Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold90
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: 178240
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:61511 original size:9 final size:9
Alignment explanation
Indices: 61497--61523 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
61487 TTCCTTCGTT
61497 GGTAGGATC
1 GGTAGGATC
61506 GGTAGGATC
1 GGTAGGATC
61515 GGTAGGATC
1 GGTAGGATC
61524 ATCGAAGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.44, T:0.22
Consensus pattern (9 bp):
GGTAGGATC
Left flanking sequence: Indices 60997 -- 61496
CTAGTTCCCCCACACCCCCACCCCCACTTCCCCCCCACAGGGTAGTATAGGTTGCCGGACTTCGA
TGTGAACTATTTTAAGTCTTTCAAGTTAACCCATCAAAGAAAACGTATAAAATACTACTTTCTCT
GGATGGAAAGCAGAGCCCAACACATCGTGCAACCTCTTGAAATTGGATATTTGACGTAGTTCCCC
GGCATGTGTTCACAGCTACCTGTACACACCTAAGATGCCATCTACCGAAACCCCGAACAACAGAA
CCGCCCGGTTTTAAGCACATAAGAATCGCCTACCTTTCACAGTTCTTGTCGACTTTTCGTACCAA
AATTAATACCCCGCATTATCACCTCACAGCGCGACTTGTTATCGCGATCTCTCTCGCAATCACAC
TGACGCCGGATTTGCAAGAAATTCGTCCACATCTTCATGATTAAATCCCTCCTCACTTCGGGCCA
TATAACAAGATGGAATATCACCGCAATCCATTTTATTCCTTCGTT
Right flanking sequence: Indices 61524 -- 62023
ATCGAAGACTGAAATCATAGGCGAGTAATCTCGGACATTAGTCTCCATCCGATACCAACTGCATA
GGAACCCTGATATTTTACGGTGATAGACTTCACTTATTGTTTGCTAAAGAGGATCCCCCGGGGCC
GTTGACTCCACTTCTCCGGGGGAGGAAGAGTCTTAGCACCGAGTCCGCAACGCCTTTTCGACCTA
TTTCGCCTATGCACGAGTGATTGACGTATTGACAATGCCTCTTTTACCAAAAGTTGTAAATCATG
TTTTGAATCGCACACAGCCAAATATTAAGTCCCGGGTTAAATTGCAATTCGATTTCATTTACCAG
ATCGGCGTACACACAAGGCAGGATTTTTGCAAAGGGCTGCTCGCTTAAGCAATATTGTCATCTTG
GAGTTAGCCCCTAACATAAGGCGTCAGGACACGTGCAGGACTTACTGAACTCGGATTTAGGACGT
CGGATGCGAGTATACAACGGATCAATGTAAAGATGGCAAAACCAA
Found at i:99750 original size:33 final size:33
Alignment explanation
Indices: 99659--99757 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
99649 CGGTCAAGCC
* *
99659 CCCCAGCTGATTGTTGGAGAGGCTGAAATTACT
1 CCCCAGCTGCTTGTTGGAGAGGCTGAAGTTACT
*
99692 CCCCAGCTGCTTGTCGGAGAGGCTGAAGTTACT
1 CCCCAGCTGCTTGTTGGAGAGGCTGAAGTTACT
* * *
99725 CCCCAGCTGCTTGTTGGACAAGCTGAGGTTACT
1 CCCCAGCTGCTTGTTGGAGAGGCTGAAGTTACT
99758 GACCTTCCTG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.26
