Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010933.1 Corchorus olitorius cultivar O-4 contig10965, 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: 4198
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Found at i:986 original size:26 final size:26
Alignment explanation
Indices: 948--998 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
938 GATACTGTAG
* *
948 AAATTGAATTTTTCTAAATAAAATAA
1 AAATTAAAATTTTCTAAATAAAATAA
974 AAATTAAAATTTTCTAAATAAAATA
1 AAATTAAAATTTTCTAAATAAAATA
999 TTTTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (26 bp):
AAATTAAAATTTTCTAAATAAAATAA
Found at i:2129 original size:351 final size:351
Alignment explanation
Indices: 1486--2183 Score: 983
Period size: 351 Copynumber: 2.0 Consensus size: 351
1476 GCCAAGCTAG
* * * ** * * *
1486 ATGTCTTGAAGTCTAAATCTGATATTTTTAGACCCAATTCATTACTGTGGAAGCCCAAAGAAGGA
1 ATGTCTTGAAGGCTAAATCTGATATTCTTAGACCCAATTCATTACTATGGAAAACAAAAAAAAGA
*
1551 GTCTAAGTCCAATCAATAATTATGATGCAGTAATGATTCAACCCTGATGCAGCATTGTTAAATCC
66 GTCTAAGTCCAATCAATAATTATGATGCAGTAATGATTCAACCCTGATGCAACATTGTTAAATCC
* *
1616 AATTCGAATAAGAACTTCACAAAAGCAGTTTTGGAAAAAAAATCATAATTTTTGATCCGGAAATC
131 AATTCGAATAAGAACTTCACAAAAGCAGTTTTGGAAAAAAAATCATAACTTTTGATCCAGAAATC
* * * *
1681 AGAAAAATGCAAATGAGGTACCGTTGGAAAGAGGATTCGAAGATCTACAACTTTTATGTTTACCT
196 AGAAAAATGCAAATGAGGTACCATTGGAAAGAGAATTCGAAGATCTACAAATTTCATGTTTACCT
* *
1746 CGAGACCTAATTCTGCAGTTCCGATGGATGATTTTTCCCTTGAAATTTGTGAACAGAATTGATCT
261 CGAGACCTAATTCTGCAGTTCCGATGGATGATTTTGCCCTTGAAATTTCTGAACAGAATTGATCT
* * *
1811 TCTCCTCAACTGGCTTGGAGAACCAT
326 TCTCCTAAACCGACTTGGAGAACCAT
*
1837 ATGTCTTGAAGGCTAAATCTGATATTCTTAGACCCAATTCGTTTA-TATGGAAAACAAAAAAAAG
1 ATGTCTTGAAGGCTAAATCTGATATTCTTAGACCCAATTC-ATTACTATGGAAAACAAAAAAAAG
* * *
1901 AGT-TCAAGTTCAATCAGTGATTATGATGCAGTAATGATTCAACCCTGATGCAACATTGTTAAAT
65 AGTCT-AAGTCCAATCAATAATTATGATGCAGTAATGATTCAACCCTGATGCAACATTGTTAAAT
** * * * **
1965 CTTATTC-AA-AAGAGGACTTCACAATAGCAGTTTTGGAAGAAAATTCATAACTTTTGATTTAGA
129 CCAATTCGAATAAGA--ACTTCACAAAAGCAGTTTTGGAAAAAAAATCATAACTTTTGATCCAGA
* *
2028 ACTCAGAAAAATGCAAATGAGGTACTATTGGAAAGAGAATTAC-AAGATCTACAAATTTCATGTT
192 AATCAGAAAAATGCAAATGAGGTACCATTGGAAAGAGAATT-CGAAGATCTACAAATTTCATGTT
* * * *
2092 TACCTCGAGACCTAATTTTGCAGTTCCGATTGATGATTTTGCCCTTGAACTTTCTGGACAGAATT
256 TACCTCGAGACCTAATTCTGCAGTTCCGATGGATGATTTTGCCCTTGAAATTTCTGAACAGAATT
2157 GATCTTCTCCTAAACCGACTTGGAGAA
321 GATCTTCTCCTAAACCGACTTGGAGAA
2184 TGTTTTGGAC
Statistics
Matches: 305, Mismatches: 37, Indels: 10
0.87 0.11 0.03
Matches are distributed among these distances:
349 4 0.01
350 3 0.01
351 294 0.96
352 4 0.01
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (351 bp):
ATGTCTTGAAGGCTAAATCTGATATTCTTAGACCCAATTCATTACTATGGAAAACAAAAAAAAGA
GTCTAAGTCCAATCAATAATTATGATGCAGTAATGATTCAACCCTGATGCAACATTGTTAAATCC
AATTCGAATAAGAACTTCACAAAAGCAGTTTTGGAAAAAAAATCATAACTTTTGATCCAGAAATC
AGAAAAATGCAAATGAGGTACCATTGGAAAGAGAATTCGAAGATCTACAAATTTCATGTTTACCT
CGAGACCTAATTCTGCAGTTCCGATGGATGATTTTGCCCTTGAAATTTCTGAACAGAATTGATCT
TCTCCTAAACCGACTTGGAGAACCAT
Found at i:2527 original size:31 final size:31
Alignment explanation
Indices: 2468--2529 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
2458 GAGTTTTGTA
*
2468 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
* *
2499 AAACTTTTGAATCGCCTATCGTATCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
2530 TTTCGAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATCATACCCTTATT
Found at i:2672 original size:85 final size:86
Alignment explanation
Indices: 2565--2736 Score: 283
Period size: 85 Copynumber: 2.0 Consensus size: 86
2555 TTATTTAAAT
* *
2565 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTACATC-TAATATCCTTATAACT
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCATAATATCCTTATAACT
* *
2629 ATTTTATTTTTACCATTTTAC
66 ATTTTATTTTTACAATATTAC
**
2650 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCATAATATCCTTATGCCT
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCATAATATCCTTATAACT
2715 ATTTTATTTTTACAATATTAC
66 ATTTTATTTTTACAATATTAC
2736 T
1 T
2737 AATTTAATTA
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
85 46 0.57
86 34 0.43
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (86 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCATAATATCCTTATAACT
ATTTTATTTTTACAATATTAC
Found at i:3417 original size:16 final size:16
Alignment explanation
Indices: 3377--3407 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3367 TTGGCTTTAG
*
3377 GTCACTCGGGTTTTGA
1 GTCATTCGGGTTTTGA
3393 GTCATTCGGGTTTTG
1 GTCATTCGGGTTTTG
3408 GGTTTTTCGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.16, G:0.32, T:0.42
Consensus pattern (16 bp):
GTCATTCGGGTTTTGA
Done.