAATCAAAGTTACT-CCT-ATA-A--T-TTTG-C------CATAAATAAACGAATCAATTAG
65 TGTCAATCAAAGTTA-TAACTGATAGATGTATTTGACATTTTGCATAAATAAAAGAATCAATTAG
*
3164 TAATTACGTTAGC
129 TAATTATGTTAGC
* * * * * *
3177 AAAAAAAATAAAATTAATTGAACATGCTAAATAAATAAATGAATCAAGATAGTCGTTAGTTAATT
1 -AAAAAAAT-AAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACT
* * *
3242 TTGTCAATCAAAGTTGTAATTGATTGATG
64 TTGTCAATCAAAGTTATAACTGATAGATG
3271 ATTATTTAAT
Statistics
Matches: 304, Mismatches: 44, Indels: 40
0.78 0.11 0.10
Matches are distributed among these distances:
127 33 0.11
130 7 0.02
131 58 0.19
132 4 0.01
133 1 0.00
135 1 0.00
136 2 0.01
138 1 0.00
139 5 0.02
140 65 0.21
141 1 0.00
142 41 0.13
143 3 0.01
144 1 0.00
145 81 0.27
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (141 bp):
AAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTT
GTCAATCAAAGTTATAACTGATAGATGTATTTGACATTTTGCATAAATAAAAGAATCAATTAGTA
ATTATGTTAGC
Found at i:3254 original size:131 final size:127
Alignment explanation
Indices: 3007--3256 Score: 356
Period size: 131 Copynumber: 1.9 Consensus size: 127
2997 ATGATTATTA
* * *
3007 AATTTTGCCATAAATAAATGAATCAATTAGTAATTATGTTAGCAAAAATAAACTGATTCAACATG
1 AATTTTGCCATAAATAAACGAATCAATTAGTAATTACGTTAGCAAAAATAAACTAATTCAACATG
*
3072 CTAAATAAACAAATGAACCAAGTTAGTCCTAAGTCAACTTTGTCAATCAAAGTTACTCCTAT
66 CTAAATAAACAAATGAACCAAGATAGTCCTAAGTCAACTTTGTCAATCAAAGTTACTCCTAT
* *
3134 AATTTTGCCATAAATAAACGAATCAATTAGTAATTACGTTAGCAAAAAAAATAAAATTAATTGAA
1 AATTTTGCCATAAATAAACGAATCAATTAGTAATTACGTTAGC---AAAAAT-AAACTAATTCAA
* * * * * *
3199 CATGCTAAATAAATAAATGAATCAAGATAGTCGTTAGTTAATTTTGTCAATCAAAGTT
62 CATGCTAAATAAACAAATGAACCAAGATAGTCCTAAGTCAACTTTGTCAATCAAAGTT
3257 GTAATTGATT
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
127 41 0.38
130 6 0.06
131 60 0.56
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (127 bp):
AATTTTGCCATAAATAAACGAATCAATTAGTAATTACGTTAGCAAAAATAAACTAATTCAACATG
CTAAATAAACAAATGAACCAAGATAGTCCTAAGTCAACTTTGTCAATCAAAGTTACTCCTAT
Found at i:3434 original size:165 final size:162
Alignment explanation
Indices: 3141--3622 Score: 685
Period size: 165 Copynumber: 2.9 Consensus size: 162
3131 TATAATTTTG
** * *
3141 CCATAAATAAACGAATCAATTAGTAATTACGTTAGCAAAAAAAATAAAATTAATTGAACATGCTA
1 CCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAAAT----TT-ATTGAACATGCTA
* *
3206 AATAAATAAATGAATCAAGATAGTCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATG
61 AATAAATAAATGAATCAAGTTAGTCGTTAGTTAA-TTTGTCAATCAAAGTTATAATTGATTGATG
3271 ATTATTTAATTTTACCATAAATCGCTACAAAAAAAATTA
125 ATTATTTAATTTTACCATAAATCGCTAC-AAAAAAATTA
* *
3310 CCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAAATTTATTGAGCATGGTAAATAA
