Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_035962
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: 463792
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Found at i:5181 original size:15 final size:15
Alignment explanation
Indices: 5161--5190 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5151 AACTCGCTCG
*
5161 CCTACTATACTATAC
1 CCTACTATACAATAC
5176 CCTACTATACAATAC
1 CCTACTATACAATAC
5191 ATTAGTAGGG
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:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
CCTACTATACAATAC
Left flanking sequence: Indices 4661 -- 5160
GGTGGCTACCTAAGGAAACTCCGATTCGATCCGCCCCCCAGCTGGGAGGCATCTACCTCATCCCG
ATCACAAGGAGAGGTTCACCATGATGGGGGTACTTTTCTTTTTTCCCTTCCGGAAAGAATGAAAT
GCATAGGGGACCATCCTTTTGTTGTGTTGCGGCATGCTCCTCAGATTTACGGATTCGCAGGGGGC
CTCAGGCCCTACTTAGTTGACTGACAATGACAAAGGCTTGCGAAACTAAGTAGGGCCTTTTGAAT
TGAATCTTAAGTAGTCTATCAGTGGTGCAAAGCGGCTTTGTGCCCCTTTTCAGTAGGGGAGCGAA
TTAGACCTTAGAAAGTCAGCGAACAGCGGTTCTTCTATGTAGGTATGGCCTTCCCCCTTGACTCT
CCTAACGTCGAGCTAAGTGACTTCGTAACCTTTGCGTAGCGTAGTAGAATGAAGGCTACGCACGG
ACGCTCTCTTATCTATTAGCCTAAGCGTCTTCGCTAACTCGCTCG
Right flanking sequence: Indices 5191 -- 5690
ATTAGTAGGGTAGGCTAACCCATAGGTCCTTAGTAGCGTTGACAAAGAAGAACAGCCGGTTAAAA
GACAGTGAATCTTTATAAATATAGATTTATAAAAGATTCTAGAATAATGAATAAGATATTTTATA
TAGGCCAGCTTGACAAGCTACCCTTCCTCTTGATCTTAGGTGCGAAGAGAAAGATCTCTTTTTTA
TGACTTCCACTTATCTATCGATCCCGGCCCGGAAAAGTGACCGACCAGGGCCCTCTTTTTGAATG
AAAGAAAGGCTTTATGAGCCCTAGCCCTGTAAGCCCACACCTGTGTAGAGTAGATCGTTCAACAC
CTGCGGCACAAACCCATTTTTGACCTATTGGTCCTAGTATCATAGGCGACCGAACGGCCGCCCCC
TAATTACTAGACCAACCTGCTGTAATAATTCCATAAACACCTAACGAAGATATGGCAAACAAATA
AAGTAGCCCTATGTTCGAATCTGACAATACCATACCATAATCAAA
Found at i:318556 original size:28 final size:28
Alignment explanation
Indices: 318516--318607 Score: 184
Period size: 28 Copynumber: 3.3 Consensus size: 28
318506 GTGGTTGTTC
318516 CCTCTCCTTTCAGTCGAGTGACTTCGTA
1 CCTCTCCTTTCAGTCGAGTGACTTCGTA
318544 CCTCTCCTTTCAGTCGAGTGACTTCGTA
1 CCTCTCCTTTCAGTCGAGTGACTTCGTA
318572 CCTCTCCTTTCAGTCGAGTGACTTCGTA
1 CCTCTCCTTTCAGTCGAGTGACTTCGTA
318600 CCTCTCCT
1 CCTCTCCT
318608 GACCGAGAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 64 1.00
ACGTcount: A:0.13, C:0.35, G:0.16, T:0.36
Consensus pattern (28 bp):
CCTCTCCTTTCAGTCGAGTGACTTCGTA
Left flanking sequence: Indices 318016 -- 318515
GTCCTATAGGAAGTGGAAGTCAGAAATCCTATCCATCTTTTTCTCTAAATCTAAATATATAATGA
AGAAATCATATCGTGCTTATATTTTAGGATCCTCTAAATCCTCAGACACCGAGACTATGGGGAAT
