Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017561.1 Corchorus olitorius cultivar O-4 contig17594, 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: 1912
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Found at i:717 original size:325 final size:325
Alignment explanation
Indices: 1--853 Score: 1314
Period size: 325 Copynumber: 2.6 Consensus size: 325
*
1 TAGAAGCGTGAAAAGCCCTCTAATCTTTTTGGCGTTGAATTAAATA-TTTTTATGAGTATTCTTG
1 TAGAAGCGTGAAAAGCCCTCTAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTCTTG
*
65 G-AAAAATTGAGGAAAAATCTTTCGTGTCAAATTTTTGCAAAATTTTAGCCGTAATCTTGTACTA
66 GAAAAAATTGAGGAAAAATCTTTCGTGT-AAATTTTTGCAAAATTTTAGCCGTAATCATGTACTA
*
129 ACCATCACGGTTTTTGG-C-AAAACG-CG-TTTGGGACCCGG-CTCAGTTTTGCATGATTTTTGG
130 ACCATCACGGTTTTTGGCCAAAAACGACGTTTTGGGGCCCGGACTCAGTTTTGCATGATTTTTGG
*
189 CGCCAAAATTCCTTGAGACATCCATATTCATCTAACCAAAATCTCTGCAACGATGGATTTAAAAA
195 CGCCAAGATTCCTTGAGACATCCATATTCATCTAACCAAAATCTCTGCAACGATGGATTTAAAAA
* * * *
254 TTTGTCTTTACGAGCATCTAAATCTTGTTTCGATTAATTTAGAAATTACTTCAGAAAAAAAACGA
260 TTTGTCTTTAAGAGAATCTAAATCTTGTTTCGATTAAATTAGAAATTACTT-A-AAAAAAAACAA
319 TAT
323 TAT
* * *
322 TAGAAGCGTGAAAAGCTCTCTAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTGTTG
1 TAGAAGCGTGAAAAGCCCTCTAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTCTTG
* *
387 GAAAAAATTGAGGAAAAATCTTTCGTGTTAATTTTTGCAAAATTTTAGCCGTAATCGTGTACTAA
66 GAAAAAATTGAGGAAAAATCTTTCGTGTAAATTTTTGCAAAATTTTAGCCGTAATCATGTACTAA
452 CCATCACGGTTTTTGGCCAAAAACGACGTTTTGGGGGTCCCGGACTCAGTTTTGCATGATTTTTG
131 CCATCACGGTTTTTGGCCAAAAACGACGTTTT-GGGG-CCCGGACTCAGTTTTGCATGATTTTTG
**
517 GCGCCAAGATTCCTTGAGACATCCATATTCATCTAACC-AAATCTCTGCAACGATGGATTTAAGG
194 GCGCCAAGATTCCTTGAGACATCCATATTCATCTAACCAAAATCTCTGCAACGATGGATTTAAAA
*
581 ATTTGTTTTTAAGAGAATCTAAATCTTGTTTCGATTAAATTAGAAATTACTT-AAAAAAAACAAT
259 ATTTGTCTTTAAGAGAATCTAAATCTTGTTTCGATTAAATTAGAAATTACTTAAAAAAAAACAAT
645 AT
324 AT
* * * * *
647 TAGAAGCGTTAAAAGCCCTCCAATCTTTTTGGTGTCGAATTATATATTTTTTATGAGTATTCTGG
1 TAGAAGCGTGAAAAGCCCTCTAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTCTTG
* **
712 GAAAAAATTGAGGAAAAATCTTTCGGGCCAATTTTTGCAAAATTTTAGCCGTAATCATGTACTAA
66 GAAAAAATTGAGGAAAAATCTTTCGTGTAAATTTTTGCAAAATTTTAGCCGTAATCATGTACTAA
* * * * *
777 CCATCACTGTTTTTGGCTAAAAAC-ACGTTTTGGGGACC-GACTCAGTTTTACATGATTTTTTGC
131 CCATCACGGTTTTTGGCCAAAAACGACGTTTTGGGGCCCGGACTCAGTTTTGCATGATTTTTGGC
*
840 GCGAAGATTCCTTG
196 GCCAAGATTCCTTG
854 GATTTAAGGA
Statistics
Matches: 490, Mismatches: 33, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
321 79 0.16
322 71 0.14
323 31 0.06
324 13 0.03
325 155 0.32
326 3 0.01
327 3 0.01
328 77 0.16
329 58 0.12
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (325 bp):
TAGAAGCGTGAAAAGCCCTCTAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTCTTG
GAAAAAATTGAGGAAAAATCTTTCGTGTAAATTTTTGCAAAATTTTAGCCGTAATCATGTACTAA
