Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MW717907
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: 154640
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:29461 original size:21 final size:21
Alignment explanation
Indices: 29436--29478 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
29426 GCTCGAGAAC
*
29436 TCACGAACTGAAGA-GCTCACG
1 TCACGAACTAAAGATGCT-ACG
29457 TCACGAACTAAAGATGCTACG
1 TCACGAACTAAAGATGCTACG
29478 T
1 T
29479 GACGCTTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (21 bp):
TCACGAACTAAAGATGCTACG
Left flanking sequence: Indices 28936 -- 29435
AGCTTCTTCTCTTTCATATGCTACATCGGCCACATCCTTTGAAGAATCCGAATATGAATCTGGTA
ACCTTGCATCCGAAGTAGCGATTCCCTTCCTCGCTCAGGAAAGTAAGAAGGAAAGGCATAAAGCA
AGTACTGCGAACCCCTTTAAGCACGAGATTAGACAGTTGTGATTGCGCTTTCACCCATGATGGGA
TTCTTTGGGCTAGGATGCTAAAGAGATGGCTATGAGAGGGTCTTAGCCTGTAGTAGCTTGACAGT
AGGAAGAGTCTAAAGGCCTAACCGCAGCTATTGAATCAACTATTCTTATTCAAGCTTTCTTGACG
TCTTTCTACGCGGAAAGCTATAGATTCATAGATCGGTCGTTCCAGATGTGATGTTGCAAGCCGCC
GATCAACGCAACCAATATCTGACGCGAGGCCTTTATACGATTACGATAAAGATCGAGTCGATTAG
TCAGCTTTGCCTTGTTGATAGGCTAAAGCATAGCAGCTCGAGAAC
Right flanking sequence: Indices 29479 -- 29978
GACGCTTCCTTCATATGCGGATACAAGGGCCCAGCCCATTATGACTAGTGAAGGCTCCTTTTTTG
TTTGCTTTACTTCCCCCCCTTATTTTTTTTTTCATAAGTGGTCATATTCATCTAGTTTTCTCGCT
TTAGGAGTCTGAACAAATTGAAGAACCTAATGGATCCAACTTATAGAAGGACCCGAACCCGCGTA
TCGCCTTGGTGGAATCTATAAAAGTTATGTCGAATTGCGATATGATTGAGAGGGCCCCTCTTTTA
ATGATGAGTAGGATCACATCACGACAGGGAACAAGCTCTTTGCGCCCCACGTATGGCTTCTACTG
TGATGTTCGATGAATAGTATGCCGAGGGGGCTGCTTTCTGTTTCGATTTCACTCGTTGAAGAATG
TCTTTCCTTTTCAAAACTTGTATCTGGCGGGTTTCTAAACTATACAATCAAAAGTGATAAGGTAA
TATTCGCCTGAAGCGAATGGAGACCTCTCTTTATCCGCCTTCGGG
Found at i:76833 original size:13 final size:13
Alignment explanation
Indices: 76815--76841 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
76805 TGTGATCTTC
76815 TCTATCTAATGAA
1 TCTATCTAATGAA
76828 TCTATCTAATGAA
1 TCTATCTAATGAA
76841 T
1 T
76842 GGGGAGTCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TCTATCTAATGAA
Left flanking sequence: Indices 76315 -- 76814
TTGGGTCGTATCCAGAGGGCATGTATATCTCCATACAAAGGAGTACCCGGTTAGGGGTAATGACT
ATCTATCCCTTTTCAGAGCAGGCCTCATCAGCCCCATCGAGAAGGATAGAAGATAGAAAGCCAGA
AAGTCTTTTGACTTTCCGGTGACCGAAGAGTCCTTAGACTCGTAGGGGTTTACCCGTAGAGTCGG
TAAACTCGAAGAGCCTTAGAATCAATTACAACAGCTGCAGCAGAAGTAGAGGGATCAGCCTTAGG
AGTCAGTCCCCCGACGTACCCAAGATCTTCGAAACATAAAAGTAAGGACCCCGATTTCATGATGA
ACCCTAGACCGAATCCAACCCTGTAATGAATAAACCCGTTTGTTACGCACAGGTCGCTCCTGAAA
CAGCGGGGGGAACACCTATTAGGGGATATCGGTATATCAATACCGATTCGATCCGAGATCTTGGA
ATTGGAATAAGTTCGGCAGCGAATCACGAAATCTTTGTGATCTTC
