Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014700.1 Corchorus olitorius cultivar O-4 contig14733, 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: 23787
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:810 original size:334 final size:332
Alignment explanation
Indices: 1--1138 Score: 1760
Period size: 334 Copynumber: 3.4 Consensus size: 332
* *
1 GATATTAGAAGCGTGAAAGGTCCTAAAATTTTTTTGACGTTGAGTTATATATTTTATACGATTAT
1 GATATTAGAAGCGTGAAAGGCCCTAAAATCTTTTTGACGTTGAGTTATATATTTTATACGATTAT
* *
66 TGTGGCAAAAAATAGAGCGCAAAAGATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAA-----T
66 TGTGGCAAAAAATTGAGCGCAAAAGTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
* *
126 A--AC-ATCAC-GACTTTTGGCACAAAACGCGTTCCGGGGCCCCGGCTCAATTTTTCTTGATTTT
131 ACTACTATCACGGA-TTTTGGCTCAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTCTTGATTTT
*
187 TTGCGTCAAGACTCATTAAAATTTCTGTATTCATC-TATCGAAATGTCAGCCGCAATGGATATAG
195 TTGCGTCAAGACTCATTAAAATTTCTGTATTCATCAT-TCGAAATGTCAGCCACAATGGATATAG
*
251 GGATTTGTTTTTACAAGCATCAGAATCTTTTTCCGATTTAATTAGAATTTTAATTTAGAAAAAAT
259 GGATTTGTTTTTACGAGCATCAGAATCTTTTTCCGATTTAATTAGAATTTTAATTTAGAAAAAAT
316 TGGAAAAAT
324 TGGAAAAAT
325 GATATTAGAAGCGTGAAAGGCCCTAAAATCTTTTTGACGTTGAGTTATATATTTTATACGATTAT
1 GATATTAGAAGCGTGAAAGGCCCTAAAATCTTTTTGACGTTGAGTTATATATTTTATACGATTAT
* *
390 TTTGGCAAAACATTGAGCGCAAAAGTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
66 TGTGGCAAAAAATTGAGCGCAAAAGTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
*
455 ACTAACTATCACGGATTTTGGCTCAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTCTTGTTTTT
131 ACT-ACTATCACGGATTTTGGCTCAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTCTTGATTTT
* *
520 TTGCGTCAAGACTCATTAAAATTTCTTTATTCATCATTCGAAATGTCAGCCACAATGAATATAGG
195 TTGCGTCAAGACTCATTAAAATTTCTGTATTCATCATTCGAAATGTCAGCCACAATGGATATAGG
** *
585 GATTTGTTTTTACGAGCATCAGTTTCTTTTTCTGATTTAATTAGAATTTTAATTTAGAAAAAAAT
260 GATTTGTTTTTACGAGCATCAGAATCTTTTTCCGATTTAATTAGAATTTTAATTTAG-AAAAAAT
*
650 TTGAAAAAT
324 TGGAAAAAT
* * * *
659 GATATTAGAATCGTGAAAGACCCTAAAATCTTTTTAACGTTGGGTTATATATTTTATACGATTAT
1 GATATTAGAAGCGTGAAAGGCCCTAAAATCTTTTTGACGTTGAGTTATATATTTTATACGATTAT
*
724 TTTGGCAAAAAATTGAGCGCAAAAGTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
66 TGTGGCAAAAAATTGAGCGCAAAAGTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
* * * *
789 ACTATCTATCACGGGTTTTGGCTCAAAAAGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTT
131 ACTA-CTATCACGGATTTTGGCTCAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTCTTGATTTT
* * * ** * **
854 TTGCGTCAAGACTCGTTAAAATATCTGTATTCATCAATCGAAATCACAGCCACAATGGATTTAAT
195 TTGCGTCAAGACTCATTAAAATTTCTGTATTCATCATTCGAAATGTCAGCCACAATGGATATAGG
* * *** *
919 GATTTG-TTTTACGAGCATCAGAATCGTTTTCCAATACGATTAGAATTTTAATTTAGAAAAAATC
260 GATTTGTTTTTACGAGCATCAGAATCTTTTTCCGATTTAATTAGAATTTTAATTTAGAAAAAATT
983 GGAAAAAT
325 GGAAAAAT
*
