Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022628.1 Corchorus olitorius cultivar O-4 contig22661, 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: 45700
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:2628 original size:12 final size:12
Alignment explanation
Indices: 2597--2632 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
2587 TTTTCCTTTT
2597 TTTATTATATATA
1 TTTATT-TATATA
2610 TTATATTTATATA
1 TT-TATTTATATA
2623 TTTATTTATA
1 TTTATTTATA
2633 ACTAACTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.36
13 10 0.45
14 4 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTATTTATATA
Found at i:3179 original size:41 final size:41
Alignment explanation
Indices: 3133--3268 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
3123 GTGTTCAACA
**
3133 TGGTCCCTGATTTAGGATACTATTTATTGTTTGATGCAATT
1 TGGTCCCTGATTTAGGATTTTATTTATTGTTTGATGCAATT
* * * ***
3174 TGGTCCTTGATCTAGGATTTTATTTTTTGATTT-ATGCGGCT
1 TGGTCCCTGATTTAGGATTTTATTTATTG-TTTGATGCAATT
* * * *
3215 TAGTCCCTGATTTAAGATTTTATTTACTATTTGATGCAATT
1 TGGTCCCTGATTTAGGATTTTATTTATTGTTTGATGCAATT
*
3256 TGGTCCCTAATTT
1 TGGTCCCTGATTT
3269 TAGAAATATA
Statistics
Matches: 73, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
40 3 0.04
41 67 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.49
Consensus pattern (41 bp):
TGGTCCCTGATTTAGGATTTTATTTATTGTTTGATGCAATT
Found at i:4781 original size:26 final size:26
Alignment explanation
Indices: 4745--4797 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
4735 ATCTAATAAG
*
4745 TACAACGACTCAGCAAGTGACAGACA
1 TACAACAACTCAGCAAGTGACAGACA
4771 TACAACAACTCAGCAAGTGACAGACA
1 TACAACAACTCAGCAAGTGACAGACA
4797 T
1 T
4798 CCCCTCAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.13
Consensus pattern (26 bp):
TACAACAACTCAGCAAGTGACAGACA
Found at i:13955 original size:18 final size:18
Alignment explanation
Indices: 13932--13966 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
13922 ACTGGTGGGA
13932 GTTAGAGACATTAAGTCG
1 GTTAGAGACATTAAGTCG
13950 GTTAGAGACATTAAGTC
1 GTTAGAGACATTAAGTC
13967 AACAGCTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (18 bp):
GTTAGAGACATTAAGTCG
Found at i:14218 original size:3 final size:3
Alignment explanation
Indices: 14212--14252 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
14202 TTTATTATTC
14212 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
14253 TCTGTTATGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:15302 original size:30 final size:30
Alignment explanation
Indices: 15266--15869 Score: 465
Period size: 30 Copynumber: 19.9 Consensus size: 30
15256 ACTCTCCAAA
15266 TGACACCAGAAGTTGTCATGATCTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
*
15296 TGACACCACAAGTTGTCATGATCTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
*
15326 TGACACCACAAGTTGTCATGATCTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
* *
15356 TGACACCACAAGTTGTAATGATCTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
* **
15386 TGACACCATAAGTTGTCAATGGCCTTACAAT
1 TGACACCAGAAGTTGTC-ATGATCTTACAAT
**
15417 TGACACCAGAAGTTGTCAATGGCCTTACAAT
1 TGACACCAGAAGTTGTC-ATGATCTTACAAT
* **
15448 TGACACCAGAAGTTATCAATGGCCTTACAAT
