Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024678.1 Corchorus olitorius cultivar O-4 contig24711, 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: 27674
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Found at i:6344 original size:8 final size:8
Alignment explanation
Indices: 6331--6362 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
6321 AATATTTAGT
6331 AAAAATCA
1 AAAAATCA
6339 AAAAATCA
1 AAAAATCA
6347 AAAAATC-
1 AAAAATCA
6354 AAAAATCA
1 AAAAATCA
6362 A
1 A
6363 GTCTTGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.75, C:0.12, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATCA
Found at i:6357 original size:15 final size:16
Alignment explanation
Indices: 6331--6362 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
6321 AATATTTAGT
6331 AAAAATCAAAAAATCA
1 AAAAATCAAAAAATCA
6347 AAAAATC-AAAAATCA
1 AAAAATCAAAAAATCA
6362 A
1 A
6363 GTCTTGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.75, C:0.12, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAATCAAAAAATCA
Found at i:7283 original size:42 final size:42
Alignment explanation
Indices: 7235--7327 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
7225 TCATAAGAAA
* * *
7235 TAAAAAAGAT-AAATTAAAGAGAGAAAATGAAAGTTTGTTTTC
1 TAAAAAAGATGAAACTAAAAAGAG-AAATGAAAATTTGTTTTC
* *
7277 TTAAAAAA-ATGAGACTAAAAAGAGGAATGAAAATTTGTTTTC
1 -TAAAAAAGATGAAACTAAAAAGAGAAATGAAAATTTGTTTTC
7319 TAAAAAAGA
1 TAAAAAAGA
7328 GGATTAAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
41 7 0.16
42 19 0.44
43 17 0.40
ACGTcount: A:0.54, C:0.03, G:0.16, T:0.27
Consensus pattern (42 bp):
TAAAAAAGATGAAACTAAAAAGAGAAATGAAAATTTGTTTTC
Found at i:18730 original size:39 final size:39
Alignment explanation
Indices: 18497--19157 Score: 447
Period size: 39 Copynumber: 17.2 Consensus size: 39
18487 GGTTTTTATC
18497 TAAGTAAACCTGCTTAGGTCTCTGTTTAGAA-----GTT
1 TAAGTAAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTT
* * * * ** * *
18531 TCA-TCGAACCTACTTAGATCTCCATTTACAATTTCCATT
1 TAAGT-AAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTT
* * * *
18570 TAAGTAAACCTGCTCAGGTCTTTGCTTAGAGTTT-CGTT
1 TAAGTAAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTT
* * * * * * * *
18608 TAAGAAAACCCGCTCAGCTCTTTGCTTAGAATTTTCATT
1 TAAGTAAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTT
* * * * * * *
18647 TAAGAAAACCTGTTTAAGATCTTTGCTTAGAGCTTT--GAT
1 TAAGTAAACCTGCTT-AGGTCTCTGTTTAGA-ATTTCCGTT
* * * * * *
18686 CAAGTAAACCTGCTTAGGTCCCTATTTAGAGTTGCCATT
1 TAAGTAAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTT
* *
18725 TAAGTAAACCTGCTTAGGTCTATGTTTAGAATTT-CATT