1 CCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAAATTTATTGAACATGCTAAATAA
* * *
3375 ATAAATGAATCCAAGTTAGTCGTTAGTCAATTCTGTCAATCAAAGTTTTAATTGATTGATAATTA
66 ATAAATGAAT-CAAGTTAGTCGTTAGTTAATT-TGTCAATCAAAGTTATAATTGATTGATGATTA
*
3440 TTTAATTTTACCATAAATCGCTACCAAAAAATTA
129 TTTAATTTTACCATAAATCGCTACAAAAAAATTA
* *
3474 CCATAAATAAATAAATCAATTAGTGATTATGTTACCAAAAAAATAAATTATTGAACATGCTAAAT
1 CCATAAATAAATAAATCAATTAGTAATTATGTTACC-AAAAAA-AATTTATTGAACATGCTAAAT
* * * * *
3539 AGACAAATGAATCAAGTTAGTCATTAGTTAACTTTGCCAATCAAAGTTATAACTGATTGATGATT
64 AAATAAATGAATCAAGTTAGTCGTTAGTTAA-TTTGTCAATCAAAGTTATAATTGATTGATGATT
3604 ATTTAATTTTACCATAAAT
128 ATTTAATTTTACCATAAAT
3623 AAATCAATCA
Statistics
Matches: 285, Mismatches: 23, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
164 72 0.25
165 142 0.50
166 30 0.11
169 41 0.14
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (162 bp):
CCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAAATTTATTGAACATGCTAAATAA
ATAAATGAATCAAGTTAGTCGTTAGTTAATTTGTCAATCAAAGTTATAATTGATTGATGATTATT
TAATTTTACCATAAATCGCTACAAAAAAATTA
Found at i:3750 original size:174 final size:174
Alignment explanation
Indices: 3526--3851 Score: 474
Period size: 174 Copynumber: 1.9 Consensus size: 174
3516 ATAAATTATT
* *
3526 GAACATGCTAAATAGACAAATGAATCAAGTTAGTCATTAGTTAACTTTGCCAATCAAAGTTATAA
1 GAACATGCTAAATAAACAAATCAATCAAGTTAGTCATTAGTTAACTTTGCCAATCAAAGTTATAA
* * * *
3591 CTGATTGATGATTATTTAATTTTACCATAAATAAATCAATCAATTAATAATTATGTTAGCAAAAA
66 CTGATTCATAATTATTTAATTTTACAATAAATAAATCAATCAATTAATAATTACGTTAGCAAAAA
*
3656 AATCAATTGATTGAACATGCTAAATAAATTGATGCCAAAAAAAA
131 AATAAATTGATTGAACATGCTAAATAAATTGATGCCAAAAAAAA
*
3700 GAACATGCTAAATAAATAAATCAATCAAGTTAGT-AGTTAGTTAACTTTGCCAATCAAAGTTATA
1 GAACATGCTAAATAAACAAATCAATCAAGTTAGTCA-TTAGTTAACTTTGCCAATCAAAGTTATA
* * * * * * **
3764 ATTGATTCATAATTATTTAATTTTGCAATAAATAAATTAGTCAGTTAGTAATTACGTTAGTGAAA
65 ACTGATTCATAATTATTTAATTTTACAATAAATAAATCAATCAATTAATAATTACGTTAGCAAAA
* *
3829 AACTAAATTGATTGAATATGCTA
130 AAATAAATTGATTGAACATGCTA
3852 GCTAAATAAA
Statistics
Matches: 133, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
173 1 0.01
174 132 0.99
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (174 bp):
GAACATGCTAAATAAACAAATCAATCAAGTTAGTCATTAGTTAACTTTGCCAATCAAAGTTATAA
CTGATTCATAATTATTTAATTTTACAATAAATAAATCAATCAATTAATAATTACGTTAGCAAAAA
AATAAATTGATTGAACATGCTAAATAAATTGATGCCAAAAAAAA
Found at i:5364 original size:15 final size:15
Alignment explanation
Indices: 5341--5429 Score: 63
Period size: 15 Copynumber: 5.7 Consensus size: 15
5331 CAACTTATAT
5341 CATCGGGACGCTTTC
1 CATCGGGACGCTTTC
* ** *
5356 CATCAGGACAATTTATAT
1 CATCGGGAC-GCTT-T-C
5374 CATCGGGACGCTTTC
1 CATCGGGACGCTTTC
**
5389 CATCATGACGACTTAT-
1 CATCGGGACG-CTT-TC
