Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_021092
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: 404466
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:14073 original size:15 final size:15
Alignment explanation
Indices: 14050--14079 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
14040 CCTACCCTAT
*
14050 GTATTGTATAGTAGG
1 GTATAGTATAGTAGG
14065 GTATAGTATAGTAGG
1 GTATAGTATAGTAGG
14080 CGAGCGAGTT
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:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (15 bp):
GTATAGTATAGTAGG
Left flanking sequence: Indices 13550 -- 14049
GTACCTTTTGATTATGGTATGGTATTGTCAGATTCGAACATAGGGCTACTTTATTTGTTTGCCAT
ATCTTCGTTAGGTGTTTATGGAATTATTACAGCGGGTTGGTCTAGTAATTAGGGGGCGGCCGTTC
GGTCGCCTATGATACTAGGACCAATAGGTCAAAAATGGGTTTGTGCCGCAGGTGTTGAACGATCT
ACTCTACACAGGTGTGGGCTTACAGGGCTAGGGCTCATAAAGCCTTTCTTTCATTCAAAAAGAGG
GCCCTGGTCGGTCACTTTTCCGGGCCGGGATCGATAGATAAGTGGAAGTCATAAAAAAGAGATCT
TGATCTTCGCACCTAAGATCCAGAGGAAGGGTAGCTTGTCAAGCTGGCCTATATAAAATATCTTT
TTCATTATTCTAGAATCTTTTCTAAATCTATTTATAAAGATTCACTGTCTTTTAACCGGCTGTTC
TTCTTTGTCAACGCTACTAAGGACCTATGGGTTAGCCTACCCTAT
Right flanking sequence: Indices 14080 -- 14579
CGAGCGAGTTAGCGAAGACGCTTAGGCTAATAGATAAGAGAGCGTCAGTGCGTAGCCTTCATTCT
ACTACGCTACGCAAAGGTTACGAAGTCACTTAGCTCGACGTTAGGAGAGTCAAGGGGGAAGGCCA
TACCTACAAGAACCGCTGTTCGCTGACTTTCTAAGGAAGGTCTAACCCTTAGCTCCCCTACTGAA
AAGGGGCACAAAGCCGCTTTGCACCACTGATAGACTACTAAAGATTCAATTCATTCAAAAGGCCC
TACTTAGTTTCGCAAGCCTTTGTCATTGTCAGTCAACTAAGTAGGGCCTGAGGCCCCCTGCGAAT
CCGTCAATCTGAGGAGCATGCCGCAACACAACAAAAGGATGGTCCCCTATGCATTTCTTTCCGGA
AGGGAAAAAAAAACAAGTACCCCCATCATGGTGAACCTCTCCTTGTGATCGGGATGAGGTAGATG
CCTCCCAGCTGGGGGGCGGATCGAATCGGAGTTTCCTTAGGTAGC
Found at i:123460 original size:15 final size:15
Alignment explanation
Indices: 123440--123469 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
123430 AGAAAGAAGG
123440 GATTGAATCTATTCC
1 GATTGAATCTATTCC
123455 GATTGAATCTATTCC
1 GATTGAATCTATTCC
123470 AATGTGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (15 bp):
GATTGAATCTATTCC
Left flanking sequence: Indices 122940 -- 123439
TCCCATATTTATTCCATTTGTGTGTATATAGACTACTCATTCGATTTTGAACCTTCTAACATCTC
GAACCTCATTTGCACCTTGAACATAACATCTCGACTCACATCACATCTCGTTTAGAGCTCAAACT
TAAGGTTTAATTACACCCCCCGAGGTGGGGCGTATAATGACGCCCCACGGCGAGGATAAGGATTC
ATAGGCGATATGGAGCTTTTGCAAATAGGCAACTTGAGGTTCCACTATAAACATAAACACCATTA
AATGGTGGACTAGTAGAAACCAAAATAGTAATACAATGAAGAACTTCAGTACATCATCAGGGTAT
AAGAAACTTTCAAAACTTTTGGGCCAGTGGATAAACGTTTTTCATATTCGAAGTATAAAATGGGG
TTGTTCCTCCATTTGTGCTTTTTTTTCTTCTTCTTTTCGAGGGGTATCCATTATGTCTAGAATAC
AAAGACGACTCCACCCCTCACCCCTCAAGTGGTCAAGAAAGAAGG
Right flanking sequence: Indices 123470 -- 123969