1 TAAGTAAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTT
* * *
18763 TAAGAAAACCTGCTTAGGTCTCTGCTTAGAATTTCTGTT
1 TAAGTAAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTT
* * * * **
18802 TAAGAAAACCTGCTTAGGTCCCCGCTTAGAATCACC-TT
1 TAAGTAAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTT
* * * **
18840 TGATTAAACCTGCTTAGGTCTCTGTTCAGAATTTTTGTT
1 TAAGTAAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTT
* *
18879 TAAGTAAACCTGCTTAGATC-CTCGTTTAGAATTTTCGTT
1 TAAGTAAACCTGCTTAGGTCTCT-GTTTAGAATTTCCGTT
* * * *
18918 TAAATAAACCTGCTTAGGCCTCTGTCTGGAATTTCCGTT
1 TAAGTAAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTT
* * * *
18957 TAAGTGAACCTGCTTAGCTCTCTGCTTAGAGTTT-CGTT
1 TAAGTAAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTT
* ** *
18995 TAAGAAAACCTGCTTAGGTCTCTACTTAGAGCTTT--GTT
1 TAAGTAAACCTGCTTAGGTCTCTGTTTAGA-ATTTCCGTT
* * * * *
19033 TAA-TCAAGCCTGCTTAGGTCTTTATTTGGAATTTCTGTT
1 TAAGT-AAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTT
* * ** * *
19072 TAAGTGAACCTGCTTAGGTCGCTACTTAGAGTTT-CGTC
1 TAAGTAAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTT
* * *
19110 TAGGTAAACCTGCTTAGGTGTCTGTTTAGAATTTTCGTT
1 TAAGTAAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTT
*
19149 TAAGAAAAC
1 TAAGTAAAC
19158 TTGGAGTTTC
Statistics
Matches: 485, Mismatches: 120, Indels: 39
0.75 0.19 0.06
Matches are distributed among these distances:
33 1 0.00
34 22 0.05
37 5 0.01
38 193 0.40
39 243 0.50
40 18 0.04
41 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (39 bp):
TAAGTAAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTT
Found at i:18831 original size:77 final size:77
Alignment explanation
Indices: 18568--19157 Score: 467
Period size: 77 Copynumber: 7.6 Consensus size: 77
18558 ACAATTTCCA
* * * * * *
18568 TTTAAGTAAACCTGCTCAGGTCTTTGCTTAGAGTTTCGTTTAAGAAAACCCGCTCAGCTCTTTGC
1 TTTAAGTAAACCTGCTTAGGTCTTTGCTTAGAATTTCGTTTAAGAAAACCTGCTTAGGTCTCTGC
*
18633 TTAGAATTT-TCA
66 TTAGAATTTCT-G
* * * * * * * *
18645 TTTAAGAAAACCTGTTTAAGATCTTTGCTTAGAGCTTT-GATCAAGTAAACCTGCTTAGGTCCCT
1 TTTAAGTAAACCTGCTT-AGGTCTTTGCTTAGA-ATTTCGTTTAAGAAAACCTGCTTAGGTCTCT
** * * **
18709 ATTTAGAGTTGCCA
64 GCTTAGAATTTCTG
* * *
18723 TTTAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCATTTAAGAAAACCTGCTTAGGTCTCTGC
1 TTTAAGTAAACCTGCTTAGGTCTTTGCTTAGAATTTCGTTTAAGAAAACCTGCTTAGGTCTCTGC
18788 TTAGAATTTCTG
66 TTAGAATTTCTG
* *** ** * * **
18800 TTTAAGAAAACCTGCTTAGGTCCCCGCTTAGAATCACCTTTGATTAAACCTGCTTAGGTCTCTG-
1 TTTAAGTAAACCTGCTTAGGTCTTTGCTTAGAATTTCGTTTAAGAAAACCTGCTTAGGTCTCTGC
*
18864 TTCAGAATTTTTG
66 TT-AGAATTTCTG
* * * * *
18877 TTTAAGTAAACCTGCTTAGATCCTCGTTTAGAATTTTCGTTTAA-ATAAACCTGCTTAGGCCTCT