5405 CATCGGGACGCTTTC
1 CATCGGGACGCTTTC
*
5420 CATCGAGACG
1 CATCGGGACG
5430 AATTGATTGG
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
14 1 0.02
15 28 0.51
16 14 0.25
17 4 0.07
18 8 0.15
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (15 bp):
CATCGGGACGCTTTC
Found at i:5372 original size:33 final size:32
Alignment explanation
Indices: 5327--5423 Score: 142
Period size: 33 Copynumber: 3.0 Consensus size: 32
5317 CTAAGTTTTA
5327 AGGACAACTTATATCATCGGGACGCTTTCCATC
1 AGGACAA-TTATATCATCGGGACGCTTTCCATC
5360 AGGACAATTTATATCATCGGGACGCTTTCCATC
1 AGGACAA-TTATATCATCGGGACGCTTTCCATC
* * *
5393 ATGACGACT-TATCATCGGGACGCTTTCCATC
1 AGGACAATTATATCATCGGGACGCTTTCCATC
5424 GAGACGAATT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 22 0.37
32 1 0.02
33 37 0.62
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (32 bp):
AGGACAATTATATCATCGGGACGCTTTCCATC
Found at i:18967 original size:31 final size:31
Alignment explanation
Indices: 18929--19095 Score: 190
Period size: 31 Copynumber: 5.4 Consensus size: 31
18919 GTCCGACGTA
**
18929 GCATGCCATGTGTACCAAAAAGCAACATGTG
1 GCATGCCATGTGTACCAAAAAGTGACATGTG
* *
18960 GCATGCCACGTGTACCAAAAAGCGACATGTG
1 GCATGCCATGTGTACCAAAAAGTGACATGTG
* * * * *
18991 GCACGTCACGTGTAACAAAAAGTGACATGTA
1 GCATGCCATGTGTACCAAAAAGTGACATGTG
* * * *
19022 TCACGCCATGTCTACCCAAAAGTGACATGTG
1 GCATGCCATGTGTACCAAAAAGTGACATGTG
** *
19053 GCATGCCATGTGTTTCAAAAAGTGACACGTG
1 GCATGCCATGTGTACCAAAAAGTGACATGTG
19084 GCATGCCATGTG
1 GCATGCCATGTG
19096 CACAAAAGGA
Statistics
Matches: 115, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 115 1.00
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (31 bp):
GCATGCCATGTGTACCAAAAAGTGACATGTG
Found at i:25706 original size:30 final size:30
Alignment explanation
Indices: 25672--25731 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
25662 TTTTATCTCG
25672 ACTTTCCTCTTATACCCTCAAATTTTAATA
1 ACTTTCCTCTTATACCCTCAAATTTTAATA
*
25702 ACTTTCCTTTTATACCCTCAAATTTTAATA
1 ACTTTCCTCTTATACCCTCAAATTTTAATA
25732 TTTTACTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (30 bp):
ACTTTCCTCTTATACCCTCAAATTTTAATA
Found at i:30666 original size:27 final size:27
Alignment explanation
Indices: 30636--30718 Score: 121
Period size: 30 Copynumber: 3.0 Consensus size: 27
30626 ATACCACTAA
*
30636 TAATAATTATTATTATAATAATAAGTT
1 TAATAATTATTATAATAATAATAAGTT
*
30663 TAATAATTATAATACCACTAATAATAAGTT
1 TAATAATTATTATA--A-TAATAATAAGTT
30693 TAATAATTATTATAATAATAATAAGT
1 TAATAATTATTATAATAATAATAAGT
30719 CTAAATTAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
27 23 0.46
28 1 0.02
29 1 0.02
30 25 0.50
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (27 bp):
TAATAATTATTATAATAATAATAAGTT
Done.