Consensus pattern (33 bp):
CCCCAGCTGCTTGTTGGAGAGGCTGAAGTTACT
Left flanking sequence: Indices 99159 -- 99658
GGTGATTGTCCGCTTTGGATAAGTTGATCTCGCTTTCGGATATGCACTGGCGAGGTGCTGCAGGG
TCCTGGGGACAACATCAAGCGAAAATAACAAAGATGAGCATTAAATGCTCCAACCGTAGAGAAGA
TGACAGTCTACGACTTGCCAGCCCGTTGCCCCAAATGAGAAACAATGGTTTCAAGCAGTAATTTT
TTACCTCCAGAATTAGACGATTTTTCCTACTTATTTGCAGCCAAAACATACATAGTTAGGCATCG
ACTCGCGTCCTCGTCAGCGGACCTGACTCTAGTAGCTATAAAAGGCCATGGAACTCCGTCTTCTA
AGCCCAATAAACCATGAAGTTCTCTACCACTGCCATCGTTGCTTACGCTGCTTACGCCATTGCCG
AACAGGCTACTGAGGAGATTGAAAATCAGATTCCTGAGACTCCTGACGCTTACGCCGAAGACATT
GTCGGGCAGGTCGAGCTCGCTGCTGAGCAGCTTGTCGGTCAAGCC
Right flanking sequence: Indices 99758 -- 100257
GACCTTCCTGATACCGAGGAAGAGCCCTCCATCCCTGACTATCCTACTGAGTTGCCTCCGGCCCT
CAACTCCACTAACGGTACCACCGGTCCTGATTTCGAGTGGGAAGGTGTTGCCAATATGAGAGGCA
TTGCTGCCGGCGCTGTCGCCATTGCTGGCCTTTTGATGTTGTAGGTAGTGTTCTAGTCAGAAGTA
TTCAAATAGTTTTGTTGATACCCTAATACTAAAGCTTTCAACATAATAACCAGGCTTAATCAAGT
ATGACGCATTCGACTACCATCGTCACGAATTGGGCTGCAATCATACCTTTGAGGCTCCCCTAAGT
ATCGTCACCTCACGTTTCAGCTGCAAGTATTAAAATATGACTTTACAAGAAAGCATGTCCATTCG
AGTTACATGACGAATAAATACTTCCAAATCTAGTTCGGATGTAGTACCGAATGAAAAAGTCGCTT
TCATACCCAAATATGTACAAGATGAATCTGCATTTTAACGGCCCC
Found at i:128157 original size:12 final size:12
Alignment explanation
Indices: 128142--128179 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
128132 ATCGTGCTCA
128142 TCATCGTCGTCC
1 TCATCGTCGTCC
* *
128154 TCATCGTCATCT
1 TCATCGTCGTCC
128166 TCATCGTCGTCC
1 TCATCGTCGTCC
128178 TC
1 TC
128180 TTCTTCAGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.11, C:0.39, G:0.13, T:0.37
Consensus pattern (12 bp):
TCATCGTCGTCC
Left flanking sequence: Indices 127642 -- 128141
CTTCATCACCCATCCGCGCACCCTGAACAGCATCGTCATCCAAATGAAGCCCATACAGTCTTTTC
TCAAGAGAAAGCAAATCTTTCCAGACAGTGTTACGCTCCCAAACAATGTGTTCCCTCAATGACAG
CTTGAGCTCATTTTTCACCAGCTCCAAATCAGCTGTGGTGGTTTTAGATGACATCCGTCCCAGCA
ACAAAGCATAAACTTTGACCATCTCATTCAAACGTTGCTCTAAAGCCGTCATGGTGTCGGTTGCA
AAAACGCGGCAATTCAAGGGCAACCATTGGGTGACGAAGTCCTGCTTAGTTGCATACTTGCACGT
TTTGTCAAACTTTTTAGTGATCTTTGTGAAAGCGATTTTGTTGAGCTCAATGTACAGCTTGAGTT
CCAGTAAACAGATGAAGATCTGAGCGGCTTGACGCTTGAGGGTGATTTTCGTTTGCTGTTTCACA
