Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_043897
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: 494369
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:68555 original size:18 final size:18
Alignment explanation
Indices: 68515--68557 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
68505 ACCGCCCTGC
68515 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
68534 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
68551 CATAGTC
1 CATAGTC
68558 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 68015 -- 68514
TCAAGTGATTCACCGAAGCGACGAGACCTTGAAAGTTGCTTTTTCAAGTGTCAGTAGCGGGACGT
TCTGTCAATCGGGGAAGGTTTTTGGTGACAACACCTGGAGATATCAGAAGTGAGAATGCTGACAT
GAGTAACGAGAAATCCTGTGAAAAACACGATCGCCTGCCAGTGGAAGGCTTTCTGCGTTCAGTCA
ATCTACGCAGAGTGAATCGGTCCCTAAGGAAGCCCCGAAAGGGCTGCCGTCCGATGGGTACACGA
AAGTGACGAAGTTGCTTTGACTACAGAACCATGCCTGTCTGTTGGAGTGAATTGGATGATCGGGC
CGAGGGCTGCCCCCTCTTCCCCTCACTCTCCTTTCCCTAAGATGAACCTTGAGTCATCAAAGCCT
TTCTGACTCGGCCTGGCCCGGTCGCCCTACGCGACTGGCGCTTCAAAAGGTAGTTGACTTGCTTA
CTCGTTAGAGTAGGGGTCGCGAGAGAGCAGAGCGTACCGCCCTGC
Right flanking sequence: Indices 68558 -- 69057
AACAAGGTTGAAACTTCCAGGAAAAAACTTCGAAATGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTATAAGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Found at i:320582 original size:31 final size:31
Alignment explanation
Indices: 320544--320677 Score: 259
Period size: 31 Copynumber: 4.3 Consensus size: 31
320534 TTTAGTACTT
320544 GTGCTAAGGAACGAAAGTCGTTTAGTACGAA
1 GTGCTAAGGAACGAAAGTCGTTTAGTACGAA
320575 GTGCTAAGGAACGAAAGTCGTTTAGTACGAA
1 GTGCTAAGGAACGAAAGTCGTTTAGTACGAA
320606 GTGCTAAGGAACGAAAGTCGTTTAGTACGAA
1 GTGCTAAGGAACGAAAGTCGTTTAGTACGAA
320637 GTGCTAAGGAACGAAAGTCGTTTAGTACGAA
1 GTGCTAAGGAACGAAAGTCGTTTAGTACGAA
*
320668 GTGCTTAGGA
1 GTGCTAAGGA
320678 TAAATCCACT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 102 1.00
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.23
Consensus pattern (31 bp):
GTGCTAAGGAACGAAAGTCGTTTAGTACGAA
Left flanking sequence: Indices 320044 -- 320543
GATCGCTTGAACTAATCAATCAATGCTTCTTTGTAAAGCGACCTTGACTCCAACATTGCACGGGG
CGCTAAAGAGTTATGAATGCAAAGAGCTCTCTCTTGCCTTATGAGGGGTGGTGGGCTTACTTAAT