CCATATTTGTTAACGAAAAGATTCCCAAAATTACAAGAAACCACCTTACCATCTCCGGGCTTCAG
AATTAGAAATTGAACTCCTTCATCCATACAGGAATTCTCTAGAAATAAGAGAACCCTATTTTTTT
ACTTTGCATGCAGTTCCGATTGGAACAAGCATTTTATGATAGAATCGTGCGAAGGGCAAGTCCAG
AAACTTAGAAACGAAATATCTGTCAAAAAAAAGTGAAAAAAAACCGGACGAAGAAATCGGACGGG
CGGTATTCGTCGGCCCGGTTTCTCCCTTTCTTGTCTAGTGTATTAGACTCCATTATAGGTCATTC
GGAAGGGCTCCGTTTCTATTTTAGGGCATAACGTTGTGGTTGTTC
Right flanking sequence: Indices 318608 -- 319107
GACCGAGAAAAAGAAGTTCCAGAGGCATCCTCCATTCATATCGATTTGGGTTTTTCTGCACCATA
TTTTGATCTGCCTCTTCTTCGATCCGGAATTCCCAACAAATCCTTGACTCCTCGAATACAATGGG
ATTTAACACCTGGCAAATCTTTCACTCTACCTCCTCTTATTAACACCATAGAATGTTCCTGCGAA
TTATGACCTTCGCCCGGAATGTGAGCAAATATATCATGTCGATTGCTCAATCGTACTTTGGCTAT
CTTACGTGGAGCTGAATTTGGTTTTTTCGGTGTTCTCGTTGAAACACGCGGGCGTACTCCTTGCT
TCTGGGGACATTGATCCGAAGCTCGAGTACGGTCCGTGCGCCGTTTTTCTTCTCTACCATGACGA
ATCAATTGATTTAATGTAGGCATCGCTCTTTCCTTTGTCCTTCCTCCCTATTTTTGCCCTATCAC
TAGTGATTACTCCCGATCCGAAGCACCCCTTTTCCATTCATAGAG
Found at i:418613 original size:17 final size:17
Alignment explanation
Indices: 418587--418621 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
418577 CTTTTCCTTC
418587 TTTTCGTTTTCGCTCCT
1 TTTTCGTTTTCGCTCCT
* *
418604 TTTTCTTTTTCGTTCCT
1 TTTTCGTTTTCGCTCCT
418621 T
1 T
418622 CCTTAGGTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.26, G:0.09, T:0.66
Consensus pattern (17 bp):
TTTTCGTTTTCGCTCCT
Left flanking sequence: Indices 418087 -- 418586
ACAAGCCGAATCCAAAGTACCTCGACACAAATAAAAAAAGAAGATAAGAAGTGCCTATCCGCTCA
TCAAGTAAAGAAAGGCATCGATACATCGAGGACCAGGGCGGTGAAGTGGGGAAGGTGGACAGTAA
GCTAGTAATTGCGTTAAGAAAAAGCGGTAGAAGGGCGTGAAGGTGTACTTTCTTTCGCGGTTGTT
GGGTATTGTATTAGTGGCAAGCCGACTGACTGATAGGGTCACGAAGAGCCCAACGAATGGAGGAC
CAGAACTGCTTTGCTTAACACACATATAGTTCAGTTCCCTCAATTCATCACCAACATGCTTGATT
CCAATCTCGAGGGACTGAACCCGCTCCTCGAGAATGAAGCTTGCTGGCGATACCGGTATCCATCT
ATAGCCGTTAGTTCATCGGTGTCGGGGGAGTTTGGCCCCAGCCTATTGTCCCTTTCCCCATGGGG
CGGGCTCCTATGATAGGGTCTAGGGAAATCTACCTCTTTTCCTTC
Right flanking sequence: Indices 418622 -- 419121
CCTTAGGTCTGTCTCCTTCGGCGGATCTTGGGACTCCTTTTGCTGGCTTCGGGCTTTGATCTTTC
TCTTATCTGGTGTGGCGTCCTGCTTCATCTTTAGGTGTCCTTATTGGTCTCTATCCGCCAGTGCG
TAGCTCCGTAACTTTCCCTCTCCCCTGCGGTAGCCGGAGCTCGCACAACCCAAAAAAGAAAAACA
AACAAAGCGTGGTTCATGGTAGGCTCTGATAATGGTTAGGGTAGGGGTTTAGTAAAGGATCTCCA
GCATGGAACGATGCTCCTTCTCATGCCCATTTGCCAACATCCAGAAAACCCGCCTTCTCACGCTA
ATGAAAGCCCTTCTTACAGAACAACTAGTGCGAGAGCCTTTCCGTCCCCTATACAGAAGGAGACT
TTCTTTTGTCTAACTCTCCAGAAGAGACCAAGTCGTTTACTTCATATTTGTGACTCTTGCCAACA
ATTGGTTCTTTAACTGACACTTGACTCGAACCGCTTGCCATATCT
Done.