Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_026891
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: 106358
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:1008 original size:2 final size:2
Alignment explanation
Indices: 1001--1027 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
991 TAGTATAGAC
1001 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1028 TGGCTAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 501 -- 1000
GGTGTATAGCTTAATTGGTAGAGCATTAGGCTTTTAACTTAATGGTCGCAGGTTCAAGTCCTGCT
ATACCCAAATGTTTTTATAGAAGTTCTCCAGGCAGTTCATATGCACATCAAAATATACATTGTAC
GTTGACTCGTCTAGTACGATTAATTACGTTAAACTAAAATATATATATATTTTTAATGTCTTTAT
GGCCGCTCACGCCCTTTTTTTTTCTTTGCGAAAAAAGGCCGCGGGCCTCTAATCTAAGCTTAGAG
TGGGTGAATAGAACGTCGCAGCGTTTGATGCGGCTCTGAAAAGATAGAAGTTAAGTAGGTGTTAC
CAACTACTTAACTATTTAACTTATCTATATTATACAATCTGCAGCAATCCTGCATTCTGCAATTA
AGGAGTTGTTTGATAGCAACTGTGAATAACAGTATAGATATAGATATTTTCATAAAATAAATAAA
TAGCTTATTTATTATTGGCCAAATACATAATATTTTAGTATAGAC
Right flanking sequence: Indices 1028 -- 1527
TGGCTAATAATGCCGTATTGATTGTTGTTTCATTAAAGCTAATTGCTGTTGGAATAAAGGCTCTA
GTAAACTAGAAGTCTCGATTACATGTGCCGCGTTTTGCGCTTTTCGGACAGCATTGCTGGAGCTG
GCAACATGAAGAGCGGATTCCCGTTATTTTCAAATTTCTAAGTAATCTACGTCACCGTCAACCTT
AATTCATGAGATATGCGTCTCTTTCATTAATTATCTAAATTATGCCAACCTATCTTATGAAAGCC
AGCCCGGCAGTATAATATAATAAATACTGGCTCGCTCGCGTATATTCCCACATTCATTCGTCAAA
TCAGGCAATCTCTATTGAATAAAAGAGAAGATATGATAATAAATTGAATAAGAAGCTTCCGAGTA
CGCAAATGGTAGGAATACACCAGAAGTATTGGCAACCTAGAAATAGGCCGGCAAAAGGTACAAGA
ATAGCATGTCGCCACTAGCTGTGTTATGGCATTGGCCGCCTCCAA
Found at i:3220 original size:14 final size:14
Alignment explanation
Indices: 3201--3230 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3191 TAGTTGTTGC
3201 ATATTCCTCTCAGG
1 ATATTCCTCTCAGG
3215 ATATTCCTCTCAGG
1 ATATTCCTCTCAGG
3229 AT
1 AT
3231 CCAGCCTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (14 bp):
ATATTCCTCTCAGG
Left flanking sequence: Indices 2701 -- 3200
TACCGACGTGTCGAACGAGGTTGCGGTGCCTCTCCGGTTTCCTTCTTTTCCTTTTGAGTTTTTTT
TTATTAGGGAGAGAGAGCCCGAAGAAATATTTTACGTGGTCGGCTCTCTCGTGCTCGAGCTTGCA
AAGGGATATTCGCTTTCTGTTGAACATGGTCATCATCTCGTTTATCCGTGAGATGTTCTTATCGA
GTTGGCTCAACTTGTGCATGTGGTTAATTTTTACTGGTCCGGATTTGTTGACTAGGCATCTGGTA
TCGTCCAGTATAGATCCGCCGCGTAGGTTTTTGAAAAGAGGCGTAGCGAGACCAAGCTTTTTGGC
TTTTTGGTTGGGGTTTTGTATTTGGCTGCGTACCCTGCGCTAAAATTTCTGTACGTTTTCGAGGC
TCTTTGTTGCCGCAATTTTATGATTAGGGTGCAAACACAGCAGCTCCTGATGACGAGTTTCAGAT
AATTTGTTAATTGGTAGAACTTGTCAAGGAACGAATAGTTGTTGC
Right flanking sequence: Indices 3231 -- 3730
CCAGCCTTTGTAGTCTTCTCGTATCCCGCTTTTAGTGCCTTAGAAATGAATCAGCGTATAAGTCT
CCTATCTCTTTTTTAACAGGTTCACAAAAATTAGATAGTCGATTAAGCCGTAGTATTTTGTTATA
TGCCATCAGGGGTGCCTTTGCAGTCCAGTTCCAATTGACTGTGAGCCAAATGAATACAAGGGTCG
