Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017848.1 Corchorus olitorius cultivar O-4 contig17881, 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: 26221
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:11109 original size:29 final size:29
Alignment explanation
Indices: 11073--11130 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
11063 TAGAAATTAG
11073 ATTGAAATATTAAAAATCTAATTAATTCT
1 ATTGAAATATTAAAAATCTAATTAATTCT
*
11102 ATTGAAATATTAAAATTCTAATTAATTCT
1 ATTGAAATATTAAAAATCTAATTAATTCT
11131 GAACCCGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (29 bp):
ATTGAAATATTAAAAATCTAATTAATTCT
Found at i:25141 original size:331 final size:319
Alignment explanation
Indices: 24313--25557 Score: 1199
Period size: 318 Copynumber: 3.9 Consensus size: 319
24303 ACCATGATGG
* * * *
24313 TAAAAA-TGACCCG-AAAGATTTTTCATCAATTTTTGGCAAAAATACTCATAAAATAA-ATATAA
1 TAAAAACTGACCCGAAAAG-TTTTTC-TCAATTTTTTGCCACAATACTCAGAAAA-AATATATAA
* * * * *
24375 TTCAACGCCAAAAATATTGGAGGACTTTTCACGCATT-TAATATCGTTTTTCATGTTTTTTTCTG
63 TTCAATGCCAAAAAGATTGAAGG-CTTTTCACGC-TTCTAATATCGTTTTTC--CTTTTTTTCCG
* * * * * *
24439 AATGAAATTCTAATTAAATCGAAACAAAATTCAAATGCACGTAAAAA-AAATCCTTAAATCCAAT
124 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAAT
* * * * * * * * * ** * *
24503 GTGACTCAGATTTGATTAGATGAATAAAGATATTCCAAGGAATCTCAGCGTCAAAAATCATGCAA
189 GTGGCTGACATTTGGTTCGATGAATATAGATATTTCAATGAGTCTTTGCGCCAAAAATTATGCAA
** * * * * * * *
24568 AACAGATCTGCGGC-CACGGAACGCGTTTTTAGTCAAAAACCGTGATGG-T-ACACA--ATTTTC
254 AATTGAGCCGGGGCTC-CGTAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACATGA-TTTA
*
24628 GGC
317 AGC
* * *
24631 TAAAAACTTACCCGAAACGTTTATTCTCAATTTTTTGCCACAATACTAAGAAAAAATATATAATT
1 TAAAAACTGACCCGAAAAGTTT-TTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATT
* * * * *
24696 CAACGCTAAAAAGATTGACGAGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTT--GAATA
65 CAATGCCAAAAAGATTGAAG-GCTTTTCACGCTTCTAATATCGTTTTTCC-TTTTTTTCCGAATT
* * *
24759 AATTTTTTAATTAAATCGAAATAAGATTCAGATACTCGTAAAAACAAATCCTTATATCCAATGTG
128 AA-TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTG
24824 GCTGACATTTGGTTCGATGAATATAGATATTTCAATGAGTCTTTGCGCCAAAAATTATGCAAAAT
192 GCTGACATTTGGTTCGATGAATATAGATATTTCAATGAGTCTTTGCGCCAAAAATTATGCAAAAT
* *
24889 TGAGACGGGGCTCCGTAACGCGTTTTTAGCCAAAAGCCGTGATGGTTAATACATGATTTAAGC
257 TGAGCCGGGGCTCCGTAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACATGATTTAAGC
* * *
24952 TAAAATTTTGCAAAAACTGACCTGAAAAGTTTTTCACCAATTTTTTGCCACAATACTCAGTAAAA
1 --------T--AAAAACTGACCCGAAAAGTTTTTC-TCAATTTTTTGCCACAATACTCAGAAAAA
* * *
25017 ATATATAATTTAATGCCAAAAAAATTGAAGGATTTTCACGCTTCTAATATCGTTTTTCCTTTTTT
55 ATATATAATTCAATGCCAAAAAGATTGAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTTTTTT
* * * *
25082 TCCGAATTTATTTCTAATTAAATCTAAACAAAGATTGAGATGCTCGTAAAAACAAATCCTTAAAT
120 TCCGAATTAATTTCTAATTAAATCGAAAC-AAGATTCAGATGCTCGTAAAAACAAATCCTTATAT
* * * * * *
25147 CCATTATGTCTGAGATTTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAAT
184 CCAATGTGGCTGACA-TTTGGTTCGATGAATATAGATATTTCAATGAGTCTTTGC-GCCAAAAAT
* * * * * * * * *
25211 CATTCAAAACTAAGCCGGGGC-CATGAAACGCGTTTTTAGCCAAAAACTGTTATGGTTAGTACAT
247 TATGCAAAATTGAGCCGGGGCTC-CGTAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACAT
**
25275 GATTTCGGC
311 GATTTAAGC
* * *
25284 TAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTCTG-AAAAATATTCAGAAAAAATATATAAT
1 TAAAAACTGACCCGAAAAG-TTTTTCTCAATTTTT-TGCCACAATACTCAGAAAAAATATATAAT
* **
25348 TCAATGCC-AAAAGATTGATGGTCTTTTCATACTTCTAATATCG---------TTTTTCCGAATT
64 TCAATGCCAAAAAGATTGAAGG-CTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTCCGAATT
* * * * * * *
25403 GATTTCTATTTAAATCGAAACAAGATTTAAATGCTCGTAAAACCAAATTCTTATATACAATGTGG
128 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGG
* *
25468 CTGATATTTGATTCGATGAATATAGATATTTCAATGAGTCTTTGCGCCAAAAATTATGCAAAATT
193 CTGACATTTGGTTCGATGAATATAGATATTTCAATGAGTCTTTGCGCCAAAAATTATGCAAAATT
25533 GAGCCGGGGCTCCGTAACGCGTTTT
258 GAGCCGGGGCTCCGTAACGCGTTTT
25558 CCCCAATTTT
Statistics
Matches: 770, Mismatches: 121, Indels: 79
0.79 0.12 0.08
Matches are distributed among these distances:
311 71 0.09
312 42 0.05
313 30 0.04
316 6 0.01
317 34 0.04
318 122 0.16
319 81 0.11
320 11 0.01
321 16 0.02
322 73 0.09
323 8 0.01
324 1 0.00
329 8 0.01
330 46 0.06
331 119 0.15
332 102 0.13
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (319 bp):
TAAAAACTGACCCGAAAAGTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTC
AATGCCAAAAAGATTGAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTCCGAATTAAT
TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTG
ACATTTGGTTCGATGAATATAGATATTTCAATGAGTCTTTGCGCCAAAAATTATGCAAAATTGAG
CCGGGGCTCCGTAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACATGATTTAAGC
Done.