CCATCACGGTTTTTGGCCAAAAACGACGTTTTGGGGCCCGGACTCAGTTTTGCATGATTTTTGGC
GCCAAGATTCCTTGAGACATCCATATTCATCTAACCAAAATCTCTGCAACGATGGATTTAAAAAT
TTGTCTTTAAGAGAATCTAAATCTTGTTTCGATTAAATTAGAAATTACTTAAAAAAAAACAATAT
Found at i:1084 original size:286 final size:283
Alignment explanation
Indices: 570--1123 Score: 808
Period size: 286 Copynumber: 1.9 Consensus size: 283
560 TCTGCAACGA
* *
570 TGGATTTAAGGATTTGTTTTTAAGAGAATCTAAATCTTGTTTCGATTAAATTAGAAATTACTTAA
1 TGGATTTAAGGATTTGTTTTCAAGAGAATCTAAATCTTGTTTCGATTAAATTAGAAATTAATTAA
**
635 AAAAAACAATATTAGAAGCGTTAAAAGCCCTCCAATCTTTTTGGTGTCGAATTATATATTTTTTA
66 AAAAAACAATATTAGAAGCGTTAAAAGCCCTCCAATCTTTTTGGCATCGAATTATATATTTTTTA
* *
700 TGAGTATTCTGGGAAAAAATTGAGGAAAAATCTTTCGGGCCAATTTTTGCAAAATTTTAGCCGTA
131 TGAGTATTCTGGGAAAAAATTGAGGAAAAATCTTTCGGGCCAATTTTTGCAAAATTTTAACCGAA
* * ** * * *
765 ATCATGTACTAACCATCACTGTTTTTGGCTAAAAACACGTTTTGG-GGACCGACTCAGTTTTACA
196 ATCATATACTAACCATCACAGTTTTAAGCTAAAAACACGTTCTGGCGGACCAACTAAGTTTTACA
829 TGATTTTTTGCGCGAAGATTCCT
261 TGATTTTTTGCGCGAAGATTCCT
* *
852 TGGATTTAAGGATTTGTTTTCACGAGCATCTAAATCTTGTTTCGATTAAATTAGAAATTAATTCA
1 TGGATTTAAGGATTTGTTTTCAAGAGAATCTAAATCTTGTTTCGATTAAATTAGAAATTAATT--
* * *
917 GAAAAAAAAAACGATATTAGAAGC-TTGAAAAGCCCTCCAATCTTTTTGGCATTGAGTTATATA-
64 ---AAAAAAAACAATATTAGAAGCGTT-AAAAGCCCTCCAATCTTTTTGGCATCGAATTATATAT
* *
980 TTTTTATGAGTATTTTGGGAAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTA
125 TTTTTATGAGTATTCTGGGAAAAAATTGAGGAAAAATCTTTCGGGCCAATTTTTGCAAAATTTTA
* * * *
1045 ACCGAAATCGTATACTAACCATCACAGTTTTAAGCTAAAAACGCGTTCTGGCGGCCCAATTAAGT
190 ACCGAAATCATATACTAACCATCACAGTTTTAAGCTAAAAACACGTTCTGGCGGACCAACTAAGT
*
1110 TTTGCATGATTTTT
255 TTTACATGATTTTT
1124 GGCGTCAAGA
Statistics
Matches: 240, Mismatches: 25, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
282 59 0.25
286 107 0.45
287 74 0.31
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (283 bp):
TGGATTTAAGGATTTGTTTTCAAGAGAATCTAAATCTTGTTTCGATTAAATTAGAAATTAATTAA
AAAAAACAATATTAGAAGCGTTAAAAGCCCTCCAATCTTTTTGGCATCGAATTATATATTTTTTA
TGAGTATTCTGGGAAAAAATTGAGGAAAAATCTTTCGGGCCAATTTTTGCAAAATTTTAACCGAA
ATCATATACTAACCATCACAGTTTTAAGCTAAAAACACGTTCTGGCGGACCAACTAAGTTTTACA
TGATTTTTTGCGCGAAGATTCCT
Found at i:1449 original size:330 final size:324
Alignment explanation
Indices: 852--1910 Score: 1387
Period size: 330 Copynumber: 3.2 Consensus size: 324
842 GAAGATTCCT
* *
852 TGGATTTAAGGATTTGTTTTCACGAGCATCTAAATCTTGTTTCGATTAAATTAGAAATTAATTCA
1 TGGATTTAAGGATTTGTTTT-ACGAGCATCTGAATATTGTTTCGATTAAATTAGAAATTAATTCA
* * *
917 G-AAAAAAAAAACGATATTAGAAGCTTGAAAAGCCCTCCAATCTTTTTGGCATTGAGTTATATA-
65 GAAAAAAAAAAACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATAT
980 TTTTTATGAGTATTTTGGGAAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTA
130 TTTTTATGAGTA-TTTGGGAAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTA
* * * * * * *