AAAACCTTGATAAGGGCACCGGTTTGTAAATCACTTATATATACTATTGTCCCAATTGCTTCTAG
AATGATATTTTTTCTAGAAGGCCACTGTAGTAAGCGGCGGGCGTTCGCCTCCTTCGAAGCGCCTC
ATACCTTGTTAAAATTGGAAGCGTTCTGAGCGAAGTTGTTTATTTTTCTTTTGTTGACGTCTAAT
ATTTTGCCGTTAAGGGCCGGCGTACTTCGCCCCGGGATGGACTAAAATGCCAACTCGGTCAGGTC
TTCGTGAAATAGAAATCTGCAAGGGTTAAGGTTGTTGTTAAGGTT
Found at i:30533 original size:18 final size:18
Alignment explanation
Indices: 30510--30546 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
30500 TTAGGCTTTT
30510 ATTAAGCAACATACAAAA
1 ATTAAGCAACATACAAAA
30528 ATTAAGCAACATACAAAA
1 ATTAAGCAACATACAAAA
30546 A
1 A
30547 AAACTAAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.16
Consensus pattern (18 bp):
ATTAAGCAACATACAAAA
Left flanking sequence: Indices 30010 -- 30509
GCAGGCTGACCCGAAAAGAACTGCGATTCTGCTTTATCATCTCATGCTAAATGAAATATATATAT
ATATATATTTCATTTAGCAAGCGCCAGCGGACTCGCGGAGGATTATTGAGCAGGCCGATAGACTA
GCCGACGAATATCTCCTTTTTTATTGCTGCTTTTGTGGTATGCTTCCTTTGCTTTGCTATCGGGT
AAGCCCTGAGCCCCTCGAGCAGTAGTGCCTTTGTTGTAATCACAAGTGATCTAACGGCCGCCCCT
AAGAAAGCCCCAGAAATTCTATGGAAAATAGAAAAAGTAGAAGTAAGCTGTGGCTTATAAATGGT
AAGATGAGGTGATAACGGTCGATTAATTTTCATGTTTTTAGTTGACTTTGATTTTAACTCAAGGT
GACAGGATTTGAACCTATGACCCTCTGTACCCAAAACAGATGCGCTACCAGACTGCGCTACACCT
TGGCTGATGTTCCCTAATGAATATTTGATAAATGTTTAGGCTTTT
Right flanking sequence: Indices 30547 -- 31046
AAACTAAGACTAATAAAAACTCTATTTTTAACACCACTGAAAAAAAGCACTATCATCTCGTTCAG
TTTCTTTTTTGCGTGAAAATACTTTTTTTGGTGGACGTTTATTATTGTTTCAGCCTTTTAATGCT
CGCTCGAAGAAGGGCAAGTCGATCATTGTCTGCCTTATTTATAAAGCTTTATAATGCAATTACAT
GTAATTGCATTATAAAGTCAAATATTCAAAGAAGATATTATTAATCTTTCAGTTATGTTATTAAT
TAAGTAATTCCATGAGAAATAGCCATGAATAATCATAGATAAATAAAAGGGCCCAGATCTAAAGG
TATTCCATAGAATATAGCATACTTACAATTTGCAATCACTACGTAATTCCATAATGCGAAAGAAG
CGTAGCAAGTTTATTGGGCCAAAGGTTCTACATAGTGAATGCATTTTGGTCTATGGGTAGTAAAC
CTTAGTATGATGATAATTTAGTTAGTGATACGCAGAGGTTTTCTA
Found at i:37922 original size:24 final size:24
Alignment explanation
Indices: 37895--37940 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
37885 TGCTAATACG
*
37895 AAAAAGAAAAAGA-AGACTAAAGA
1 AAAAAAAAAAAGAGAGACTAAAGA
* *
37918 AAAAAAAAATAGAGATACTAAAG
1 AAAAAAAAAAAGAGAGACTAAAG
37941 TGAGCACTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.72, C:0.04, G:0.15, T:0.09
Consensus pattern (24 bp):
AAAAAAAAAAAGAGAGACTAAAGA
Left flanking sequence: Indices 37395 -- 37894
CTCAGTGAAATTGAACTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTAAGACCCCGTGC
ACCTTTACTATAGCTTTGCAGTGACAACCTTGATTGAATGTGTAGGATAGGTGGGAGGTGGTGAC
GTTGCACGTCACCACCAATCTTGAAATACCACTCTTTCGTCTAAGGATGTCTAACTGCCGAAACA
GAGGCGGGACACTGCATGGTGGTTAGTTTATCTGGGGCGGATGCCTTTAAGTAAGGGGCGCTTGG
ATGGTAACATCCCAGGCCAATCTGGCTATATGCTGAAATCTCCATTTCTTGGACAATCAGCAGGG
AAGGCTGAAAAAAGCCACTGCGAAAAATTTATTTGGCTCCCTCAACGACTGCATGCCAGGTATCC
