Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011001.1 Corchorus capsularis cultivar CVL-1 contig11022, 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, 706
Length: 1178
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Found at i:445 original size:138 final size:138
Alignment explanation
Indices: 209--555 Score: 475
Period size: 138 Copynumber: 2.5 Consensus size: 138
199 CCAAAAGCTA
** * *
209 ATGATTATTTAATTTTGCCACAAATAAATGAATCAATTAGT-ATTATGTTACAAAAAAATAAATT
1 ATGATTATTTGTTTTTTCCATAAATAAATGAATCAATTAGTAATTATGTTAC--AAAAA-AAATT
* *
273 GATTGAACATCCAAAATAAGTAAATGAATCAAGTTAGTCCTT-AGTTAACTTTGCCAATCAAAGT
63 GATTGAACATCCAAAATAAATAAATGAATCAAGTTAGTCCTTGA-TCAACTTTGCCAATCAAAGT
337 TATAATTGATGG
127 TATAATTGATGG
* *
349 ATGATTATTTGTTTTTTCCATAAATAAATAAATCAATTAGTAATTATATTACAAAAAAAATTGAT
1 ATGATTATTTGTTTTTTCCATAAATAAATGAATCAATTAGTAATTATGTTACAAAAAAAATTGAT
* * * *
414 TGAACATGCTAAATAAATAAATGAATCAAGTTAGTCGTTGATCAACTTTGTCAATCAAAGTTATA
66 TGAACATCCAAAATAAATAAATGAATCAAGTTAGTCCTTGATCAACTTTGCCAATCAAAGTTATA
*
479 ATTGATTG
131 ATTGATGG
* * *
487 ATGATTATTTGATTTTGT-CATAAATGAATGAATCAATTAGTAATTATGTTAGCAAAAAAAATAG
1 ATGATTATTTG-TTTTTTCCATAAATAAATGAATCAATTAGTAATTATGTTA-CAAAAAAAATTG
551 ATTGA
64 ATTGA
556 TAGAACATAC
Statistics
Matches: 185, Mismatches: 18, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
138 113 0.61
139 27 0.15
140 36 0.19
141 9 0.05
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (138 bp):
ATGATTATTTGTTTTTTCCATAAATAAATGAATCAATTAGTAATTATGTTACAAAAAAAATTGAT
TGAACATCCAAAATAAATAAATGAATCAAGTTAGTCCTTGATCAACTTTGCCAATCAAAGTTATA
ATTGATGG
Found at i:773 original size:167 final size:166
Alignment explanation
Indices: 457--775 Score: 417
Period size: 167 Copynumber: 1.9 Consensus size: 166
447 GTCGTTGATC
* * * ** * *
457 AACTTTGTCAATCAAAGTTATAATTGATTGATGATTATTTGATTTTGTCATAAATGAATGAATCA
1 AACTTTGCCAATCAAAGTTATAACTAATTGATGATTATTACATTTTGCCATAAATAAATGAATCA
* * * * *
522 ATTAGTAATTATGTTAGCAAAAAAAATAGATTGATAGAACATACTAAATAAATTAGGGAATCAAA
66 ATTAGTAATTATGTTAGC-AAAAAAATAAATTGATACAACATACTAAATAAATAAAGGAACCAAA
* *
587 TTAGTCGTTAATTAATTGCCAAAAAAAATTAGTAATT
130 TTAGTCGCTAATAAATTGCCAAAAAAAATTAGTAATT
*
624 AACTTTGCCAATCAAAGTTATAACTAATTGGTGATTATTACATTTTGCCATAAATAAATGAATCA
1 AACTTTGCCAATCAAAGTTATAACTAATTGATGATTATTACATTTTGCCATAAATAAATGAATCA
* * * *
689 ATTAGTAATTATGTTAGC-AAAAAATAAATTGATTCAACATGCTAAATAAATAAATGAACCAAGT
66 ATTAGTAATTATGTTAGCAAAAAAATAAATTGATACAACATACTAAATAAATAAAGGAACCAAAT
753 TAGTC-CTAAGTCAAAATTGCCAA
131 TAGTCGCTAA-T--AAATTGCCAA
776 TCAAAGTTAC
Statistics
Matches: 130, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
164 3 0.02
165 43 0.33
167 84 0.65
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (166 bp):
AACTTTGCCAATCAAAGTTATAACTAATTGATGATTATTACATTTTGCCATAAATAAATGAATCA
ATTAGTAATTATGTTAGCAAAAAAATAAATTGATACAACATACTAAATAAATAAAGGAACCAAAT
TAGTCGCTAATAAATTGCCAAAAAAAATTAGTAATT
Found at i:1044 original size:137 final size:139
Alignment explanation
Indices: 889--1178 Score: 460
Period size: 137 Copynumber: 2.1 Consensus size: 139
879 GTTAGTGATT
* * *
889 GTTAGTTAATTTTTTCAATCAAAGTTGTAATTGATTGATAATTATTTAATTTTTCCAT-AAATCG
1 GTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATAATTATATAATTTTACCATAAAATCG
*
953 CTA-AAAAA-ATTAACATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAATTAT
66 CCACAAAAAGATTAACATAAATAAATAAATCAATTAGTAATTATGTTACC-AAAAAATAAATTAT
1016 TGAACATGTC
130 TGAACATGTC
*
1026 GTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAATCG
1 GTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATAATTATATAATTTTACCATAAAATCG
* *
1091 CCACCAAAAAGATTACCATAAATAAATAAATCAATTAGTGATTATGTTACCAAAAAATAAATTAT
66 CCA-CAAAAAGATTAACATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAATAAATTAT
*
1156 TGAACATGTT
130 TGAACATGTC
*
1166 GTTAATTAATTTT
1 GTTAGTTAATTTT
Statistics
Matches: 140, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
137 54 0.39
138 8 0.06
140 40 0.29
141 38 0.27
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.38
Consensus pattern (139 bp):
GTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATAATTATATAATTTTACCATAAAATCG
CCACAAAAAGATTAACATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAATAAATTATT
GAACATGTC
Done.