Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012953.1 Corchorus olitorius cultivar O-4 contig12986, 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: 17135
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1483 original size:28 final size:28
Alignment explanation
Indices: 1391--1514 Score: 171
Period size: 28 Copynumber: 4.5 Consensus size: 28
1381 AATGTACTTG
* * * *
1391 AAATGACTAAAATGCCCCTGAATATG-T
1 AAATGACCAAAATGCCCCTGGACATGCA
*
1418 AAATGACCAAAATGCCCCT-GACATACA
1 AAATGACCAAAATGCCCCTGGACATGCA
*
1445 AAATGACCAAAATGCCCCTGGATATGCA
1 AAATGACCAAAATGCCCCTGGACATGCA
*
1473 AAATGACCAAAATGCCACTGGACATGCA
1 AAATGACCAAAATGCCCCTGGACATGCA
1501 AAATGACCAAAATG
1 AAATGACCAAAATG
1515 AGAAGTAAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
26 3 0.03
27 37 0.43
28 46 0.53
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.18
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGACATGCA
Found at i:9839 original size:262 final size:263
Alignment explanation
Indices: 9337--10293 Score: 1150
Period size: 265 Copynumber: 3.6 Consensus size: 263
9327 ATATTGTCCA
* * * * *
9337 CAGAGTTGAGTGACATAAACTACCTCGACTCTTAAGTTGGA-TTTAGACCATATACCTTGATTGC
1 CAGAGTTGAGTGACATAAACTACCTTGACTCTTAAGTTGGACTTGA-ACCAAATACCTCGATTGG
* *
9401 ACTTGGGCTTGGTCACCTTGACTTATTTGCACCTGACCGACTTGGATCAAATTCTCGAACATGGA
65 ACTTGGGCTTGGACACCTTGACTTATTTGGACCTGACCGACTTGGATCAAATTCTCGAACATGGA
* * * * * *
9466 TAGTTGCGGACTAAATATTATTATTTATTTCCATTTTTAGTAAATATTTTATCGCCATTTCATGT
130 TAATTGCGGACTAAATA-T-TTA--T-TGT-CATTTTAAGTAAAAATTTTATCGCTATTTTATGT
* *
9531 CCAATATCCCACAACGACAAAGTAATATCTGCTTCACTCATTTATAATAAGCAACGTTCCTAATA
189 CCAATATCCCACAACGACAAAATAATATCTGCTTCACTCCTTTATAATAAGCAACGTTCCTAATA
9596 CGATTGTTCT
254 CGATTGTTCT
* * * * * * *
9606 CAGGGTTTAGTGACATAAACTACCTTAACTCTTAAGTTAGAGTTGAACCAAATACCTCAATTAGA
1 CAGAGTTGAGTGACATAAACTACCTTGACTCTTAAGTTGGACTTGAACCAAATACCTCGATTGGA
* * * *
9671 CTTGGGCTTGG-CACCTTGACTTATTTGGACTTGACCGACTTGGACCAAATTCTTGGACATGGAT
66 CTTGGGCTTGGACACCTTGACTTATTTGGACCTGACCGACTTGGATCAAATTCTCGAACATGGAT
** * *
9735 AATTTTGGACGAAATATTTATTGTCATTTTAAGTAAAAATTTTAAT-GTTATTTTATGTCCAATA
131 AATTGCGGACTAAATATTTATTGTCATTTTAAGTAAAAATTTT-ATCGCTATTTTATGTCCAATA
* * * *
9799 TCCCACAACGACAAAACAATATCTGCTTCAGTCCTTTATAATAAGTAACGTTCCTATTACGATTG
195 TCCCACAACGACAAAATAATATCTGCTTCACTCCTTTATAATAAGCAACGTTCCTAATACGATTG
**
9864 CCCT
260 TTCT
* * * * * * *
9868 TAAAGTTGAGTGGCATAAACTACCTTGACTCTTAAGTTGGACTAGGACCAAATAGCTTGATTGGA
1 CAGAGTTGAGTGACATAAACTACCTTGACTCTTAAGTTGGACTTGAACCAAATACCTCGATTGGA
* * * *
9933 CTTGGGCTTGGACGCCTTGACTTGTTTGGGCCTGACTGACTTGGATCAAATTCTCGAACATGGAT
66 CTTGGGCTTGGACACCTTGACTTATTTGGACCTGACCGACTTGGATCAAATTCTCGAACATGGAT
* * * *
9998 AGTTGCGGACTAAATATTTATTGCCATTTTAAGTAAATAAAATTTGTCGCTATTTTATGTCCAAT
131 AATTGCGGACTAAATATTTATTGTCATTTTAAGT-AA-AAATTTTATCGCTATTTTATGTCCAAT
* * * * *
