Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_060995
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: 103937
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Found at i:17695 original size:19 final size:20
Alignment explanation
Indices: 17653--17695 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
17643 GGATGTTGGT
* *
17653 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
17673 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
17692 CATG
1 CATG
17696 GAGGAGTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
CATGACTATCGAAAAGTTCA
Left flanking sequence: Indices 17153 -- 17652
GAGCTAAAAATGCATTTTTTTTCTTTTTTCTTCTTCTTCTTAATTTTTCCATTTTCAAATTTATG
GGAGACTTGTCATATTTAGAATCTTTCTGTGGTGTGCTTTGTTTTTCATTACTTTGTACATTTTT
CCTATCATTTGAATATAGGCGCGATACGTGGGCAAACGAGGGGCGTAAGCTTGGAATGAGGGAAA
AGGGAAAACCGCGTAGGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTAGCGAAAAA
AAGAAACAAAGAAATAAAAAGAAAGAAAATTTTTCCTTTTTATTTCTTTCAAATAAATCAAAACT
ATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAAAAAGCCAAAATTTTGG
CTTTTTATTCTCTGCTTGCTTTTTCGCAAGCTTATTCTCTCGTCCTTGAAAATAGTTGGAATAGA
TTTTTTCTTGTTCGCGCTTTACCAAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 17696 -- 18195
GAGGAGTTTGCATCTTTATTATGGGTGTTATTTTGTCGTGCGACCCGGCAGCTTATGCGCGACCA
TCTCGTGTTTAAGCTCACGCCATGTGGGCGTGAACTCTGGTTGAATTCGGGTTCTAAATCCCGCC
GCTGAGATGCTCAGTCGACTCTTGAACCTTGATAGGAAGACGGCTTCTTCCCAAATTAGTGCAAA
AGGTTCAAGGACTTAGGATGAACTTAATGTGAATGGGTATAAGCTTCGCTGCTCAAAAACACCCA
GTATTGACCACACTGAGAGACTTGCCGATGGCAAAAAAGGCCGCGGGTAACGCTAGTTGGCGAAA
TGGCGTTAAGCATTCCTGGCAATACGGAAAGAGAGGTCGTGATGATATCATCTACGTTCGTACTG
TCCCTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGAATAATTCCCATTAAGTT
CCAGGAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAACA
Found at i:27514 original size:29 final size:29
Alignment explanation
Indices: 27481--27539 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
27471 ATGAGCTTTC
27481 ATTGCTTTTTACCTTTTTTCTGAGAGTAA
1 ATTGCTTTTTACCTTTTTTCTGAGAGTAA
*
27510 ATTGCTTTTTACTTTTTTTCTGAGAGTAA
1 ATTGCTTTTTACCTTTTTTCTGAGAGTAA
27539 A
1 A
27540 AGGAAACTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.53
Consensus pattern (29 bp):
ATTGCTTTTTACCTTTTTTCTGAGAGTAA
Left flanking sequence: Indices 26981 -- 27480
AATAAGTACTGCTTTGCCCTTTTTTTCATGGCAAGGGCGATATAAACCGGAACAGGCACATAGAG
GACAATGAAAAAAACCATCATTAGTAACCATTTAATCACTTACTAACTTCATCCATGACACGGCC
TCTACTAGCACCAGAAAAAAATATATATATATATATTTTTTTTGCTGCGCTCTCCGCGCTTATCT
TCGCCCTATAGCACTATCTGAATCTTTGAATGATTATAAAGTTTTTTCAAAAAACAAAAAACGAA
AAAACATATTTGATAATTATTAAACAAAATACTCTGAAAAGAATCAAGATCCAATTTCGTGTTAT
TTCATGGTGAACATAATCTGTCAGAATTTCTTCAATTCCCACATGAATATGCCAGAATAACAAAA
TGTTTAACAGAATCAAAGTAGAAACATTTGATAGAAGAATGGTTGGGATTAGAGAAGCAGCAGTC
ATTCTTTGGAGAAGCCAATGCCCCAAGGTTTCTCTATGAGCTTTC
Right flanking sequence: Indices 27540 -- 28039
AGGAAACTGGCCTTTTTGGTCCGGCCCCTTCTTGTAGAAGCGTATGTGACAATTGTCCGTCATAC
GGCTCTGCCTATCTAAAAAGTATCCCGTCGGCCGAAATAGTACTGGAACAGGTTGTAGGCTTGTC
TTAGTAAAGCCCCCGCAAGATAAAGTAGACCCGATTCCGAGGCATCGCTGAGCTATCAGGGAAAA
AAGTCTATATATATAGACTTTTTTTTCGGGGTTCTCGTATTTCGTGCTTATGAGAAATAGAATCG
GATAATATTCGATACAGCTAAAAAAGCTGCACAGAATAACATAATAATTCCGGAAGTATATACTT
TGGATAATTCTGGAAAAAAACCTAGATCCCACAATAAATGACGAATTCCATTACTCATATGATAA
CACAAAGCCAATAAATTGAAATTGACTACGCTTAGGATCAACCAATGGAAATAGAAAGTGAAGAA