AATGTGGGTTTGACCCACAAAAGCCATGGGAAAGGTGGTTTTGACCAACCAAAGACATGGGAAAG
GCTAAAGGAAAGGAACATAAAAAAAGCGAATCATCATGAGATCCTAAATTATTATACAAAACTCA
TATCTCGTTAATTAGTCGCGGGGCATTGTTCATTTTTCGACGAACCCACTTCCTTTTCCATCTGC
CGGATCAACTCGAATGCCTCCCCAGTCGGTTTCAACAACTTTTCGTACTTCCTCGACCGCTTGGC
CTTCTACTCGGGGGTCACTAGACAACTTTTTGTACAGTTGCATCCGGACCGGAACTATATCTATC
TATATACGGAATATATACGGAATACGTAATTTTTACATCATTTTGTGGCAATTTGACTTAATAGA
AATGAGCTAACTCTCTCTTTTCGACTCTTTTCGAAAGTTTCCCCTAAGCTGGTGAATGCACCTTA
ACGTTAAGAAATCTTCTTATCTATTTCAATTGGAAGTTTCACTGG
Found at i:123513 original size:31 final size:31
Alignment explanation
Indices: 123473--123535 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
123463 CTATTCCAAT
* *
123473 GTGGGTTTGACCCACAAAAGCCATGGGAAAG
1 GTGGGTTTGACCAACAAAAGACATGGGAAAG
* *
123504 GTGGTTTTGACCAACCAAAGACATGGGAAAG
1 GTGGGTTTGACCAACAAAAGACATGGGAAAG
123535 G
1 G
123536 CTAAAGGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.32, T:0.17
Consensus pattern (31 bp):
GTGGGTTTGACCAACAAAAGACATGGGAAAG
Left flanking sequence: Indices 122973 -- 123472
TACTCATTCGATTTTGAACCTTCTAACATCTCGAACCTCATTTGCACCTTGAACATAACATCTCG
ACTCACATCACATCTCGTTTAGAGCTCAAACTTAAGGTTTAATTACACCCCCCGAGGTGGGGCGT
ATAATGACGCCCCACGGCGAGGATAAGGATTCATAGGCGATATGGAGCTTTTGCAAATAGGCAAC
TTGAGGTTCCACTATAAACATAAACACCATTAAATGGTGGACTAGTAGAAACCAAAATAGTAATA
CAATGAAGAACTTCAGTACATCATCAGGGTATAAGAAACTTTCAAAACTTTTGGGCCAGTGGATA
AACGTTTTTCATATTCGAAGTATAAAATGGGGTTGTTCCTCCATTTGTGCTTTTTTTTCTTCTTC
TTTTCGAGGGGTATCCATTATGTCTAGAATACAAAGACGACTCCACCCCTCACCCCTCAAGTGGT
CAAGAAAGAAGGGATTGAATCTATTCCGATTGAATCTATTCCAAT
Right flanking sequence: Indices 123536 -- 124035
CTAAAGGAAAGGAACATAAAAAAAGCGAATCATCATGAGATCCTAAATTATTATACAAAACTCAT
ATCTCGTTAATTAGTCGCGGGGCATTGTTCATTTTTCGACGAACCCACTTCCTTTTCCATCTGCC
GGATCAACTCGAATGCCTCCCCAGTCGGTTTCAACAACTTTTCGTACTTCCTCGACCGCTTGGCC
TTCTACTCGGGGGTCACTAGACAACTTTTTGTACAGTTGCATCCGGACCGGAACTATATCTATCT
ATATACGGAATATATACGGAATACGTAATTTTTACATCATTTTGTGGCAATTTGACTTAATAGAA
ATGAGCTAACTCTCTCTTTTCGACTCTTTTCGAAAGTTTCCCCTAAGCTGGTGAATGCACCTTAA
CGTTAAGAAATCTTCTTATCTATTTCAATTGGAAGTTTCACTGGACACATCAAGGTTTTTTGCTG
GAGCGAAGATGCGATAGCTTTCCGAGAGGCCAAAGAATAATAGCT
Found at i:124578 original size:12 final size:12
Alignment explanation
Indices: 124561--124586 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
124551 CGAAATTGCC
124561 TAGAATTACCTA
1 TAGAATTACCTA
124573 TAGAATTACCTA
1 TAGAATTACCTA
124585 TA
1 TA
124587 CTAGATAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
TAGAATTACCTA
Left flanking sequence: Indices 124061 -- 124560
AGAGGAGTTCATTGCTGCCTTTCTTTATCCCGGTTTCTCCCGTCTGGACCTGGCGGAGTGGGATG
GGGCTAGCCCCGCAGAAGAAGAGAAGAGCAGAACCCGCTGTTGCTGTCCACGAAGTAGCAAAGGG
CACCCAAGAATCAACATAAGCCAAATCCGGGTAAGTGGAATCCCTTTATCCTGAATTCGTTCCTG