1 TGACACCAGAAGTTGTC-ATGATCTTACAAT
**
15479 TGACACCAGAAGTTGTCAATGGCCTTACAAT
1 TGACACCAGAAGTTGTC-ATGATCTTACAAT
* ** **
15510 TGACACCAGAAGTTGTCAATGCTC-GGCAGC
1 TGACACCAGAAGTTGTC-ATGATCTTACAAT
*** ** * ** ***
15540 TGAGTTTGCAG-TCTTGCACACCAGGGTA-AATT
1 TGA--CACCAGAAGTTG-TCATGATCTTACAA-T
* *
15572 TCACATTCTCA-AAGCTT-T--TGATCTT-CAGT
1 TGACA--C-CAGAAG-TTGTCATGATCTTACAAT
** * * *
15601 CTGACATCTTGAAGAATAGGTTAT-ATC--GCAAT
1 -TGACA-CCAGAAG--T-TGTCATGATCTTACAAT
* * * *
15633 TGAGACCAGTAGTTGTTATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
* *
15663 TGACACCAGGAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
* *
15693 TGACACCAGGAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
* ** *
15723 TGACACCAGAAGTTATCATGATCTTGTAGT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
* *
15753 TGACACCAGAAGTTATCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
*
15783 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
* * *
15813 TGACACCAAAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
*
15843 TGACACCAGAAGTTGTCATGATTTTAC
1 TGACACCAGAAGTTGTCATGATCTTAC
15870 CTTTCAAATT
Statistics
Matches: 483, Mismatches: 68, Indels: 46
0.81 0.11 0.08
Matches are distributed among these distances:
27 5 0.01
28 4 0.01
29 6 0.01
30 318 0.66
31 132 0.27
32 10 0.02
33 5 0.01
34 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTACAAT
Found at i:15416 original size:31 final size:31
Alignment explanation
Indices: 15266--15530 Score: 385
Period size: 31 Copynumber: 8.7 Consensus size: 31
15256 ACTCTCCAAA
*
15266 TGACACCAGAAGTTGTC-ATGATCTTACAAT
1 TGACACCAGAAGTTGTCAATGACCTTACAAT
* *
15296 TGACACCACAAGTTGTC-ATGATCTTACAAT
1 TGACACCAGAAGTTGTCAATGACCTTACAAT
* *
15326 TGACACCACAAGTTGTC-ATGATCTTACAAT
1 TGACACCAGAAGTTGTCAATGACCTTACAAT
* *
15356 TGACACCACAAGTTGT-AATGATCTTACAAT
1 TGACACCAGAAGTTGTCAATGACCTTACAAT
* *
15386 TGACACCATAAGTTGTCAATGGCCTTACAAT
1 TGACACCAGAAGTTGTCAATGACCTTACAAT
*
15417 TGACACCAGAAGTTGTCAATGGCCTTACAAT
1 TGACACCAGAAGTTGTCAATGACCTTACAAT
* *
15448 TGACACCAGAAGTTATCAATGGCCTTACAAT
1 TGACACCAGAAGTTGTCAATGACCTTACAAT
*
15479 TGACACCAGAAGTTGTCAATGGCCTTACAAT
1 TGACACCAGAAGTTGTCAATGACCTTACAAT
15510 TGACACCAGAAGTTGTCAATG
1 TGACACCAGAAGTTGTCAATG
15531 CTCGGCAGCT
Statistics
Matches: 226, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
30 103 0.46
31 123 0.54
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (31 bp):
TGACACCAGAAGTTGTCAATGACCTTACAAT
Found at i:19732 original size:118 final size:123
Alignment explanation
Indices: 19447--19760 Score: 342
Period size: 127 Copynumber: 2.6 Consensus size: 123
19437 TAAAGTGCGT
* *
19447 TGCACTCTTTTTCCCTTATGATCGGTTTTGTCCCACAGGGTTTTTCGACTTAAGGTTTTTAATGA
1 TGCACTCTTTTTCCCTTATGATCGGTTTTGTCCCACTGGGTTTTCCGACTTAAGGTTTTTAATGA
* *
19512 GGCAACAATAGCACATCTAGATTGAATTGTCCTAAAGACATTTACATGGACTTAATTGCCC
66 GGCAACAAGAGCACATATAGATTGAATTGTCCTAAAGACA--TACATGGACTTAATTG-CC
* * * **
19573 TAGCACT-TTTGTTCCCTTTTGTTCGGTTTTTTCCCACTGGGTTTTCCGACACAAGGTTTTTAAT
1 T-GCACTCTTT-TTCCCTTATGATCGGTTTTGTCCCACTGGGTTTTCCGACTTAAGGTTTTTAAT
* * *
19637 GAGGCAATAAGAGCACATATA-A-T-ATTTGTCC-AGAAGACA-A-ATGGACTTGATATG-C
64 GAGGCAACAAGAGCACATATAGATTGAATTGTCCTA-AAGACATACATGGACTTAAT-TGCC