991 GATATTAGAAGCGTGAAAGGCCCTAAAATCTTTTTGACGTTGAGTTATATATTTTATACGATAAT
1 GATATTAGAAGCGTGAAAGGCCCTAAAATCTTTTTGACGTTGAGTTATATATTTTATACGATTAT
1056 TGTGGCAAAAAATTGAGCGCAAAAGTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
66 TGTGGCAAAAAATTGAGCGCAAAAGTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
*
1121 ACTACCCATCAC-GATTTT
131 ACTA-CTATCACGGATTTT
1139 TGGTAAAAAA
Statistics
Matches: 745, Mismatches: 56, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
324 118 0.16
329 2 0.00
331 5 0.01
332 150 0.20
333 208 0.28
334 262 0.35
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (332 bp):
GATATTAGAAGCGTGAAAGGCCCTAAAATCTTTTTGACGTTGAGTTATATATTTTATACGATTAT
TGTGGCAAAAAATTGAGCGCAAAAGTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
ACTACTATCACGGATTTTGGCTCAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTCTTGATTTTT
TGCGTCAAGACTCATTAAAATTTCTGTATTCATCATTCGAAATGTCAGCCACAATGGATATAGGG
ATTTGTTTTTACGAGCATCAGAATCTTTTTCCGATTTAATTAGAATTTTAATTTAGAAAAAATTG
GAAAAAT
Found at i:1374 original size:333 final size:331
Alignment explanation
Indices: 1--1375 Score: 1735
Period size: 333 Copynumber: 4.2 Consensus size: 331
* *
1 GATATTAGAAGCGTGAAAGGTCCTAAAATTTTTTTGACGTTGAGTTATATATTTTATACGATTAT
1 GATATTAGAAGCGTGAAAGGCCCTAAAATCTTTTTGACGTTGAGTTATATATTTTATACGATTAT
* *
66 TGTGGCAAAAAATAGAGCGCAAAAGATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAA-----T
66 TGTGGCAAAAAATTGAGCGCAAAAGTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
* * *
126 A--A-CATCACGACTTTTGGC-ACAAAACGCGTTCCGGGGCCCCGGCTCAATTTTTCTTGATTTT
131 ACTACCATCACGA-TTTTGGCTAAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCTTGATTTT
* * * * *
187 TTGCGTCAAGACTCATTAAAATTTCTGTATTCATCTATCGAAATGTCAGCCGCAATGGATATAGG
195 TTGCGTCAAGACTCATTAAAATATCTGTATTCATCAATCGAAATCTCAGCCACAATGGATATAAG
*
252 GATTTGTTTTTACAAGCATCAGAATCTTTTTCCGATTTAATTAGAATTTTAATTTAGAAAAAATT
260 GATTTGTTTTTACGAGCATCAGAATCTTTTT-CGATTTAATTAGAATTTTAATTTAGAAAAAATT
317 GGAAAAAT
324 GGAAAAAT
325 GATATTAGAAGCGTGAAAGGCCCTAAAATCTTTTTGACGTTGAGTTATATATTTTATACGATTAT
1 GATATTAGAAGCGTGAAAGGCCCTAAAATCTTTTTGACGTTGAGTTATATATTTTATACGATTAT
* *
390 TTTGGCAAAACATTGAGCGCAAAAGTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
66 TGTGGCAAAAAATTGAGCGCAAAAGTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
* * * *
455 ACTAACTATCACGGATTTTGGCT-CAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTCTTGTTTT
131 ACT-ACCATCAC-GATTTTGGCTAAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCTTGATTT
* * * * * *
519 TTTGCGTCAAGACTCATTAAAATTTCTTTATTCATCATTCGAAATGTCAGCCACAATGAATATAG
194 TTTGCGTCAAGACTCATTAAAATATCTGTATTCATCAATCGAAATCTCAGCCACAATGGATATAA
**
584 GGATTTGTTTTTACGAGCATCAGTTTCTTTTTCTGATTTAATTAGAATTTTAATTTAGAAAAAAA
259 GGATTTGTTTTTACGAGCATCAGAATCTTTTTC-GATTTAATTAGAATTTTAATTTAG-AAAAAA
*
649 TTTGAAAAAT
322 TTGGAAAAAT
* * * *
659 GATATTAGAATCGTGAAAGACCCTAAAATCTTTTTAACGTTGGGTTATATATTTTATACGATTAT