Right flanking sequence: Indices 76842 -- 77341
GGGGAGTCCGCTTTGAAATCGTCCGCCCTGCACCCACCCCCCGAGTATATGCTTCAACAGGAATC
ACACAAGGGTAGATTGATACAATAGAAACCTCTGGTAAAATGCCCCCCCGTAACCCAGCAGATAA
AGTACATTACAGAGTCCGTTTTAGGGATTGGCGACTTACCCATTCAGTGACTTTGGCGCTGGACG
TTCCCCAAATGGGTACTATCGGGTCGGGTGAATTCAATAATAGACGCCTGTTGGCATTCCAGCCT
TCCTTCTCCTTTCAGGGCCTATCCGAAAGAGAATCCAGTACTTCTTGGTCGTGAATATCTGAATA
GGACGAACCGCTCCGTGGATATCTTTGCTTCGGAACAAAACAATTATAATTAGTCGGTCAACTGG
AATGTGTATTATCCATATAGGGGATCTTTCAATTGAGAAGATCCGTCGACCCGAGACGAAGAGAA
ATGTCTATCTATTTTATTTAGTTATTCAGTTAAACCAATGATTCG
Found at i:79136 original size:18 final size:18
Alignment explanation
Indices: 79115--79153 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
79105 GTCACGGTCG
79115 ATATCGTCACTATCATCA
1 ATATCGTCACTATCATCA
79133 ATATCGTCACTATCATCA
1 ATATCGTCACTATCATCA
79151 ATA
1 ATA
79154 AGAAAACCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (18 bp):
ATATCGTCACTATCATCA
Left flanking sequence: Indices 78615 -- 79114
TACTAATCGATAGGACCTCATTGGTAAGTGCTACAAGATCTCGTACATCGGAACCCATGGTTATG
GACCCGAATCCATTAGTATGGAACATTTTCTTTTCCAAGTGAAATCCCCTAGTATATGAAAGAGT
GAAAAAGTGCTTTCGTTGTTGTGGAATAAGAAGCCTTCGTATCTTAATGCATGTATTTAATTTAT
TCGGAGCTATTAGAGCGGGATCCACTTTTTGGGGAATATGAGTCGAAGCAATAACAAGAATATTT
CTAGTGGAACATCTTTCACAATCCCTGGAGAGATAGTTCACTAATAGACCGAGGGATAAGTAATT
CGACTCATTCACATCCAGATCATGAATGGATGGAATCCATATTATGCAAGGAGACATTGCTTTTG
CTAATTCGAATTGAAGGGTGATATAAAATCGGTCTATTTCCGGCATCATATCCATAGTTAGCACA
TTCATCATAGTTAGAAGCTCCAGCTCCGTATCAAGGTCACGGTCG
Right flanking sequence: Indices 79154 -- 79653
AGAAAACCCTTAGGCTTGTTATCCAGGAACTTGTTCAGAAATACTGTAATGAAAGGAACATAGGA
GTTTGTCGCTAGGTATTTGACCAAATAGGATCGTCCAGTTCCTATAGAACCTATCACTAAAATAC
CCCTAGAGAGGGATAGGGCTAAGCGGAGCGAAAAAGGTTTTCCATGAAATGGGAAATGAAAACTA
TTAGCCCCACAGGGGGTTTGTGAATAAGTGATTGTCTGATAATGAGCAAGGAATATCCGTCTTTC
TGCTAAACAGGATGTATTGAACTCATAATTCATTAGATACTTTTTATGAATGTCAACTAAGTATC
GTAAGTAAATTGCTCCCGGTTGTTCAATCATTTGATAACCGGAGTCATTCTTTGATAAATGATCA
CTATGAGTCAGACTCAATAGAATTTGATCAATCCTTTTTTTTTCACCCAATCTCTTCGTTATTCT
ATGAGATAATTTGGTAGAGGGACTAGAAAGAAGGTAGTGGCTTAC
Found at i:114411 original size:21 final size:21
Alignment explanation
Indices: 114385--114428 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
114375 CGCATCCCCT
114385 ATGAAGAGAAGAATCAAAAGG
1 ATGAAGAGAAGAATCAAAAGG
114406 ATGAAGAGAAGAATCAAAAGG
1 ATGAAGAGAAGAATCAAAAGG
114427 AT
1 AT
114429 TGAACTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.57, C:0.05, G:0.27, T:0.11
Consensus pattern (21 bp):
ATGAAGAGAAGAATCAAAAGG
Left flanking sequence: Indices 113885 -- 114384