AACAATGCAATAATGATTGGATAATGATACAGTCTGAACTTCCAGTAAACTGGAAGCCTAAAGTA
CTGTTCACTACGAAACAGTGATAGGACATTCAAACTGCTAATACG
Right flanking sequence: Indices 37941 -- 38440
TGAGCACTTCAATTGAATCAAATACAACGACAAGTATGTTGCAGAGTGAATGAACATAATTGCCC
AAAGAGTAACGGAGGTGTGCGAAGGTAGGCTCGAGCTAATATTATGACAGCTTTAGAGCGTAATG
GTAGAAGCCTGCCTGACTGTGAGACTTACCAGTCGAACAGAGACGAAAGTCGGCCATAGTGATCC
GGGAGTCCCGTGTGGAAGGGCTCTCGCTCAACGGATCAAAGGTACGCCGGGGATAACAGGCTGAT
GACTCCCAAGAGCTCTTATCGACGGAGTCGTTTGGCACCTCGATGTCGACTCATCACATCCTGGG
GTTGAAGAAGGTCCCAAGGGTTCGGTTGTTCGCCGATGAAAGTGGTACGTGAGTTGGGTTTAGAA
CGTCGTGAGACAGTTCGGTTCCTATCTACCGTTGGTGTTTAAGAGAGAACTGCGAGAAGCCAACC
CTAGTACGAGAGGACTGGGTTGGGTCAACCTATGGTGTACCGGTT
Found at i:41633 original size:82 final size:81
Alignment explanation
Indices: 41496--41645 Score: 248
Period size: 82 Copynumber: 1.8 Consensus size: 81
41486 TAAATACTCG
*
41496 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTTCA
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCA-TTTTCA
41561 CCAAGCGAGTATGCTCA
65 CCAAGCGAGTATGCTCA
* *
41578 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
41642 CCAA
65 CCAA
41646 ATGAGCTTAG
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
81 10 0.16
82 52 0.81
83 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (81 bp):
CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 40996 -- 41495
ACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTAGAAATAACATCAG
TATTTCAACAACTTTTTGAGCTCATTTTTTACCCATATAATTCTTTATGCTCTTGTTTGAACAAG
CCAATTTGTGCTTCATCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCACCAGAGGAT
AACCACTTAGTAACTTGGGTCCCCACTTTGCCAATTAAAGCCTGCGGCTTTATTGACAGAACTGG
GGACCCAAGTTTGTAGCGAACCTTTTTTTTTTAATATTTCGGGAACCCCCCAAAAATATTAAAAA
TATTTTTTGCTGCGAAAAACAGCGTCCTCAAAAATTATAAAGATTTAAACTAATGGATGATTTGT
TTTTTTGGCGAATAACGGGATTCGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTAT
TAAGTTATACTCGCCCTTTTTCCAATTTAGACATTTAAATACTCG
Right flanking sequence: Indices 41646 -- 42145
ATGAGCTTAGGGAAGCGAAGCGCAGAGTGGAAACACAATCTTTTTGTTTCGTTTTATTTTCGCCA
TTTTATTTTATAGACATCCCCGGCTTATTCCGGCTCGGCTGGACCTGCGGCATTTTTTCAAATAT
TTGAAAAATCTATAGTCCCTTGTCTTAAGGCGTGTAGAGACTCCTTTTTTATTGATTTATACTAG
TCTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTCATCTAACCACGGTTGCCTTGG
CAATGGCAATTACTCTTATACGATATGCAGAATACTCCAAAACCTCTATTTATTCTATTTAGAAC
TAAAAGAAGATAATGCTTTTTTATAAAAAAATCATAAAGTGCAAAGATTCAAATTTTGAGCTTTG
TTTTACGTAGTTTTGCCATCTATATAATAGAATATAGTAAGAAATAATAAGTTGGCGAGGAATAA
AAAAAAAATATATATATATATATTTTTTTTTATTCTGTGGTCCTG
Found at i:54723 original size:11 final size:11
Alignment explanation
Indices: 54707--54731 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54697 AAGGCAGGGG
54707 CGCGCTGCAGC
1 CGCGCTGCAGC
54718 CGCGCTGCAGC
1 CGCGCTGCAGC
54729 CGC
1 CGC