TAAATAGAGTCAAAGGAATTGGCCTATGGTACAGCTAAACCTCCATTGGTGGAGCAAAGGAGGAA
TCCATTTCTCTACTCATTCTATTCACTATTCTAGGGCCGATCTGGATCATTCATCAAAAGCATCA
GCCTTTCTTTTGCTTTTGGGCAAAGATAAAGAGGTGTGCTGCCGCTTGTCTTGAATCACTATGTC
CAATTCTTCAGGTTACAATCACCCTTTGAAGCAATCCTTTTCTTTCTATGCACTTTTATGCCCTC
TCTTGCCTCTATTGAATCTTCGGCCTTGGTTCTTTCCTTTCTATATGCTTGTCCAATCTTTTTCT
TTGAAGCAATAGAGTTTTCAAGAAGGTTTATATCATTTAGTACTT
Right flanking sequence: Indices 320678 -- 321177
TAAATCCACTTTCAGAAAACCTTTTAGGGACTCATCAAAGTCTTTTCTTTTCCTCTACAACGGGG
AGGGTTTCACCGCTACAAAGCAGTTTCACCAATCTTGTGAAAAAGACAGGTCTTTTCCAGGCTCG
AAAGCCATCCATATCATATATCATTTCAGTCCTAGTTCCCATATACCCAGTGTAGTAGATGAGTT
CATAGCTATTTCTTTCTCCTAGTGACTACTCCGAGTAAAGACTACTGACCTTAACCCGTTAACGG
GTTTTTGGACATTACTAAATAGATTATGAAGAATCCTCTTCCCCTTATTCCCAGTCTGACTCTTC
CAATTTGTAGAGTTGGGCAGGTGAATCAAGATAAATGACTAGGGGATTTCCTGCCAGAGTTCCCT
CCCTTGGGGTGTCATCAATGTTGGCCGATCAGTTAATACTGAAGCTGAACCATCTGCTGCCGCTG
GAGTGCCTTTCCCGCAATATATGTTGTCAGGTAAGTATCCTTAGT
Found at i:320588 original size:15 final size:15
Alignment explanation
Indices: 320570--320651 Score: 60
Period size: 15 Copynumber: 5.3 Consensus size: 15
320560 GTCGTTTAGT
320570 ACGAAGTGCTAAGGA
1 ACGAAGTGCTAAGGA
* * *
320585 ACGAAAGTCGTTTA-GT
1 ACG-AAGT-GCTAAGGA
320601 ACGAAGTGCTAAGGA
1 ACGAAGTGCTAAGGA
* * *
320616 ACGAAAGTCGTTTA-GT
1 ACG-AAGT-GCTAAGGA
320632 ACGAAGTGCTAAGGA
1 ACGAAGTGCTAAGGA
320647 ACGAA
1 ACGAA
320652 AGTCGTTTAG
Statistics
Matches: 49, Mismatches: 12, Indels: 12
0.67 0.16 0.16
Matches are distributed among these distances:
14 6 0.12
15 21 0.43
16 16 0.33
17 6 0.12
ACGTcount: A:0.38, C:0.13, G:0.29, T:0.20
Consensus pattern (15 bp):
ACGAAGTGCTAAGGA
Left flanking sequence: Indices 320070 -- 320569
TTCTTTGTAAAGCGACCTTGACTCCAACATTGCACGGGGCGCTAAAGAGTTATGAATGCAAAGAG
CTCTCTCTTGCCTTATGAGGGGTGGTGGGCTTACTTAATTAAATAGAGTCAAAGGAATTGGCCTA
TGGTACAGCTAAACCTCCATTGGTGGAGCAAAGGAGGAATCCATTTCTCTACTCATTCTATTCAC
TATTCTAGGGCCGATCTGGATCATTCATCAAAAGCATCAGCCTTTCTTTTGCTTTTGGGCAAAGA
TAAAGAGGTGTGCTGCCGCTTGTCTTGAATCACTATGTCCAATTCTTCAGGTTACAATCACCCTT
TGAAGCAATCCTTTTCTTTCTATGCACTTTTATGCCCTCTCTTGCCTCTATTGAATCTTCGGCCT
TGGTTCTTTCCTTTCTATATGCTTGTCCAATCTTTTTCTTTGAAGCAATAGAGTTTTCAAGAAGG
TTTATATCATTTAGTACTTGTGCTAAGGAACGAAAGTCGTTTAGT