* * *
19692 TGCACTCTTTTTTCCTTATGA-CTGGTTTTGTCCCATTGGGTTTTCC-AGCTTAAGGTTTTTAAC
1 TGCACTCTTTTTCCCTTATGATC-GGTTTTGTCCCACTGGGTTTTCCGA-CTTAAGGTTTTTAAT
19755 GAGGCA
64 GAGGCA
19761 TTAGCTACAT
Statistics
Matches: 161, Mismatches: 20, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
117 2 0.01
118 52 0.32
119 5 0.03
120 10 0.06
121 3 0.02
123 1 0.01
124 13 0.08
125 1 0.01
126 5 0.03
127 69 0.43
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.38
Consensus pattern (123 bp):
TGCACTCTTTTTCCCTTATGATCGGTTTTGTCCCACTGGGTTTTCCGACTTAAGGTTTTTAATGA
GGCAACAAGAGCACATATAGATTGAATTGTCCTAAAGACATACATGGACTTAATTGCC
Found at i:26972 original size:452 final size:453
Alignment explanation
Indices: 26113--27026 Score: 1706
Period size: 452 Copynumber: 2.0 Consensus size: 453
26103 ATTATTATAA
*
26113 ATAAAGGTGAATTAATGTCCATTAAACATTAAAATTTGAAGAATTTTTTCAGTTTTAGATTCTGA
1 ATAAAGGTGAATTAATGTCCACTAAACATTAAAATTTGAAGAATTTTTTCAGTTTTAGATTCTGA
*
26178 AAAGTTAAAAAGTTGTCATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTGTT
66 AAAGTTAAAAAGTTGACATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTGTT
26243 CCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAATTTTTTTTTTTTTGAAGA
131 CCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAA----TTTTTTTTTGAAGA
26308 ATTTTTTAAGTTTTAGAATCTAAAAGTCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAAT
192 ATTTTTTAAGTTTTAGAATCTAAAAGTCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAAT
26373 GTTTCTGTTTTTTGTTGGAATAATCAATTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGAC
257 GTTTCTGTTTTTTGTTGGAATAATCAATTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGAC
*
26438 AACTTCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATAAGGGG
322 AACTTCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATAAGGCG
*
26503 AAAAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAGGCTGCCATCTGATATCTTT
387 AAAAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTT
26568 AC
452 AC
**
26570 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
1 ATAAAGGTG-AATTAATGTCCACTAAACATTAAAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
26635 AAAAGTTAAAAAGTTGACATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTGT
65 AAAAGTTAAAAAGTTGACATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTGT
26700 TCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAA-TTTTTTTTGAAGAA-T
130 TCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAATTTTTTTTTGAAGAATT
26763 TTTTAAGTTTTAGAATCTAAAAGTCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATGTT
195 TTTTAAGTTTTAGAATCTAAAAGTCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATGTT
26828 TCTGTTTTTTGTTGGAATAATCAATTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACAAC
260 TCTGTTTTTTGTTGGAATAATCAATTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACAAC
*
26893 TTCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATGAGGCGAAA
325 TTCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATAAGGCGAAA
26958 AAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTTAC
390 AAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTTAC
27022 ATAAA
1 ATAAA
27027 TCGTACTTAA
Statistics
Matches: 449, Mismatches: 7, Indels: 7