10063 ATCCCACAACAACAAAATAATA-CATGTTTCACTCCTTTATAATAAGCAATGTTGCTAATATGAT
194 ATCCCACAACGACAAAATAATATC-TGCTTCACTCCTTTATAATAAGCAACGTTCCTAATACGAT
10127 TGTTCT
258 TGTTCT
* * * *
10133 CAGTGTTGAGTAGA-ATAAACTACCTTGACTCTTAAGTTGAACTTGGACCAAATAACTCGATTGG
1 CAGAGTTGAGT-GACATAAACTACCTTGACTCTTAAGTTGGACTTGAACCAAATACCTCGATTGG
* * * * ** * *
10197 ACTTGGGTTTGGGCACCTTGACTTGTTTGGACTTGACCGACTTGGATCGTATTCTCGGATATGGA
65 ACTTGGGCTTGGACACCTTGACTTATTTGGACCTGACCGACTTGGATCAAATTCTCGAACATGGA
*
10262 TAATTGTGGACTAAATATTTATTGTCATTTTA
130 TAATTGCGGACTAAATATTTATTGTCATTTTA
10294 TCTCCAATAT
Statistics
Matches: 584, Mismatches: 96, Indels: 20
0.83 0.14 0.03
Matches are distributed among these distances:
262 155 0.27
263 78 0.13
264 5 0.01
265 217 0.37
266 4 0.01
267 1 0.00
268 60 0.10
269 61 0.10
270 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (263 bp):
CAGAGTTGAGTGACATAAACTACCTTGACTCTTAAGTTGGACTTGAACCAAATACCTCGATTGGA
CTTGGGCTTGGACACCTTGACTTATTTGGACCTGACCGACTTGGATCAAATTCTCGAACATGGAT
AATTGCGGACTAAATATTTATTGTCATTTTAAGTAAAAATTTTATCGCTATTTTATGTCCAATAT
CCCACAACGACAAAATAATATCTGCTTCACTCCTTTATAATAAGCAACGTTCCTAATACGATTGT
TCT
Found at i:10810 original size:229 final size:220
Alignment explanation
Indices: 10372--10812 Score: 517
Period size: 223 Copynumber: 2.0 Consensus size: 220
10362 CGATTGCCCT
* * *
10372 TAGAGTTCAGTGGCATAAACTATCTTCACTCTTAAGTTGGACTTGGACCTACCTTGATTGAACTT
1 TAGAGTTCAGTGACATAAACTACCTTCACTCTTAAGTTGGACTTAGACCTACCTTGATTGAACTT
* * * * *
10437 GGATTTGGACACCTTGACTTGTTTGGGTCTAACCGATTTAGACCAGATTCTCAGACATGGATAGT
66 GGACTTGGACACCTTGACTTGTTTAGGCCTAACCGACTTAGACCAAATTCTCAGACATGGATAGT
*** * * * *
10502 TGTGGACTAAATAGTTATTGACATTTTAAGTAAATATTTTATTTCCATTTTATGTCCAATATTCC
131 TACAGACTAAATAATTATTGACATTTTAAGTAAATATTTTATGTCCAGTTTATGTCCAATATCCC
*
10567 ACAACAATAAAACAATATTTTTCCA
196 ACAACAACAAAACAATATTTTTCCA
* * * * * *
10592 TAGAGTTGAGTGACATAAACTACCTTGACTTTTAAGTTGGATTTAGACCAAATATCTTGATTGGA
1 TAGAGTTCAGTGACATAAACTACCTTCACTCTTAAGTTGGACTTAGACC---TACCTTGATTGAA
* * * *
10657 CTTGGGCTTGGACACCTTGACTTGTTTAGGCCTGACCGACTTGGATCAAATTCTC-GAACATGGA
63 CTTGGACTTGGACACCTTGACTTGTTTAGGCCTAACCGACTTAGACCAAATTCTCAG-ACATGGA
*
10721 TAGTTACAGACTAAATATTATTAATTATTGTCATTTTAAGTAAATATTTTATCGT-CAGTTTATG
127 TAGTTACAGACT--A-A--A-TAATTATTGACATTTTAAGTAAATATTTTAT-GTCCAGTTTATG
*
10785 TCCAATATCCCACAACGACAAAACAATA
185 TCCAATATCCCACAACAACAAAACAATA
10813 CATGTTTCAC
Statistics
Matches: 182, Mismatches: 28, Indels: 13
0.82 0.13 0.06
Matches are distributed among these distances:
220 42 0.23
222 1 0.01
223 73 0.40
225 1 0.01
226 1 0.01
228 1 0.01
229 62 0.34
230 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (220 bp):
TAGAGTTCAGTGACATAAACTACCTTCACTCTTAAGTTGGACTTAGACCTACCTTGATTGAACTT
GGACTTGGACACCTTGACTTGTTTAGGCCTAACCGACTTAGACCAAATTCTCAGACATGGATAGT
TACAGACTAAATAATTATTGACATTTTAAGTAAATATTTTATGTCCAGTTTATGTCCAATATCCC
ACAACAACAAAACAATATTTTTCCA
Found at i:11113 original size:263 final size:262