AAGAAGCGGAAGAGGCAGAAGAATTGGTCGACCCTTTCTTTCATCCCCGCTAGCGCTAGATTAGA
TCATGAAAGAGCGAAAGAGCTGAGCTAATAAGAACCCCTTGCTGCAGTAGCAAAAGACGAAGCGG
AGTCTGCTGCTTCATTTCCATATATAGAGGAGAGGGTTCCAGCTAACGTGTTAGCTAAGCGGTCC
GGCACCGGAAACCGATGACGCGATAGGAGATTGATTCCATTCTCAGCTTAAGTAGGCCCGCAATC
TCAAGAAGAAGGAGGTATGGAGTCGGAATAAGAATCGAAATTGCC
Right flanking sequence: Indices 124587 -- 125086
CTAGATAAGCTTCTTAGGGCTAAGGTATTCGTCCTTGCTGGGTAAAGACCAACCAATAGAAGAAG
GTTAGCAAGCTTGGGTCGAAAGCAAAGCGTGGGAGGCTCTCGAATCAGCATCAGAAAAAGAAGAA
ACCGAAAAAGAACCATTATCCCTTGCGGAAAAACCATAATCAGCCAGCTGTGCACAAAAGCAGAA
GTTCTAAAAGATTGCTCATAATGAACTGAATTCGAAGGACCGGACTGACTTGTCTTATTTGTTCC
GATATAAAGAAAGAGGTCCAGTTCTCCGTAAGCTAGCTCCTCCTGCTCCTTACGTTAGTTCAAAA
TAGCCCGCCCAGTCCCGGAAGGACTTTAACCGTAATTCCCTTTTCTTGCTTTGCATTAGCGATGA
GAGGCTAAATAGCAAAATAGAAAAATAAAGAATCTTAGAATTCCATCAATTCAGTTCGAATCAAT
TCTTTTTTTCGGTAACCTTTACTAAAATGGGGGCTTTTGCCCTTA
Found at i:177958 original size:45 final size:45
Alignment explanation
Indices: 177908--177998 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
177898 TTTTCCCAAA
*
177908 AGGAAAAAGACGGAAGTCCGAAAGGGGCATCTGATATGGAGAAGG
1 AGGAAAAAGAAGGAAGTCCGAAAGGGGCATCTGATATGGAGAAGG
* *
177953 AGGAAAAAGAAGGAAGTCCTAAAGGGGCTTCTGATATGGAGAAGG
1 AGGAAAAAGAAGGAAGTCCGAAAGGGGCATCTGATATGGAGAAGG
177998 A
1 A
177999 TATAAAAAGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.41, C:0.10, G:0.36, T:0.13
Consensus pattern (45 bp):
AGGAAAAAGAAGGAAGTCCGAAAGGGGCATCTGATATGGAGAAGG
Left flanking sequence: Indices 177408 -- 177907
TATTACTGAAAATAGGGTGCCATTCCGGTGGCAACGACAATGGAATAAGCACATAATTAAACAAT
ACCCCAAAGAAGAAGAAGAGAATAAATTTCAATGGATCGAGCGGGTCAAAACCGTAACCCTTGCT
TTTTTTGTTGTTATAGGGTCTTTCGATATATGGGATTTCGATATTCAATTAGAATGGTATTTCAC
TCTTCGGCTATTCCTCACGATTGCTCCTTGTGATGCAGGGGACTCCACATCAAGCTCTCTTGATC
AATTTCAGAATCATATACTCCTATTCATCGAAAAGTCTTGGTTTCTTTTTAGCTGCGGTTTCGGA
GTAATTCTCGTAGGATTTGGCATACGACTCTTTCGCCTATACCAGAAAGGTGTGATTGAACAACA
TTTCAAATACGTTCAATCGGTAATGGAGTGAAATCGTGAGAAAGAGGAGACTCTTTATTGTTCCA
AATTTAGCGGGTCCCTGAAAGGAATAGTTATGGAATTTTCCCAAA
Right flanking sequence: Indices 177999 -- 178498
TATAAAAAGGATCAGGGATCCCCCCGGGTAGAGTAATGGAAGGTCCGATTTCTTCTTGTCCTTTA
TGACTGGGATTTGTTGACTCCCTAACCTAATGTAACTCCCACGGCTAGTATGAAGACTGCCTGCA
CGAGAGGTTTTAGGATAGGCTCTTGGAGCTCACAAATGCGCTGTTGACATGAGATAATGAATTCT
TGACAATGTTGATTGATTTCTACGGACCTAGGAGGGAGGGAAGGAAAGGTAAAGCTGGCGGAGAC
CCTGGCTGAGTAATTGACTGAGAATGTAAGTCAGTGAGGTTCCTGGTATAGTGAAGTGATAAGAT
CCTTGACTATACCAGGAGGAAGACAGGCGGGGATGAGCTGAACGAGAGCGAGGCTAGTCTCAGCG
GGAGGGCTGTCGGTCTGGTCCCATCTAAGACATAGAAGGACGAAAAAGGGTTTTGAGAAGAAGCT
CTTCCTGAAGTGAAGAATGACCAAATAGATTCAAAGTGGGGCCCT
Found at i:256915 original size:18 final size:18
Alignment explanation