54732 TTCTTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.48, G:0.36, T:0.08
Consensus pattern (11 bp):
CGCGCTGCAGC
Left flanking sequence: Indices 54207 -- 54706
TAGCCTTAATAGGAGTTGTTACTAGTGTTATCAGTTGTTTTTATTATATACGCTTTGTCAAAATC
ATGTATTTTGATACACCTAAAAAATGGATTCTATATAAAACAATGGATCGTGAAAAATCCTTACT
ACTAGCAATTACTTTATTTTTCATTACGTTTTTCTTTTTATACCCTTCTCCCCTATTCTTAGTCA
CCCATCAAATGGCACTAAGTCTATCTTTCTAAGCCGCTGGCTGCAACGCCGGCGCACCAATGACT
CTCCGTACCGTTTCCCATCATTTGTTATGCGAATAATGTGGGCGCCAGCCTTCGGCCTGTAGCGC
CAAGCCCACCGCACCCACCGCAGCGCGAGGCTGCCCCCCCATCGGCCTGGCATACATTTTAAGCG
GAAAAAGGGACTTGAACCCTCAACCTCAGCCTTGGCAAGGCTATACTCTACCATTAAGCTATTTC
CGCAGCACAATAATAAAAAAGTAACAAGGGTCCGAAAGGCAGGGG
Right flanking sequence: Indices 54732 -- 55231
TTCTTTATTACTACTAAGAAGGGCAGCCTCGCTACAGCCGCTTCTTTATTATTAGATGTATTATC
TTAGTAAACCATGCTTGGAAAGATTCGAACTCTCAACCCCCAAATCCGTAGTTTGGTGCTCTATC
CGATTGAGCTACAAGCATAAATTTCTTAAGCACTACGTGTCATGTAGGCTGCATTATTACAAAGA
AAAAACATATATATATGAAAAAAGAATAGCAGTTCGGGCAGCATTCTCTAGAGATTAGTATTACC
GTATTGCATTATTTTAAGTATGCCTTCTGTGACTGCACTGTGTAGTCAACATCCGCAGTTACGTG
CATTACTAACGTAATTAAGTTCGAATGTTGATTCGATTAGATTAGATTAGATTAGCTTGCGTTTT
TACTGCTAAAATAGATATATATATATATTTTGTTTTCTTATCTAATTTCTCCGAAAAGGGGAAAT
GCAGACGCTATTTTATTAAAGGTCGCTCTTGATGTAATGTTCAAC
Found at i:62281 original size:13 final size:12
Alignment explanation
Indices: 62264--62293 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
62254 TTAAGCTTAA
*
62264 ATTTTTTTTTCT
1 ATTTTTTTTTTT
62276 ATTTTTTTTTTT
1 ATTTTTTTTTTT
62288 ATTTTT
1 ATTTTT
62294 ATTCGATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (12 bp):
ATTTTTTTTTTT
Left flanking sequence: Indices 61764 -- 62263
CTATGTTATTGCAGAACTGAATCAAAGCCAAGTGGTTTTTCCATTATATGAATAATCCACAAGTT
GCATAATCTGCTACTTTTTTGAATCCCTTTAAGCATTGTATTGGTTTAACTGTGTGTTTCCAAGA
GGTTGATTATACTTATTAAAGCAAATAACCAAAGCCTTTGTAGGCTCTGTTTTTTACATATTATG
GGCACATGGTTAACGGGAGATTAATACTGATCATGTAGAACAGATTCAGTTGTGCGAAGCACTTA
TAATGCATTATGCATCGTGTTTAGTTTGCTTGTAGTTATCAAGCTACGCGCGTAGGCGGGTAAAC
TGGCTACACTCGATTGCTTCGCCTGTGGCTTCGTCCATAGCACGTGCCAGTAACCGTTCCGCGAT
TTGCCAGTGAGGAACGCAGCCCCCGGGGAAGGAACGCCCTATTTTATTTAGCAGGCTTAATTCCC
AAACTGAAGGCCCAGGGGCCCTTTTTACTTAAGAATTAAGCTTAA
Right flanking sequence: Indices 62294 -- 62793
ATTCGATAATGAGCTCTGAAAAAAAAGTGGGTAAATTTGGGCCTGAAGCGGGGCGGCTTGGCAAA
ATAAATAAATATATATATATATGCCGCACTATGCGGTCTGGTGCTCTCAGCGTTAAAATCATCAG
CAATGGCGTTAGAGTTTCCATAGTACAATGAATTGGAAGTGAAACAATCAGTTTTTTTATCATTA
TACAGTTATGGTACGAACTGGGTCTTCATAAAAAAAAATATTTTTTTGGTTTATGCCATCATAGT
TGTTCAATTATGCTAGTTTCGAATACCAAACAAGAGCCGCGTGCTTGAAAATCTTGCAAGCACTT
TGAGGGGGAGTATTTCGAAGGCTTAAGTTCGACTCAATAACAGCGATGTTTGGGGATAATTTATG
ATATATGACTTGCTTTCATCAAGCATGTTGCGTGATTACTGAAGCTTTCTCTGCCCAACATAATG
ACCTATAATTATTTTAAAAAGCTTACTCTATCTATTGGCCCCTTC
Done.