Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_007945
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: 105340
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:19355 original size:19 final size:20
Alignment explanation
Indices: 19313--19355 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
19303 GGATGTTGGT
* *
19313 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
19333 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
19352 CATG
1 CATG
19356 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 18813 -- 19312
CTAGAGCTAAAAATGCATTTTTTTTCTTTTTTATTTTCATTTTCAATTTTTTTATTTTCAAATTT
ATGGGAGACTTGTCATATTTAGAATCTTTCTGTGGTGTGCTTTGTTTTTTATTATTTTGTACGTT
TTTCTTATCATCTAAATATAGGCGCGATACGTGGGCAAACAAGGAGCCTAGGCTTGGAATAGAAA
AAAAAAGAAAAGCGCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTAACGAA
AAAAAGAAACAAAGAAATAAAAAGAAAGAAAATGCATTTTTATTTCTTTCAAATAAATCAAAAAT
ATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAAAAAGCCAAAATTTTGG
CTTTTTATTCTCTGCTTGCTTTTTCGCAAGCTTATTCTTCCGTCCCTGAAAATAGTTGGAATAGA
TTTTTTCTTGTTCGCGCCTTACCAAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 19356 -- 19855
GAGGAGTTTGCATCTTTATTATGGGTGTTATTTTGTCGTGCGACCCGGCAGCTTATGCGCGACCA
TCTCGTGTTTAAGCTCACGCCCACATGGCGTGAACTCTGGTTGAATTCGGGTTCTAAATCCCGCC
GCTGAGATGCTCAGTCGACTCTTGAACCTTGATGGGAAGACGGCTTCTTCCCAAATTAGTGCAAA
AGGTTCCAGGACTTAGGATGAACTTAATGTGAATGAGTATAAGCTTCGCTGCTCAAAAACACCCA
GTATTGACCACACTGAGAGACTTGCCAATGGCAAGAAAGGCCGCGGGTAACGCTAGTTGGCGAAA
TGGCGTTAAGCATTCCTAGCGATACGGAAAGAGAGGTCGTGATGGATGATATCATCTACGTTCGT
ACTGTTCCTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGGATAATTCCCATTA
AGTTCCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGG
Found at i:27133 original size:19 final size:19
Alignment explanation
Indices: 27109--27146 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
27099 ATATCGGCCC
27109 GCAGGGTTTCTTTTTCCAT
1 GCAGGGTTTCTTTTTCCAT
27128 GCAGGGTTTCTTTTTCCAT
1 GCAGGGTTTCTTTTTCCAT
27147 TCTGGTCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (19 bp):
GCAGGGTTTCTTTTTCCAT
Left flanking sequence: Indices 26609 -- 27108
CTGGCATTGAAGACAGTATGATTTTTAGTATATCCCTGTCAATGGTCTCCTTCTGTCTGATATTG
GTGTCATCGATTCAGGTCCCGCTGCCCTCGTTGGACATAAGGCATTATTCATAAGTCCAGGTTGC
CCACGATGTTTTGCAGATCTGAATAGGTTTCCCTAGCTTTGCGACGGGTATCTCATGAATTAATT
ATCTAAATTATGATTGCTTTTTTCTTTCTTTGCGGTTGAATATAGTCTGCTAAGGTACAGCAGAC
GGTTAGGCCCTTTCCCTTTTGTTAGCAGTTTTACTTTGTACTACGTATGGCTGAAGCGGGTACTA
TGGGCCCTCTGCCATCCACTTTGGTCCAGCTGACTGAAGTGGATTTCACCGGTGTTGCCTACAGT
TCTTGGCTAAGTTTAATTCAAGGCCATTTTGTGTCGAGATGTCGTTTAGTCTTTTGTCCCCATTA