1 GATATTAGAAGCGTGAAAGGCCCTAAAATCTTTTTGACGTTGAGTTATATATTTTATACGATTAT
*
724 TTTGGCAAAAAATTGAGCGCAAAAGTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
66 TGTGGCAAAAAATTGAGCGCAAAAGTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
* * * *
789 ACTATCTATCACGGGTTTTGGCTCAAAAA-GCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTT
131 ACTA-CCATCAC-GATTTTGGCTAAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCTTGATTT
* * *
853 TTTGCGTCAAGACTCGTTAAAATATCTGTATTCATCAATCGAAATCACAGCCACAATGGATTTAA
194 TTTGCGTCAAGACTCATTAAAATATCTGTATTCATCAATCGAAATCTCAGCCACAATGGATATAA
* * * *
918 TGATTTG-TTTTACGAGCATCAGAATCGTTTTCCA-ATACGATTAGAATTTTAATTTAGAAAAAA
259 GGATTTGTTTTTACGAGCATCAGAATCTTTTTCGATTTA--ATTAGAATTTTAATTTAGAAAAAA
*
981 TCGGAAAAAT
322 TTGGAAAAAT
*
991 GATATTAGAAGCGTGAAAGGCCCTAAAATCTTTTTGACGTTGAGTTATATATTTTATACGATAAT
1 GATATTAGAAGCGTGAAAGGCCCTAAAATCTTTTTGACGTTGAGTTATATATTTTATACGATTAT
1056 TGTGGCAAAAAATTGAGCGCAAAAGTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
66 TGTGGCAAAAAATTGAGCGCAAAAGTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
* * * ** * *
1121 ACTACCCATCACGATTTTTGG-TAAAAAAACGCGTTTCGGGGTCACGATTCTGTTTTGCCTGATT
131 ACTA-CCATCACGA-TTTTGGCT-AAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCTTGATT
* * * * * * * * * *
1185 TTTGGCG-CTGAGACACCTTGAAATATCTTTATTCATTTAATC-AAATCTTAGCCACATTGGATT
193 TTTTGCGTC-AAGACTCATTAAAATATCTGTATTCA-TCAATCGAAATCTCAGCCACAATGGATA
* * * * * *
1248 TAAGGATTTGTTTTTACGTGAATCTGAATATTGTTTCGATTTAATTAGAA-ATTAATTCTA-AAT
256 TAAGGATTTGTTTTTACGAGCATCAGAATCTT-TTTCGATTTAATTAGAATTTTAATT-TAGAAA
* ** *
1311 GAATAAGAAAAAC
319 AAATTGGAAAAAT
* * ** ** *
1324 GATATTAAAAGCGTGAATGGTTCTCCAATCTTTTTTGA-GTTGAATTATATAT
1 GATATTAGAAGCGTGAAAGGCCCTAAAATC-TTTTTGACGTTGAGTTATATAT
1376 ATATATATAT
Statistics
Matches: 931, Mismatches: 93, Indels: 45
0.87 0.09 0.04
Matches are distributed among these distances:
324 118 0.13
329 2 0.00
331 4 0.00
332 163 0.18
333 340 0.37
334 293 0.31
335 9 0.01
336 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (331 bp):
GATATTAGAAGCGTGAAAGGCCCTAAAATCTTTTTGACGTTGAGTTATATATTTTATACGATTAT
TGTGGCAAAAAATTGAGCGCAAAAGTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
ACTACCATCACGATTTTGGCTAAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCTTGATTTTT
TGCGTCAAGACTCATTAAAATATCTGTATTCATCAATCGAAATCTCAGCCACAATGGATATAAGG
ATTTGTTTTTACGAGCATCAGAATCTTTTTCGATTTAATTAGAATTTTAATTTAGAAAAAATTGG
AAAAAT
Found at i:7951 original size:11 final size:12
Alignment explanation
Indices: 7934--7967 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
7924 ATAAATATGT
7934 TCTCCATTTTCA
1 TCTCCATTTTCA
*
7946 -CTCCATTATCA
1 TCTCCATTTTCA
7957 TCTCCATTTTC
1 TCTCCATTTTC
7968 TAAAAAGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.18, C:0.35, G:0.00, T:0.47
Consensus pattern (12 bp):
TCTCCATTTTCA
Found at i:12203 original size:238 final size:238
Alignment explanation