Indices: 256875--256917 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
256865 ACCGCCCTGC
256875 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
256894 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
256911 CATAGTC
1 CATAGTC
256918 AACAAGGTTG
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:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (18 bp):
CATAGTCGCGAGCTGTTT
Left flanking sequence: Indices 256375 -- 256874
CACCGAAGCGACGAGACCTTGAAAGTTGCTTTTTCAAGTGTCAGTAGCGGGACGTTCTGTCAATC
GGGGAAGGTTTTTGGTGACAACACCTGGAGATATCAGAAGTGAGAATGCTGACATGAGTAACGAG
AAATCCTGTGAAAAACACGATCGCCTGCCAGTGGAAGGCTTTCTGCGTTCAGTCAATCTACGCAG
AGTGAATCGGTCCCTAAGGAAGCCCCGACCCCGAAAGGGCTGCCGTCCGATGGGTACACGAAAGT
GACGAAGTTGCTTTGACTACAGAACCATGCCTGTCTGTTGGAGTGAATTGGATGATCGGGCCGAG
GGCTGCCCCCTCTTCCCCTCACTCTCCTTTCCCTAATATGAACCTTGCTTGAGTCATCAAAGCCT
TTCTGACTCGGCCTGGCCCGGTCGCCCTACGCGACTGGCGCTTCAAAAGGTAGTTGACTTGCTTA
CTCGTTAGAGTAGGGGTCGCGAGAGAGCAGAGCGTACCGCCCTGC
Right flanking sequence: Indices 256918 -- 257417
AACAAGGTTGAAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTATAAGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Found at i:345077 original size:24 final size:24
Alignment explanation
Indices: 345057--345105 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
345047 TAGCCATTTG
*
345057 AATTGAAGAGTGAAATACCATTCT
1 AATTGAAGAGCGAAATACCATTCT
*
345081 AATTGAATAGCGAAATACCA-TCT
1 AATTGAAGAGCGAAATACCATTCT
345104 AA
1 AA
345106 CAAAAAAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (24 bp):
AATTGAAGAGCGAAATACCATTCT
Left flanking sequence: Indices 344557 -- 345056
CTTTGGCTCGAGCTACTTTTTCTCCTGGGAACAGCTAGCTTGCTGCCCAACAAAAGCCATCTATA
TCGTAATTCAATCTACCTAGACTCTCACCGGGGGGATCCCTGATCCTTTTTATATCCTTATCAAT
AGAAGATAGAAAGGTCTGTTTCTCTTCTTTGGCTTGTTTATTCTCTTCTTTTGTTTTTTGTTTCA
ATTCTAGAACGATCCCGGAGAGGGATCCATGCACCCTGGAACAAAAGATAGGCTCCGCTCTTTCA
CGATTTAAATCACAGACTTGATCTATGTAATAAGAATTTTTTTTAATAATGGCACTGTAGTATAA
GCAGAATCAGAGTATGATCAGTATGAAGAAGAGTAAGATCAGTATGACCAAACCGTAGACCAAAA
TAGATGGGTGTTCTTTTAATAAATGGTATAGATCGTCCCCAACTTGATCAAGAGGGCTTGATAGG
GAGTCCCCTGCATCACAAGGAGCAATCGTGAGGAATAGCCATTTG
Right flanking sequence: Indices 345106 -- 345605
CAAAAAAAGCAAGGGTTACGGTTTTGACCCGCTCGATCCATTGAAATTTATTCACTTCTTTCCCT
TTTCCTAGCCTTTACCAAACGATTAGCGAAATGAAATCGAGGAATCAAGGACGATTCGATGACTC
TCTCCAATAGATCTCGATTTGCGGACGATGTCGTTAAAGAGTCGACACCGCTTTGCACAAGAATC
GGTTCTTTGTATGGATGGACAGAAGGGCTCAGCCAGACCCGGTTCAATTCGTTTTTTGCGGGAAT
ACCAGGTTCAAGTTCAAGGGAAGAGAAAAGAAAGCGTAACTCTTTGCTTGTTGTCCTCTTACTCT
TTGAGCCTGCCTTGTGGAGGTCTCTCGGGTGTCTACGGCGGATCCGATCAGTCTCGTGCGTTAAG
AAGTCTTTTCCGATCTTCCACTAAGAAAGGTATCGTCACGACAACTAAATTTGCCCGGGAAACTA
GTCGGGGCTCCCCATGGTTTAGTAATAGGGAGGGGATAATGTCTA
Done.