ATTTGGGTAATCTGCTCCCTGGTGCGGGCTCTGTAATATCGGCCC
Right flanking sequence: Indices 27147 -- 27646
TCTGGTCTTACCATAATTTATCGATGGCAGACTGAGAGCTTGACAGCGCGCACTCATGTGCATTA
CCACAAGGAGTTCCTTGTGATTAACTGCAGGTCCAGTTTGACCGAAAGAGACTTCGATTTGCCAG
AGCAGGGGCTCATCTCATACAAGAGCAGGCTAGCGTAGTGGTCTTGGGTTGTTTGGGCTAGAATC
ATTCGTTTGCTTTGTGAACCTTCAGGTTATTGGCTAAGTAAAGAAGTAGATCGCAGGTCAAACGT
ATTACGCCGCCTGTGGTCTTTCGGGCGCTTTTGCGCTTTATGGGATAGCAAAAAAGCAAGTTGAA
AGCCTAAAAGACATACCCTGGGATCTTGCTTGTTTTTTTTCCAACTACGTTTCTAGAGCATGCTG
TGGTTCCCACCCGTTTACACGGTGGTTGGGTAAGCTCTATGCCTGGCACGCGGAATAGGGTCTCG
CGTGGTTTGCTATATGGCAGCTAGCGCAAAACTGCGAATAATTTC
Found at i:37787 original size:12 final size:12
Alignment explanation
Indices: 37770--37794 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37760 ACGTGACTTT
37770 ATAATAGTAATG
1 ATAATAGTAATG
37782 ATAATAGTAATG
1 ATAATAGTAATG
37794 A
1 A
37795 CGTGATGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
ATAATAGTAATG
Left flanking sequence: Indices 37270 -- 37769
AGAAGCCAACCCTAGTACGAGAGGACTGGGTTGGGTCAACCTATGGTGTACCGGTTGTTATGCCA
ATAGCAGCGCCGGGTAGCTAAGTTGGTATAGAAGAACTGCTGAAAGCATCTAAGCGGGAAATCCT
TCTCTATACAAGTTCTCATAAAAGGTGAAAGACCATCACTTTGATAGGCGAGAGGTATAAACACC
GTGAGGTGTGAAACAAGGCTTACGGCTCTTGTTGAGCTTACTCGTACTAATTATTATCTACTTCT
CGGGAGCCCAGGGCTCTCCGGAGATAACCTCTTAATTAAGCAGAGATTGCTGCGGTCTGTACGGA
AAGTAAAAAAAAAATTTATCATAGAAGATTGTTAGTTCTTCACATTTCTGTGGATTTTCTAGTAG
AGTACCTAAAAATATAGTAAGCTACTGAATCTTTTTGCTTCTTTTTGTTATCTTCAAAATTACTG
TAAGACTAGTTATTCTACATAAATATAATGTCATCACGTGACTTT
Right flanking sequence: Indices 37795 -- 38294
CGTGATGACAAAAAAAAAGGATTTGATTCGTGCTGGTCAAAAAAAGGAACTATGTACAATGAATA
AAATCAATATTAATAATAAATGTGTATTTATAACCCCTTTTTAATACCTCTCCTTAATAAGCCTC
CGCCGGAGGCGCTTGTCATCGCGTGGTTTCTATTATAAGATAACACGATGACATTATTATACCCG
TTAATTAATACGTTCCCGCCGGGGGCGTTGGCCAACAAGCCTCTATACCATATTCTAATAAAGCC
CGCAATTATTTCAATTTAACACGTACGCAACTGTGTTATTTCTTTTTGGAACATTTTTGATTTCA
AAATGATTATTCTGACATAAAAGTCCATAATGAAATTACGGCATTTCCGAGATGTTTTCTTATTT
AAGTATCATGGTTTTTAGATTTACTATTGTGTCTATCCTGCCGGGTTGTTATGAGGTTCCGGAAA
AAATGAACCGAACTTAGATTTAATCGAAGTAGCGAGAACCTAGCT
Found at i:41032 original size:81 final size:81
Alignment explanation
Indices: 40897--41046 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
40887 AAAATACTCG
*
40897 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
40962 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
40978 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
41042 CCAAG
65 CCAAG
41047 TGAGCTGCCG
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 40397 -- 40896
ATTATACGGACAACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTAG
AAATAACATCAGTATTTCAACAACTTTTTGAGCTCATTTTTTACCCATATAATTCTTTATGTTTT
TGTTTGAACAAGCCAATTGATGCTTCACCCACTATACAAGAAAAGACGCAAGGAGGGCCGAAGGC
AGAGGATACCCACTGCCGTAACTTGGGCCCCCACTTTGCCAATTAAGGCCGCAGGCTTTATTGAC
AGAACAGGGGCGCGTAGTTTATAGCGAAGCTTTCTTTTTTTCAATGGAAATCCCCAAAAAATATT
TTTTGCTGCGAAAAGCAGCGCCCTCGAAGATTGTAAAGATTTAAGCTAATCGATGATTTGTTTTT
TTGGCGAATAACGGGAATCGAACCCGTGTTTTCAAATTCACAATCTGACACTTTAACCTATTAAG
TTATACTCGCCCTTTTTTCCAATTTAGACGACATTAAAATACTCG
Right flanking sequence: Indices 41047 -- 41546
TGAGCTGCCGGGAAGCGAAGCGCTGAATGGAAACACAATCTTTTTGTAAAGAAGATAATGCTTTT
TTAGAAAAAAATCATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACGTAGTTTTGCCATC
TATATAATAGAATATAGTAAGAAATAATAAGTTGCCGAGGGCGCAGCAAAATATATATAATATAT
ATATATTTTTTTTCATTCTGTTGTTAAGTAAGGGGCGCTTGGATGGTAACATCCCAGGCCAACCT
GGCTAAAAATACTTATGACAGGATAAGATACTAGTTACCTGTCTAAAAGTACTAATCAAGGGTGT
AATTCCGAGAAAGACTGTTTCGTCCCTGAAATGGAACTCTTCAGAACCCTTGTTATCGGTTTACA
GCCTAAGGAAATTCCTGTGGTCGAGAATCTACTTTGTCAGGTCGTGCTATTGCTTACTTTTCAGT
CGGCGTAGGCGAGTTACGAACTTCGCATTAATTTGCGAGTAAGAT
Found at i:84617 original size:22 final size:22
Alignment explanation
Indices: 84589--84632 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
84579 GGCGCTTAGA
84589 GGCTGCAAGTGATGCATGTGTG
1 GGCTGCAAGTGATGCATGTGTG
*
84611 GGCTGCAAGTTATGCATGTGTG
1 GGCTGCAAGTGATGCATGTGTG
84633 AGCGTTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.14, G:0.39, T:0.30
Consensus pattern (22 bp):
GGCTGCAAGTGATGCATGTGTG
Left flanking sequence: Indices 84089 -- 84588
TTGTCAAAAATTTACACAGAGCTTCTTAGCGACTCATTCAGTTTAAAAAGATTCAACTAAAAAAA
AATTTTCAGGCCGCGGGTTTTGTTTCCGTGCTTCCGGGTGGAGGGTGAAAGCGGCCAGGGCGCAG
CCAATTTTTTTTCTTCCGCCCTCTGGCTACGCCCCTAGTAAGGCTTCGTCATACGAGCGGAGCTC
GAAAACCCTCCATCCCCACATTAACAACATGTAGATTTGTAAAAAACAGGAAGGCAACAAAACAT
TAACAAAATCGGGCCAGGAACGCTTATTTGTAGAATGTACTATTTGTAGGTTCTGTAGGTTTTTA
CTGCGTATTTGTACTATTAGATATTCTTTACGTATGCAATAAGGGCATTCTAATGCCGGCAAAGA
TAACTGGATGACCCAGATTGACTATGTATTGCCGTAATGCATCTGGCCGCAGGCTCGCGCTTAGA
TAGAGTAATGCATCAGTCTTTTCTGGAAACTTTCTGGCGCTTAGA
Right flanking sequence: Indices 84633 -- 85132
AGCGTTAACAAAAACAATATATATTACATAGCTCCAGCAAATCAAGTCTATCGCTCCGCAACAAT
TTCTAAAATGAATCAATCATTTTGATGATTGATAGCTACCTCCACCAAATTCTGGCTGGTGTAAT
CAGGAGAAAAGGGATTCGAACCCTTAACCTGTGGTTTTGGAGACCATTGTTCTACCATTGGAACT
ATTCTCCTAAAAAAAAAAGTGGTTCTTGGTTTATGGAATTTGCACCTATTTGTGTCTATTTAGTA
ATAAGTTTGCTACTTTCTTTGATCTTAATCGGTGTTTCCTTTCTATTTGCTTCTTCTTCTAATTC
GGCTTATCCAGAGAAATTGTCAGCTTACGAATGCGGGTTTGATCCTTTTGATGATGCCAGAAGTC
GTTTTGATATACGATTTTATCTCGTTTCTATTTTATTTATTATATTTGATTTGGAAGTCACCTTT
TCATTTCCTTGGGCAGTTTCTCTTAACAAGATTGGTTTGTTTGGA
Done.