1 TTTAAGTAAACCTGCTTAGGTCTTTGCTTAGAA-TTTCGTTTAAGA-AAACCTGCTTAGGTCTCT
* *
18941 G-TCTGGAATTTCCG
64 GCT-TAGAATTTCTG
* * * * *
18955 TTTAAGTGAACCTGCTTAGCTCTCTGCTTAGAGTTTCGTTTAAGAAAACCTGCTTAGGTCTCTAC
1 TTTAAGTAAACCTGCTTAGGTCTTTGCTTAGAATTTCGTTTAAGAAAACCTGCTTAGGTCTCTGC
**
19020 TTAGAGCTT-TG
66 TTAGAATTTCTG
* ** * ** *
19031 TTTAA-TCAAGCCTGCTTAGGTCTTTATTTGGAATTTCTGTTTAAGTGAACCTGCTTAGGTCGCT
1 TTTAAGT-AAACCTGCTTAGGTCTTTGCTTAGAATTTC-GTTTAAGAAAACCTGCTTAGGTCTCT
* *
19095 ACTTAGAGTTTC-G
64 GCTTAGAATTTCTG
* * * * *
19108 TCTAGGTAAACCTGCTTAGGTGTCTGTTTAGAATTTTCGTTTAAGAAAAC
1 TTTAAGTAAACCTGCTTAGGTCTTTGCTTAGAA-TTTCGTTTAAGAAAAC
19158 TTGGAGTTTC
Statistics
Matches: 404, Mismatches: 94, Indels: 30
0.77 0.18 0.06
Matches are distributed among these distances:
75 1 0.00
76 33 0.08
77 246 0.61
78 120 0.30
79 4 0.01
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (77 bp):
TTTAAGTAAACCTGCTTAGGTCTTTGCTTAGAATTTCGTTTAAGAAAACCTGCTTAGGTCTCTGC
TTAGAATTTCTG
Found at i:19047 original size:193 final size:191
Alignment explanation
Indices: 18560--19088 Score: 535
Period size: 193 Copynumber: 2.7 Consensus size: 191
18550 CTCCATTTAC
* * * *
18560 AATTTCCATTTAAGTAAACCTGCTCAGGTCTTTGCTTAGAGTTTCGTTTAAGAAAACCCGCTCAG
1 AATTTCCATTTAAGTAAACCTGCTTAGGTCTCTGCTTAGAGTTTCGTTTAAGAAAACCTGCTTAG
* * * * * ** * *
18625 CTCTTTGCTTAGAATTTTCATTTAAGAAAACCTGTTTAAGATCTTTGCTTAG-AGCTTTGATCAA
66 GTCTCTGCTTAGAA-TTT-ATTTAATAAAACCTGCTT-AGGTCTTTG-TTAGAATTTTTGTTTAA
* * * * *
18689 GTAAACCTGCTTAGGTCCCTATTTAGAGTTGCCATTTAAGTAAACCTGCTTAGGTCTATGTTTAG
127 GTAAACCTGCTTAGATCCCTATTTAGAATTGCCATTTAAATAAACCTGCTTAGGCCTATGTCTAG
* *
18754 AATTT-CATTTAAGAAAACCTGCTTAGGTCTCTGCTTAGAATTTCTGTTTAAGAAAACCTGCTTA
1 AATTTCCATTTAAGTAAACCTGCTTAGGTCTCTGCTTAGAGTTTC-GTTTAAGAAAACCTGCTTA
* * * * * *
18818 GGTCCCCGCTTAGAA-TCACCTTTGATTAAACCTGCTTAGGTCTCTGTTCAGAATTTTTGTTTAA
65 GGTCTCTGCTTAGAATTTA--TTTAATAAAACCTGCTTAGGTCTTTGTT-AGAATTTTTGTTTAA
* ** * * *
18882 GTAAACCTGCTTAGAT-CCTCGTTTAGAATTTTCGTTTAAATAAACCTGCTTAGGCCTCTGTCTG
127 GTAAACCTGCTTAGATCCCT-ATTTAGAATTGCCATTTAAATAAACCTGCTTAGGCCTATGTCTA
18946 G
191 G
* * *
18947 AATTTCCGTTTAAGTGAACCTGCTTAGCTCTCTGCTTAGAGTTTCGTTTAAGAAAACCTGCTTAG
1 AATTTCCATTTAAGTAAACCTGCTTAGGTCTCTGCTTAGAGTTTCGTTTAAGAAAACCTGCTTAG
* * * * * * * *
19012 GTCTCTACTTAGAGCTTTGTTTAATCAAGCCTGCTTAGGTCTTTATTTGGAATTTCTGTTTAAGT
66 GTCTCTGCTTAGA-ATTTATTTAATAAAACCTGCTTAGGTCTTT-GTTAGAATTTTTGTTTAAGT
*
19077 GAACCTGCTTAG
129 AAACCTGCTTAG
19089 GTCGCTACTT
Statistics
Matches: 274, Mismatches: 51, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
191 3 0.01
192 13 0.05
193 188 0.69
194 69 0.25