AAAAGCGTACCGGTAAAGATAATAAGAAGTAAGGTTAAGATCGCC
Found at i:40733 original size:81 final size:81
Alignment explanation
Indices: 40598--40747 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
40588 AAAATACTCG
*
40598 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
40663 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
40679 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
40743 CCAAG
65 CCAAG
40748 TGAGCTTAGG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
81 63 0.97
82 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (81 bp):
CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 40098 -- 40597
TTCAATCTACTTTGGTCAATCATATGGATATAAAAAAAGCGGCTAATTTAGAAATAACATCAGTA
TTTCAACAACTTTTTGAGCTCATTTTTTACCCATATAATTCTCTATGTTTTTGTTTGAACAAGCC
AATTTATGCTTCACCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCACCGAAGGATAA
CCACTTAGTAACTAACTTGAGCCCCCACTTTGCCAATTAAGGCCGCAGGCTTTATTGACAGAACT
GGGTGGGGCGCGTAGTTTATAGCGAAGCTTTTTTTTTTCAATATTTTGGGAAATCCCCCAAAAAT
ATTTTTTGTTGCGAAAAGCAGCGCCCTCGAAGATTGTAAAGATTTAAGCTAATGGATGATTTGTT
TTTTTGGCGAATAACGGGATTTGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATT
AAGTTATACTCGCCCTTTTTTTTAATTCAGACATTAAAATACTCG
Right flanking sequence: Indices 40748 -- 41247
TGAGCTTAGGGAATCGAAGCGCAGAATGGAAACACAATCTTTTTGTTTCGTTTTCCTTTTGCCAT
TTCATTTTATAGACATCTCCGGCTTATCCCGGCTCGGCTGAATCTGCGGCATTTTTTCAAATATT
TGAAAAATCTATAGTCCTCTGTCTTAAGGTGTGTAGAGACTCCTTTTTTATTGATTTATACCAGT
CTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTAATCTAACCATGGTTGCCTCGGC
AATGGCAATGACTTTCATACAATATGCAGAATACTCCAAAACCTCTATTTAGAACTAAAAAAAGA
TAATGCTTTTTTATAAGAAAATCATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACGTAG
TTTTGCCATCTATATAATATAATATAATAAAAAATAATAAGTTGGCGAGGAAGTAAAAATATATA
TATATCTATATATATATATATATTTTTTTTTTATTCTGTGGTCTT
Found at i:41203 original size:2 final size:2
Alignment explanation
Indices: 41196--41225 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
41186 GGAAGTAAAA
*
41196 AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41226 TTTTTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Left flanking sequence: Indices 40696 -- 41195
ATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCACCAAGTGAGCTTAGGGAA
TCGAAGCGCAGAATGGAAACACAATCTTTTTGTTTCGTTTTCCTTTTGCCATTTCATTTTATAGA
CATCTCCGGCTTATCCCGGCTCGGCTGAATCTGCGGCATTTTTTCAAATATTTGAAAAATCTATA
GTCCTCTGTCTTAAGGTGTGTAGAGACTCCTTTTTTATTGATTTATACCAGTCTATCTTAGATCC
GAGATAGTGCCGAAAAAATGATTCAATTTAATCTAACCATGGTTGCCTCGGCAATGGCAATGACT
TTCATACAATATGCAGAATACTCCAAAACCTCTATTTAGAACTAAAAAAAGATAATGCTTTTTTA
TAAGAAAATCATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACGTAGTTTTGCCATCTAT
ATAATATAATATAATAAAAAATAATAAGTTGGCGAGGAAGTAAAA
Right flanking sequence: Indices 41226 -- 41725
TTTTTTTTTATTCTGTGGTCTTGCAATTGTGCTCAAAGATAAGGGCCCCAGCCCCCTATCTCTCA
TCGTTTTCGTCAATCAAATAAAGGCTTCGTTTAGCCAGGGGCTATTTTTCTCCCCCGCTGAATTG
CTTCGCGAACAAAGTGGGCGAAAAAAATCTTTATTTTTTTTGTCCGCCTTATTCTCTTCTATCAT
TTAAATGGCCCTATGAGCTTTTGCCAAGCAAAATATTGATTGCATAAGCCATCGGCTTCTACAAA
GACCAATAAAGTGATAACAGCAGCGTAGCCAAGCTTGTTCCGCCCGCTGTGCGCAAAAAAAGAGT
TTTTTTCCGGCACTTAGTAAAACAAAATTTTGACACTCCTCGTGTTGCGGATGGTGAGTGGATTA
CTAATAAAATGGAGTGATCCAAGATGACCTCTTTTTCAATTTCAATTATGTCATTATATAGTAAT
GGCATGCGGCGAACTCTATTGGATGCGCCAAAAACTTGATTTGTT
Done.