0.97 0.02 0.02
Matches are distributed among these distances:
452 262 0.58
453 14 0.03
457 9 0.02
458 164 0.37
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (453 bp):
ATAAAGGTGAATTAATGTCCACTAAACATTAAAATTTGAAGAATTTTTTCAGTTTTAGATTCTGA
AAAGTTAAAAAGTTGACATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTGTT
CCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAATTTTTTTTTGAAGAATTT
TTTAAGTTTTAGAATCTAAAAGTCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATGTTT
CTGTTTTTTGTTGGAATAATCAATTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACAACT
TCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATAAGGCGAAAA
AGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTTAC
Found at i:27089 original size:16 final size:16
Alignment explanation
Indices: 27070--27101 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27060 TGATTGGTAT
27070 TAAAGTCATTATATTA
1 TAAAGTCATTATATTA
*
27086 TAAATTCATTATATTA
1 TAAAGTCATTATATTA
27102 ATCTCCTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (16 bp):
TAAAGTCATTATATTA
Found at i:28297 original size:14 final size:14
Alignment explanation
Indices: 28278--28311 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28268 TTTTATAATT
28278 ATTTTACTTTTACC
1 ATTTTACTTTTACC
* *
28292 ATTTTATTTTTACT
1 ATTTTACTTTTACC
28306 ATTTTA
1 ATTTTA
28312 ATTTAAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTTACTTTTACC
Found at i:37248 original size:189 final size:189
Alignment explanation
Indices: 36928--37304 Score: 720
Period size: 189 Copynumber: 2.0 Consensus size: 189
36918 GGTTCTTCCC
*
36928 CTTATCTGTGAGGAGTTGGTAATATATACCTATTTGACCTCTCTGTCTCACTTCATGTCCAGTTA
1 CTTATCTGTGAGGAGTTGGCAATATATACCTATTTGACCTCTCTGTCTCACTTCATGTCCAGTTA
36993 GCACATTATGTTTGCATATGTTGTAGCAGAAGAAGACTCTGCTATAATCAAAGAGTCAAGATGTG
66 GCACATTATGTTTGCATATGTTGTAGCAGAAGAAGACTCTGCTATAATCAAAGAGTCAAGATGTG
37058 CATGTAATTTAGAACTCACTCCCCTGTCCTGCAATGGTTG-ATCATATTTTAATAATTTG
131 CATGTAATTTAGAACTCACTCCCCTGTCCTGCAATGGTTGCA-CATATTTTAATAATTTG
*
37117 CTTATCTGTGAGGAGTTGGCAATATATACCTATTTGACCTCTCTGTCTCACTTCATTTCCAGTTA
1 CTTATCTGTGAGGAGTTGGCAATATATACCTATTTGACCTCTCTGTCTCACTTCATGTCCAGTTA
37182 GCACATTATGTTTGCATATGTTGTAGCAGAAGAAGACTCTGCTATAATCAAAGAGTCAAGATGTG
66 GCACATTATGTTTGCATATGTTGTAGCAGAAGAAGACTCTGCTATAATCAAAGAGTCAAGATGTG
37247 CATGTAATTTAGAACTCACTCCCCTGTCCTGCAATGGTTGCACATATTTTAATAATTT
131 CATGTAATTTAGAACTCACTCCCCTGTCCTGCAATGGTTGCACATATTTTAATAATTT
37305 TTAATTTGCA
Statistics
Matches: 185, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
189 184 0.99
190 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (189 bp):
CTTATCTGTGAGGAGTTGGCAATATATACCTATTTGACCTCTCTGTCTCACTTCATGTCCAGTTA
GCACATTATGTTTGCATATGTTGTAGCAGAAGAAGACTCTGCTATAATCAAAGAGTCAAGATGTG
CATGTAATTTAGAACTCACTCCCCTGTCCTGCAATGGTTGCACATATTTTAATAATTTG
Found at i:38201 original size:5 final size:6
Alignment explanation
Indices: 38183--38209 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
38173 ATAGCTTTCT
38183 CCACCC CCACCC CCACCC CCACCC CCA
1 CCACCC CCACCC CCACCC CCACCC CCA
38210 TTCTTTCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.81, G:0.00, T:0.00
Consensus pattern (6 bp):
CCACCC
Done.