195 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (191 bp):
AATTTCCATTTAAGTAAACCTGCTTAGGTCTCTGCTTAGAGTTTCGTTTAAGAAAACCTGCTTAG
GTCTCTGCTTAGAATTTATTTAATAAAACCTGCTTAGGTCTTTGTTAGAATTTTTGTTTAAGTAA
ACCTGCTTAGATCCCTATTTAGAATTGCCATTTAAATAAACCTGCTTAGGCCTATGTCTAG
Found at i:19139 original size:115 final size:115
Alignment explanation
Indices: 18879--19151 Score: 325
Period size: 115 Copynumber: 2.4 Consensus size: 115
18869 AATTTTTGTT
* * * *
18879 TAAGTAAACCTGCTTAGATCCTCGTTTAGAATTTTCGTTTAAATAAACCTGCTTAGGCCTCTGTC
1 TAAGTAAACCTGCTTAGGTTCT-GTTTAGAACTTTCGTTTAAATAAACCTGCTTAGGCCTCTATC
* * *
18944 TGGAATTTCCGTTTAAGTGAACCTGCTTAGCTCTCTGCTTAGAGTTTCGTT
65 TGGAATTTCCGTTTAAGTGAACCTGCTTAGCTCGCTACTTAGAGTTTCGTC
* ** * * * *
18995 TAAGAAAACCTGCTTAGGTCTCTACTTAGAGCTTT-GTTT-AATCAAGCCTGCTTAGGTCTTTAT
1 TAAGTAAACCTGCTTAGGT-TCTGTTTAGAACTTTCGTTTAAAT-AAACCTGCTTAGGCCTCTAT
* * *
19058 TTGGAATTTCTGTTTAAGTGAACCTGCTTAGGTCGCTACTTAGAGTTTCGTC
64 CTGGAATTTCCGTTTAAGTGAACCTGCTTAGCTCGCTACTTAGAGTTTCGTC
* *
19110 TAGGTAAACCTGCTTAGGTGTCTGTTTAGAATTTTCGTTTAA
1 TAAGTAAACCTGCTTAGGT-TCTGTTTAGAACTTTCGTTTAA
19152 GAAAACTTGG
Statistics
Matches: 129, Mismatches: 24, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
114 3 0.02
115 94 0.73
116 29 0.22
117 3 0.02
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (115 bp):
TAAGTAAACCTGCTTAGGTTCTGTTTAGAACTTTCGTTTAAATAAACCTGCTTAGGCCTCTATCT
GGAATTTCCGTTTAAGTGAACCTGCTTAGCTCGCTACTTAGAGTTTCGTC
Found at i:19462 original size:29 final size:29
Alignment explanation
Indices: 19430--19567 Score: 170
Period size: 29 Copynumber: 4.8 Consensus size: 29
19420 TCGCACGCTC
*
19430 AGGGGCATTTTGGCCATTTTTGCACATCT
1 AGGGGCATTTTGGTCATTTTTGCACATCT
*
19459 AGGGGCATTTTGGTCATTTTTGCATATCT
1 AGGGGCATTTTGGTCATTTTTGCACATCT
* ** *
19488 AGGGGTATAATGGTCATTTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCACATCT
* * *
19517 AAGGGCATTTTGGTCATCTTTACACATTCT
1 AGGGGCATTTTGGTCATTTTTGCACA-TCT
*
19547 -GGGGCAGTTTGGTCATTTTTG
1 AGGGGCATTTTGGTCATTTTTG
19568 GATACTCTAG
Statistics
Matches: 90, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
29 88 0.98
30 2 0.02
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.40
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTGCACATCT
Found at i:23229 original size:16 final size:16
Alignment explanation
Indices: 23208--23244 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
23198 TTGTCCATTT
23208 TTTTTGGATTTGTGCA
1 TTTTTGGATTTGTGCA
*
23224 TTTTT-GATTTGTTCA
1 TTTTTGGATTTGTGCA
23239 TTTTTG
1 TTTTTG
23245 CTTTTGAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.11, C:0.05, G:0.19, T:0.65
Consensus pattern (16 bp):
TTTTTGGATTTGTGCA
Done.