Alignment explanation
Indices: 10595--11308 Score: 862
Period size: 263 Copynumber: 2.7 Consensus size: 262
10585 TTTTCCATAG
* * *
10595 AGTTGAGTGACATAAACTACCTTGACTTTTAAGTTGGATTTAGACCAAATATCTTGATTGGACTT
1 AGTTGAGTGACATAAACTACCTTGACTCTTAAGTTGGACTTGGACCAAATATCTTGATTGGACTT
* * * * *
10660 GGGCTTG-GACACCTTGACTTGTTTAGGCCTGACCGACTTGGATCAAATTCTCGAACATGGATAG
66 GGGCTTGAG-CACCTTGACTTGTTTGGGCTTGACCAACTTGGACCAAATTCTCGGACATGGATAG
* * * *
10724 TTACAGACTAAATATTATTAATTATTGTCATTTTAAGTAAATATTTTATCGTCAGTTTATGTCCA
130 TTGCGGAC-AAA-A-TA-T--TTATTGTCATTTTAAGTAAAAATTTTAT-GTCATTTTATGTCCA
10789 ATATCCCACAACGACAAAACAATACATGTTTCACTCCTTTATAATAAGCAACGTTCCTAATACGA
188 ATATCCCACAACGACAAAACAATACATGTTTCACTCCTTTATAATAAGCAACGTTCCTAATA-GA
10854 -TTGTTCTCAA
252 TTTGTTCTCAA
* * *
10864 AGTTGAGTGACATATACTACCTTGACTCTTATGTTGGACTTGGACCAAATATCTCGATTGGACTT
1 AGTTGAGTGACATAAACTACCTTGACTCTTAAGTTGGACTTGGACCAAATATCTTGATTGGACTT
* * * * *
10929 AGGCTTGAGCACCTTGACATGTTTGGGCTTGACCAACTTGGACCATATTCTCGGACATGGACAAT
66 GGGCTTGAGCACCTTGACTTGTTTGGGCTTGACCAACTTGGACCAAATTCTCGGACATGGATAGT
* * * *
10994 TGTGGACAAAATATTTATTGTCATTTGAAGTAAAAATTTTAGTATCATTTTATGTCCAATATTCC
131 TGCGGACAAAATATTTATTGTCATTTTAAGTAAAAATTTTA-TGTCATTTTATGTCCAATATCCC
* * *
11059 ACAACGACAAAACAGTACTTGTTTCACTCCTTTATAATAAGCAACGTTCCTAATATATTTGTTCT
195 ACAACGACAAAACAATACATGTTTCACTCCTTTATAATAAGCAACGTTCCTAATAGATTTGTTCT
*
11124 CAG
260 CAA
* * * * **
11127 AGTTGAGTGGCATAAACTACCTTGACTCGTAAGTCGAACTTGGACCAAATA-CATTGATTAAACT
1 AGTTGAGTGACATAAACTACCTTGACTCTTAAGTTGGACTTGGACCAAATATC-TTGATTGGACT
** * * * * *
11191 TGGGGATGAACATCTTCACTTGTTTGGG-TCTGACCAACTTAGACCAAATTCTCGGACATGAATA
65 TGGGCTTGAGCACCTTGACTTGTTTGGGCT-TGACCAACTTGGACCAAATTCTCGGACATGGATA
** *
11255 GTTGCGGACTTAATATTTATTG-CTATTTTATGTAAAATATTTTATTGTCATTTT
129 GTTGCGGACAAAATATTTATTGTC-ATTTTAAGTAAAA-ATTTTA-TGTCATTTT
11309 CCAATATCCA
Statistics
Matches: 382, Mismatches: 56, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
262 4 0.01
263 239 0.63
264 15 0.04
265 1 0.00
266 2 0.01
267 1 0.00
268 3 0.01
269 116 0.30
270 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (262 bp):
AGTTGAGTGACATAAACTACCTTGACTCTTAAGTTGGACTTGGACCAAATATCTTGATTGGACTT
GGGCTTGAGCACCTTGACTTGTTTGGGCTTGACCAACTTGGACCAAATTCTCGGACATGGATAGT
TGCGGACAAAATATTTATTGTCATTTTAAGTAAAAATTTTATGTCATTTTATGTCCAATATCCCA
CAACGACAAAACAATACATGTTTCACTCCTTTATAATAAGCAACGTTCCTAATAGATTTGTTCTC
AA
Found at i:11657 original size:41 final size:41
Alignment explanation
Indices: 11600--11681 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
11590 TCTATCCCTA
11600 GTAATTCCTTTGATTGCTAGATGCGACACCGAAGCGAAGGC
1 GTAATTCCTTTGATTGCTAGATGCGACACCGAAGCGAAGGC
11641 GTAATTCCTTTGATTGCTAGATGCGACACCGAAGCGAAGGC
1 GTAATTCCTTTGATTGCTAGATGCGACACCGAAGCGAAGGC
11682 TTTGGCCGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (41 bp):
GTAATTCCTTTGATTGCTAGATGCGACACCGAAGCGAAGGC
Done.