TCAAAATCAACATGCAGTAACAAAGCAGAGTTTTTATCGTGCTCA
Right flanking sequence: Indices 128180 -- 128679
TTCTTCAGCAGCAATGTACGGTTGCTTCTCGAAATCATGATCCTGGTCGACGTGATTGATGGTAT
CAAATACCAGGGCGTTGGTGATTGTGCGAGACAACGTTGAGCGAACATTGTATTGTTGATGTGCG
TAATTGTAATCGGGCTCCTGATAAGCCTGTGTGAACCGAAAAACGCCATCGACATCAATATTCAT
TTTGTGAAGATCTGCTAAAAGATGATTGTAATTTTTGAAGATCTCCTTCTCCTTAGCATCATAGA
ACTCAGCTACTTTAGCAACCTCAACTATCAACTGCTTAGCAAACACCTTGAGAGCGTCGAAGCTA
GGCAGTTGAGGGTCCTTGTAATCGTCATTCGAGTTTTGAGAACGAAAGGTGACTACATTCGTCAA
ATCGTAACCAGTCTCTGCCACATCCAGCGCTTTCTCAATTTTGCCATCTTCCTCTGATGACGTAC
CGGCTTCGAGGTCCTCAACTTTGTTCTTCTTAAGCTTTCGGAATA
Found at i:141523 original size:15 final size:15
Alignment explanation
Indices: 141503--141532 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
141493 CATTCCCTCG
141503 TCGTCATCGTCGTCA
1 TCGTCATCGTCGTCA
*
141518 TCGTCATCGTTGTCA
1 TCGTCATCGTCGTCA
141533 CTTTGAAAGG
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:0.13, C:0.30, G:0.20, T:0.37
Consensus pattern (15 bp):
TCGTCATCGTCGTCA
Left flanking sequence: Indices 141003 -- 141502
CTAGAATCACACTCGGGCCAGCGTCCAAAGAGCTCGTGAAAAGATCCCGAGAGTCAGGAACCACT
TGAAGTAAAGGTTGAACGAGATCCGCCAATCTTTGGCGCAATGAGACACCCTTGCGTGCGCCCAA
AGCATAACCTCTTTCAAATGGAGTTGCACCATGTCCGTGGTTCATTTCTGCCATGAGGATCTCTG
GTGGATTGTTTTGCGAGTCCAATGAATCATTGGCAATTTCTTCAAATTCAGGAATCCCACCTGAG
GTTGAAACAATCACGGGAGACGGAGAGAAGCCCGTTTCAAGTCTCATTGTTTCTTGGGGAAGATA
GGGTTTCATGCCTATGGAATCTTGAGGAGATTGGAATACCTGTTTTTCTCGGTTCACGGTACCAG
AATCAATCTTCAGATCATAGACAGTGAAATCACATGGAGACACAGGGCTACTCGGGGAACGTTGC
ACATTTGGTATCAACAAGTTGGAGTCGTCACTAATCATTCCCTCG
Right flanking sequence: Indices 141533 -- 142032
CTTTGAAAGGGCAAAAGATCGCTTTTCGGTGGCCTCTCTTCGCTGCCCAAGAGTTTGCTGGTGGT
CCGAGAACTAGTGTCAACCGACTCTCCCTCTATGCGACCGCCCGTCACCAGTGAAAAGTCTTTAA
CATTACGCCGAGAAACATCAGAATCATGGTCAGAGGCCAGCATTAATGGTTTTGTACTCGTTTTG
TGCGATAATTCAACAACCGGCTTACATCGTTCGTCGTTTTCTGAGGAAAGTTCTTTGGACGCATT
TGCCCAAGCCACCCCAAACCCTCTCTTATAAGCCAGCTTGAAAGTGATATCCACCGGAATCGCTG
GCATCAATGTTTGCACTTCCTCTTTTGGGACATTAAGCCGCAGAAGATACAGAGCAAATCGTTTG
CGTCCAATACGTTCTAGCTGACGGAACAGCTCCACTTTTTTCAGAGTTCGGCTTTCTAACACTGA
TGAGGTATTTTGAATCTCATTCGATAAAACACGCTTTTTTGTCAT
Done.