Right flanking sequence: Indices 320652 -- 321151
AGTCGTTTAGTACGAAGTGCTTAGGATAAATCCACTTTCAGAAAACCTTTTAGGGACTCATCAAA
GTCTTTTCTTTTCCTCTACAACGGGGAGGGTTTCACCGCTACAAAGCAGTTTCACCAATCTTGTG
AAAAAGACAGGTCTTTTCCAGGCTCGAAAGCCATCCATATCATATATCATTTCAGTCCTAGTTCC
CATATACCCAGTGTAGTAGATGAGTTCATAGCTATTTCTTTCTCCTAGTGACTACTCCGAGTAAA
GACTACTGACCTTAACCCGTTAACGGGTTTTTGGACATTACTAAATAGATTATGAAGAATCCTCT
TCCCCTTATTCCCAGTCTGACTCTTCCAATTTGTAGAGTTGGGCAGGTGAATCAAGATAAATGAC
TAGGGGATTTCCTGCCAGAGTTCCCTCCCTTGGGGTGTCATCAATGTTGGCCGATCAGTTAATAC
TGAAGCTGAACCATCTGCTGCCGCTGGAGTGCCTTTCCCGCAATA
Found at i:433816 original size:36 final size:36
Alignment explanation
Indices: 433775--433847 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
433765 AGAGGGAGGG
433775 ATTCCCCCATCCGAACCATACATCATGAGTATTCCC
1 ATTCCCCCATCCGAACCATACATCATGAGTATTCCC
*
433811 ATTCCCCCATCTGAACCATACATCATGAGTATTCCC
1 ATTCCCCCATCCGAACCATACATCATGAGTATTCCC
433847 A
1 A
433848 GAAAAGCACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.29, C:0.37, G:0.08, T:0.26
Consensus pattern (36 bp):
ATTCCCCCATCCGAACCATACATCATGAGTATTCCC
Left flanking sequence: Indices 433275 -- 433774
GGAGGATCCCGAATCCCGGGGATCCCGAGGCGGCTCCCAAATAAGACGCTAACTTTCAAATCACT
ACGAAAGACAACAATTCCCAACATTCTCATGATTAACCAAAGTCATATCCGTCAAGGTCGGCATC
TCGGATTCCCTTGTTACGGATATCGGCAAAGATCAAATCCGCCCGTTGTTTCACGTAGTTGTTAT
CCGGGTTTTCGGCTATCACTTGCAAGATCTCAAGCAGGCCGGCTTTACTATTAAATTTTTCTTTA
GCGATGAGTTCAAAGACTCTACGCGCCTTGTTGTGGGACGGCATCGGTCCCCCATCAGGTGTCCC
CATGCTATGCACGTACGTGAGGATGACACGATGAAGGGCCCAATACCCGTTCGGTAGGTTTGGAC
TCTCATGGCGGTCATCGGTGTACACAGGAGGTTGTTGCGCCGGTGGATTCGCTACAGGTGGTGCC
TGGTTTACGCCGGTTCCCGAACTTGATGCTTCGGAAGAGGGAGGG
Right flanking sequence: Indices 433848 -- 434347
GAAAAGCACTAACATAATGACTAAAGTAATCTACAAAGCAGACTTTAAAAACCAAAAAAAGGGAT
GAAATACATAAGATCCGTATGATATCCACTACAAAGAAAGAAATCGACCCCAACTTATTACGAAT
CCTCAAACTATAAAGACGACAGAAAAATAGAGAGACCATAAGCACCGTGCAACGAGCTACTATCA
TTTCTTCATTATAGATTGAGATCTTCTTCGAACTTAATGCACAAATAGATGGAATAGCAGCAAAT
AGCATCTTTCTAGCTTGCATATTAGTGGAACTCAATCTCATTTAGAAAGGTTCTATCTATCTTTC
AGCAACTAAACGGGAAGTGGTTTAGGAAAGGACTTTAGAATCAATCGGATGCGCTCGCCCAGCGA
GAAAGGCCCTGACCCTGCCAACCAAGTCAAAAGAAAAAAGAAAGAAGAGAACGAAAGGGTTTACT
TGCTTACTTGTTAGAGTAAGGAGAAAAGAGAACTTCGTATTTTGG
Done.