Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_039768
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 402545
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Found at i:45488 original size:12 final size:12
Alignment explanation
Indices: 45471--45495 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45461 GATAGATAGA
45471 ACCTTTCTAACT
1 ACCTTTCTAACT
45483 ACCTTTCTAACT
1 ACCTTTCTAACT
45495 A
1 A
45496 AATGAGATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.00, T:0.40
Consensus pattern (12 bp):
ACCTTTCTAACT
Left flanking sequence: Indices 44971 -- 45470
GTCAAGCTCGGTACAAGTTCTAGACAAATTCTAGGCTTTTGGGTATCTCAATCTTAAGATAAGCT
CCCCATTATCTACGACCCCTTAACCGGATCGAAAGGGAAGAGGAATAGCGCGGAGCGAGTACTTA
TTATGGAAAGACAGGCTTGGAAGAAGAAAATGAAATAAGAACAACCGCGCTGGTCGTAATAGCTT
CGGATGATATGATGGGTCAATCATTTGCTTCATTGGTTTCAACGGTGGCAGCTGCGGAATCCGCT
ATTGGGTTAGCCATTTTCGTTATCACTTTCCGAGTCCGAGGGACTATTGCTGTAGAATTTATTAA
TAGCATTCAAGGTTAAACATGACTCCTAGAGAATTACCAAAATACGAAGTTCTCTTCTTTTTGAT
TTTGACTTGGTTGGCAGGGTCAGGGCCTTTCTCGCTGGGCGAGCGCATCCGATTGATTCGAAAGT
CCTTTCCTAAACCACTTCCCGTTCAGTTGCTGAAAGATAGATAGA
Right flanking sequence: Indices 45496 -- 45995
AATGAGATTGAGTTCCACGCAAGCTAGAAAGATGCTTTTTGCTGCTATTCCATCTATTTGTGCAT
TAAGTTCGAAGAAGATCTCAATCTATAATGAAGAAATGATAGTAGCTCGTTGTTTTATAGGCTTC
ATCATATTCAGTCGGAAGAGTTTAGGTAAGACTTTCAAAGTGACTCTCGACGGGAGAATCCAGGC
TATTCAGGAAGAATCGCAGCAATTCCCCAATCCTAACGAAGTAGTTCCTCCGGAATCTAATGAAC
AACAACGATTACTTAGGATCAGTTTGCGAATTTGTGGCACCGTAGTAGAATCATTACCAATGGCA
CGCTGTGCGCCTAAGTGCGAAAAGACAGTGCAAGCTTTGTTATGCCGAAACCTAAATGTTAAGTC
AGCAACACTTCCAAATGCCACTTCTTCCCGTCGCATCCGTCTTCAGGACGATCTAGGCACAAAGT
TTCACTTATTAGTTAGGAGGAGATTTTGCCCCCAGTGTATCTCGA
Found at i:149809 original size:15 final size:15
Alignment explanation
Indices: 149789--149818 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
149779 TAAGGTGCCG
149789 TTTTCAAGAAATTCA
1 TTTTCAAGAAATTCA
*
149804 TTTTCAAGCAATTCA
1 TTTTCAAGAAATTCA
149819 AAAGAGACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.40
Consensus pattern (15 bp):
TTTTCAAGAAATTCA
Left flanking sequence: Indices 149289 -- 149788
GACCCCACATTGAATACCTTTCTCAGTTCTCAGTGTGCGAAAGATAAAGATGTTGTATGCTTTCG
TTCTGGCTGAAAGCAACAAGAAAGGAAGAAGATGAGATGGTAGGAAAGACTTGAACTGAGACCGT
GAGCTACAAGCGACTCTAGCATAGCAGTAGGAGCCGAAGGACGAAGAACTGCTTCAAGCCACGCC
GCGAGAGCAGCTGAACGAGGAGAGAACAAAGAGACTGTCTGAGCGGCGAGAACTTGATCTCATCG
GTAAATGGGGTACCACTATCGAATCAAAGAGAAAGTTCTCGATATTATCCAATAACTGGACTGGA
GCTTCTAGCACCGACATAGACATATTAAGTGAAAGGAGTCGGGATTTGTCCCAAAAGGGGGTCCC
ACGATGAAATGACTGGTCGGTGAAGCCCTATGATGACTAGCTTTGAAGCCAGGAGTGCAAACTCT
GCTCTGACTAATAGAAGTCTCATTTCCTATCCTGTTAAGGTGCCG
Right flanking sequence: Indices 149819 -- 150318
AAAGAGACTATCGCTTTGTCATTCAATTCTTCTTATCTTATTCTCCTGCTACAAATGCCAAAACA
GAGATCTCAAGATCAGCTCTTTCGATCGCCGAGTCAGAAAAGATTGAAGCATAGCGCTTTTCTTT
TGATCTAGAGGGATTGATTCAATAGAATATCCCTAAAGGAAGTGGTGTCTGGACGCCTTTCCTTT
CAATCAAAGCGGATTCGAGCTCGCCCGCTCTAACGGCTTGTTTCCGAAGGTCTGATTCAAATAAA
CCGAGAAGGGCTCCTTCCTACTTATCTTAGGGATCACAGAAATGATTATCTTGTTCGTGGCAATC
AATGTCGCTAAAAGTGGAACGTATGGACTGCTGTGTAGAATAGGAGCGATAGGCCCGCCCTACTG
GACGTGGAAATGACGGAATCATAAAAATTCGCAATAGCAGGAGCAAAGAAATTTCATCCGCTTTT
AGCCAATGCTGAATGCCTCTTTGCTTTGGGAGGCAATCAATAGGA
Found at i:187899 original size:18 final size:18
Alignment explanation
Indices: 187878--187920 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
187868 CAACCTTGTT
187878 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
187896 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
187914 GACTATG
1 GACTATG
187921 GCAGGGCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAACAGATCGC
Left flanking sequence: Indices 187378 -- 187877
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGCCCAGTCGTTACGCCTTTCGTGCGGGTCGGAACTTACCCGACAAGGAATTTCGCTAC
CTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCT
CCTTCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTT
Right flanking sequence: Indices 187921 -- 188420
GCAGGGCGGTACGCTCTGCTCTCTCGCGACCCCTACTCTAACGAGTAAGCAAGTCAACTACCTTT
TGAAGCGCCAGTCGCGTAGGGCGACCGGGCCAGGCCGAGTCAGAAAGGCTTTGATGACTCAAGCA
AGGTTCATCTTAGGGAAAGGAGAGTGAGGGGAAGAGGGGGCAGCCCTCGGCCCGATCATCCAATT
CACTCCAACAGACAGGCATGGTTCTGTAGTCAAAGCAACTTCGTCACTTTCGTGTACCCATCGGA
CGGCAGCCCTTTCGGGGTCGGGGCTTCCTTAGGGACCGATTCACTCTGCGTAGATTGACTGAACG
CAGAAAGCCTTCCACTGGCAGGCGATCGTGTTTTTCACAGGATTTATCGTTACTCATGTCAGCAT
TCTCACTTCTGATATCTCCAGGTGTTGTCACCAAAAACCTTCCCCGATTGACAGAACGTCCCGCT
ACTGACACTTGAAAAAGCAACTTTCAAGGTCTCGTCGCTTCGGTG
Done.