GAATGGTAAGCATTACTCATTTGAAAGTTTCCCACGGTGATTTAATATCTTTTCAAGAAAATGAC
GCGAGAATCCGCGGTGAAGAAATAAGGAGATTTTTCTATATCGAAATATTAGTTGAAAAAATCAT
AGGCAAATTCCTGGATCACCCGGTAAGAATGTGGAGAAGAACCAAAACAGAATGGTTCCACCTAC
TAAAAACTAAGAGGGGATGCCGCCTACTACTAAAATCCCGGTTTTTGCAACAGTTGCGTTCTTAT
ATGCAAGAAGAAGACTTAGAAAGAACAAAGAAGTTTGGATCCGAAAAAGTATGCTTAGGCAGTTC
CTTCGCTGAGCACAACAGAATGAAGAGGAATTTGTATCATTTCAAATCCCTATTCTTATCGAAGA
GAAGGAACGAGAAAAACCGAAATCTTCCTACTCGAACAAGAAGTCCTATAGTTTACAACTCTTCT
TTATATAGTAAATATAGTAAAAAGACCTATTTCTCCGCATCCCCT
Right flanking sequence: Indices 114429 -- 114928
TGAACTACCTACTCATTATTCGGAGGTGAATCATAGAACACCAAAAGCTGTGGTATCTTATGGAC
CTAACATAGGTCACATCCCTCACGACATAAGATTGAAAGATCTAAACCTTCTTCTTCGGAGCGGA
AACGGACGTGGCCAAAACATATAAAGATCGGCGTAGTCGCTCAGAGGGACATATCTATCCGGATA
GAGGATAGTCTAGATCGATTCATAGATAGATCTATATCCATATAGATAGGTATCCCCGTGGATAG
AGATAAAGATAGGGATCCATCTAGATCTTGATTCACTATTTCCATTTTTTTTTTTTCTTGATTCT
GATTGATTGCCTTTTTTTTGACGACAAGTTTTAAATCGGCAAGGAAACATCGTTTTTCAATTATT
ACTTGCTGGGTCGGAGCGTAGACGAGCGAGTAGAGCCCAGGAAACAGGGAAGCCCGTCATAGAGC
AGTCGACTAGAAGTAGAAGACTGCTGGCCTGAGAGAAGGCGGCCT
Found at i:140291 original size:14 final size:14
Alignment explanation
Indices: 140272--140302 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
140262 TTTCGAATTC
140272 TAATATAATAATAA
1 TAATATAATAATAA
140286 TAATATAATAATAA
1 TAATATAATAATAA
140300 TAA
1 TAA
140303 GCAAGCACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATATAATAATAA
Left flanking sequence: Indices 139772 -- 140271
TAGCAGGCAGGCGGGAGAGGTTACTAATTTGACATGGGTGGGATCTAAAATGAGAACGTTTTTTG
TGGGATCCAAAATCATAATGGGAAGTTCTACCCGGAATATAGAGGGGAATGAATCGATCAATCGC
ACCCACCCTTTGGATGAAAAATGCACTTCGTTACATGAAGCATGGGTGATATTTATGAATTGGTC
GGAGGGTGGGAATAAAAGGCATTGATTTATCAAGAAGAATAGTTTTCATTTCGTATATGCTTCGC
CCGTACTGAAAGAGTAAACAAGCATCAAACGCCTGCTCTTCCCCTTCTTTCCATCCAGTAAAAGA
TTTTCTTGTACCCCCTGTGTCTAGGGATTCCTGGGGCATGAGTTAAGCATATAGTTGATTGCTCC
TTTCTTTCGATTTCGGAGATTAGAGCAGAAGAACTCCGTAACGACGGAGAAAGGTTTCGCCGAAG
CAAGTGCCTTAGTTCTTCTTCATATTTTTGGTATTTTTCGAATTC
Right flanking sequence: Indices 140303 -- 140802
GCAAGCACACTTGCCCATATATATTTACAATTTTTCTTTTTCATTTTCACTCGATTCATAAACTT
CTCTCAACCCAATTAGATTCTTTTTTCGACCCAACCCCGGAGAGGAGAGGCTATATGGGGCATCT
ATCTACGGGGGCCTGCATCTTATTATAGGGAAAGGGGGGAAGGACGAACTTCATTCGGTAGCAGC
GGGGTATCGAGTCATTGGTAACACCGCCTCATTTCGGAACCAGATCGAAACCCGACTCACTTAAA
TGTCCTAGCGAGGGGTATCGATAAGGGTTGGATGCGAACCCCTCCCATGAGAAATAAAGGAGCCT
AGCAGCCTTTTTTCTGTCTATTCCTGATCGAATTCCCTCCCTGTCATCGTATCTTGTGTTAGAAT
CGCTTTCGGGCTTCTTAGCGCTTTCCCATCAGTGGAAGTTTTGTCTCCCGTCCCTACCGATAGTA
ACTGATCAACCTACTGTTGGAGTTCAAGAGCATATCTTTTTCCAT
Done.