1045 ACCGAAATCGTATACTAACCATCACAGTTTTAAGCTAAAAACGCGTTCTGGCGGCCCAATTAAGT
194 GCCGAAATCGTGTACTAACCATCACGGTTTTAGGCT-AAAACGCGTTCTAGCGGCCCGACTAAGT
* * * *
1110 TTTGCATGATTTTTGGCGTCAAGACTCTTTGGAATATCTATTTTCATATAACCAAATCTCAGCAA
258 TTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATTTTCATCTAACCAAATCTCAGCAA
1175 TG
323 TG
* *
1177 ATGGATTTAAGGATTTGTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTAGAAATTAATTC
1 -TGGATTTAAGGATTTGTTTTACGAGCATCTGAATATTGTTTCGA-TTAAATTAGAAATTAATTC
* * * *
1242 AAGAAAAAAAAAGAAAACGTTATTAGATGCGTGAAAAGCCGTCCAATCTTTCTGGCGTTGAATTA
64 -AG--AAAAAAA-AAAACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTA
* * *
1307 TATATTTTTTATGAGTA-TTGGGGAAAAATTTAGGAAAAATCTTTCGGGTCCATTTTTGCAAAAT
125 TATATTTTTTATGAGTATTTGGGAAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAAT
* *
1371 TTTAGCTGAAATCGTGTACTAACCATCACGGTTTTAGGCTAGAAACGCGTTCTTGCGGCCCGACT
190 TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTAGGCTA-AAACGCGTTCTAGCGGCCCGACT
*
1436 AAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATTTTCATCTAACCAAATCTCA
254 AAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATTTTCATCTAACCAAATCTCA
*
1501 GCAACG
319 GCAATG
*
1507 TTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTAAATTAGAAATTAATTC
1 -TGGATTTAAGGATTTG-TTTTACGAGCATCTGAATATTGTTTCGATTAAATTAGAAATTAATTC
* *
1572 AGGAAAAAAAAAACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATTTA
64 AGAAAAAAAAAAACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATA
** * * *
1637 TTTTTTATGAGTATTTAGGCCAAAAATTGAGGAAAAAATATTCTC--GTTAATTTTCGCAAAATT
129 TTTTTTATGAGTATTT-GGGAAAAAATTGAGG-AAAAATCTT-TCGGGTCAATTTTTGCAAAATT
* * * * *
1700 TTAGCCGAAATCGTGTACTAATAACCATCACGGTTTTTGGCTAAAACGCATTCCAAC-GCCCTGG
191 TTAGCCGAAATCGTGTAC---TAACCATCACGGTTTTAGGCTAAAACGCGTTCTAGCGGCCC-GA
* * * * *
1764 CTTAGTTTTGCATGGTTTTTAGGTGGCAAGACTCCTTGAAATATCTATTTTTATCTAACCAAATC
252 CTAAGTTTTGCATGATTTTT-GGCGCCAAGACTCCTTGAAATATCTATTTTCATCTAACCAAATC
1829 TCAGACACAT-
316 TCAG-CA-ATG
* * * *
1839 TGGA-TTAAGGATTTATTTTTTACAAGCATCTGAATATTGTTTCGATTTAAGTAGAAATTAATTC
1 TGGATTTAAGGA-TT-TGTTTTACGAGCATCTGAATATTGTTTCGATTAAATTAGAAATTAATTC
1903 AGAAAAAA
64 AGAAAAAA
1911 TG
Statistics
Matches: 648, Mismatches: 63, Indels: 39
0.86 0.08 0.05
Matches are distributed among these distances:
325 23 0.04
326 102 0.16
327 10 0.02
328 44 0.07
329 15 0.02
330 241 0.37
331 197 0.30
332 15 0.02
333 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (324 bp):
TGGATTTAAGGATTTGTTTTACGAGCATCTGAATATTGTTTCGATTAAATTAGAAATTAATTCAG
AAAAAAAAAAACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATATT
TTTTATGAGTATTTGGGAAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGC
CGAAATCGTGTACTAACCATCACGGTTTTAGGCTAAAACGCGTTCTAGCGGCCCGACTAAGTTTT
GCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATTTTCATCTAACCAAATCTCAGCAATG
Done.