Indices: 11785--12260 Score: 907
Period size: 238 Copynumber: 2.0 Consensus size: 238
11775 CTAACTTGTT
*
11785 CTTTAATCTTGGAGGACTTGGTATTCACTCTCTTATCATATCATATATAAATATATTAAAACAGA
1 CTTTAATCTTGGAGGACTTGGTATTCACTCTCTTATCATATCATATATAAATATATTAAAACAAA
11850 AGAAGTTGGAAAAAGGTAGGAATTTTGAATATTTATAATTTAAATTAATTTAACAATCCTTATCA
66 AGAAGTTGGAAAAAGGTAGGAATTTTGAATATTTATAATTTAAATTAATTTAACAATCCTTATCA
* *
11915 ATTTTACCGAACATATCAACTATAAATATGAATCATTGCCTTTGCACTTTACAACTTTTATCTTT
131 ATTTTACCAAACATATCAACTATAAATATGAATCATTGCCTTTGCACTTTAAAACTTTTATCTTT
11980 CTATTATTTCTTCTTCTTTGAATATTTATTTTATTATTCTACC
196 CTATTATTTCTTCTTCTTTGAATATTTATTTTATTATTCTACC
12023 CTTTAATCTTGGAGGACTTGGTATTCACTCTCTTATCATATCATATATAAATATATTAAAACAAA
1 CTTTAATCTTGGAGGACTTGGTATTCACTCTCTTATCATATCATATATAAATATATTAAAACAAA
*
12088 AGAAGTTGGAAAAAGGTAGGAATTTTGAATATTTATAATTTAAATTAATTTTACAATCCTTATCA
66 AGAAGTTGGAAAAAGGTAGGAATTTTGAATATTTATAATTTAAATTAATTTAACAATCCTTATCA
12153 ATTTTACCAAACATATCAACTATAAATATGAATCATTGCCTTTGCACTTTAAAACTTTTATCTTT
131 ATTTTACCAAACATATCAACTATAAATATGAATCATTGCCTTTGCACTTTAAAACTTTTATCTTT
*
12218 CTATTATTTCTTCTTCTTTGCATATTTATTTTATTATTCTACC
196 CTATTATTTCTTCTTCTTTGAATATTTATTTTATTATTCTACC
12261 ATTTTCTTTC
Statistics
Matches: 233, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
238 233 1.00
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.43
Consensus pattern (238 bp):
CTTTAATCTTGGAGGACTTGGTATTCACTCTCTTATCATATCATATATAAATATATTAAAACAAA
AGAAGTTGGAAAAAGGTAGGAATTTTGAATATTTATAATTTAAATTAATTTAACAATCCTTATCA
ATTTTACCAAACATATCAACTATAAATATGAATCATTGCCTTTGCACTTTAAAACTTTTATCTTT
CTATTATTTCTTCTTCTTTGAATATTTATTTTATTATTCTACC
Found at i:13198 original size:1 final size:1
Alignment explanation
Indices: 13192--13230 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
13182 CCCCTTTCAC
13192 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13231 CTTAATACCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13513 original size:51 final size:52
Alignment explanation
Indices: 13436--13540 Score: 194
Period size: 51 Copynumber: 2.0 Consensus size: 52
13426 AATATATTGT
13436 AATTTCTTTTTTTTTCCTGACAAAGTATACCTCAAAATCTAACAAACTAAAG
1 AATTTCTTTTTTTTTCCTGACAAAGTATACCTCAAAATCTAACAAACTAAAG
*
13488 AATTT-TTTTTTTTTTCTGACAAAGTATACCTCAAAATCTAACAAACTAAAG
1 AATTTCTTTTTTTTTCCTGACAAAGTATACCTCAAAATCTAACAAACTAAAG
13539 AA
1 AA
13541 CAAGTAAACT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 47 0.90
52 5 0.10
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (52 bp):
AATTTCTTTTTTTTTCCTGACAAAGTATACCTCAAAATCTAACAAACTAAAG
Found at i:23729 original size:2 final size:2
Alignment explanation
Indices: 23724--23784 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
23714 AAAAATTAAA
23724 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
23766 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
23785 AGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.