Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold273
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 639416
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 15802 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:613212 original size:45 final size:46
Alignment explanation
Indices: 613086--613212 Score: 107
Period size: 45 Copynumber: 2.7 Consensus size: 46
613076 GTTTGATATG
*
613086 ATCTGCTCTACTGTAACTTCAGAGAGATAACATCTATAATCCATAGCTTCA
1 ATCTGCTCTACTGTAACTTCAGAGAGATAAGATC----A-CCATAGCTTCA
* * * * *
613137 ATCTGTTCCACTGCAACTTCAG-GAAAATAAGATC-CGC-TATCTTCA
1 ATCTGCTCTACTGTAACTTCAGAG-AGATAAGATCAC-CATAGCTTCA
*
613182 GTCTGCTCTACTGTAACTTCAGAGAGATAAG
1 ATCTGCTCTACTGTAACTTCAGAGAGATAAG
613213 GTTTGTATCT
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
45 32 0.52
46 2 0.03
50 1 0.02
51 27 0.44
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (46 bp):
ATCTGCTCTACTGTAACTTCAGAGAGATAAGATCACCATAGCTTCA
Found at i:613690 original size:220 final size:217
Alignment explanation
Indices: 613393--613818 Score: 636
Period size: 220 Copynumber: 1.9 Consensus size: 217
613383 TGCAACTTCA
* * * *
613393 AGGGGATAAGGCTGGTGCTTTCGATCTGCTTCACTGCTAGTATAGGAAGACAAGATTTACAATCT
1 AGGGGATAAGGCTGGTGCTTTCGATCTGCTTCACTGCCAGTACAGAAAGACAAGATCTACAATCT
* *
613458 TCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTACCT
66 TCAACCTACTCCACTGCTACTCAGGGAGATAGGACTAGTGGCTTAAATCTGCTT-CCTACTACCT
* * * * * *
613523 TGGGAAGATAAGATTCACCGTCATCGATCTGTTCCACTACTGCTTAGGGAGACAGGATCTGCAAT
130 TCGAAAGATAAAATTCACCATCATCG-TCTGCTCCACTACTGCTTAGGGAAACAGGATCTGCAAT
613588 CTTCAACCTACTCCAGTATTGCTC
194 CTTCAACCTACTCCAGTATTGCTC
**
613612 AGGGAGATAAGGCTGGTGCTTTCGATCTGCTTCACTGCCAGTACAGAAAGGTAAGATCTACAATC
1 AGGG-GATAAGGCTGGTGCTTTCGATCTGCTTCACTGCCAGTACAGAAAGACAAGATCTACAATC
* * * *
613677 TTCGACCTACTCCACTGCTACTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCTACTATCT
65 TTCAACCTACTCCACTGCTACTCAGGGAGATAGGACTAGTGGCTTAAATCTGCTTCCTACTACCT
* * *
613742 TCGAAAGATAAAATTTACCATCTTCGTCTGCTCCACTACTGCTTAGGGAAACAGGATTTGCAATC
130 TCGAAAGATAAAATTCACCATCATCGTCTGCTCCACTACTGCTTAGGGAAACAGGATCTGCAATC
613807 TTCAACCTACTC
195 TTCAACCTACTC
613819 TACTACTACT
Statistics
Matches: 185, Mismatches: 21, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
218 48 0.26
219 33 0.18
220 104 0.56
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (217 bp):
AGGGGATAAGGCTGGTGCTTTCGATCTGCTTCACTGCCAGTACAGAAAGACAAGATCTACAATCT
TCAACCTACTCCACTGCTACTCAGGGAGATAGGACTAGTGGCTTAAATCTGCTTCCTACTACCTT
CGAAAGATAAAATTCACCATCATCGTCTGCTCCACTACTGCTTAGGGAAACAGGATCTGCAATCT
TCAACCTACTCCAGTATTGCTC
Found at i:614213 original size:24 final size:24
Alignment explanation
Indices: 614162--614214 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
614152 TACCCTTACT
* *
614162 GTAATCTTCAAAGTTCAATCCGCT
1 GTAATCTTCAAAGTTCAATCCACC
* *
614186 GTAATCTTCAAGGTTCAGTCCACC
1 GTAATCTTCAAAGTTCAATCCACC
614210 GTAAT
1 GTAAT
614215 TTTGGGACGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (24 bp):
GTAATCTTCAAAGTTCAATCCACC
Found at i:614877 original size:108 final size:108
Alignment explanation
Indices: 614685--614890 Score: 295
Period size: 108 Copynumber: 1.9 Consensus size: 108
614675 GAAAAATGCT
* *
614685 TGAAAAAGATTATCATAATGGACAAGATCAAATTTTATCGAGAGCAAAGCTCTAAACAAATAAAT
1 TGAAAAAGATTATCACAATGGACAAGATCAAATTTTATCGAGAGCAAAGCTCGAAACAAATAAAT
* *
614750 TAATCAGGATAGCAAATTTTGCTAAAATTCAAAGTGAATAAGA
66 TAATCAAGATAGCAAATTTTGCTAAAATACAAAGTGAATAAGA
** * * * * *
614793 TGAAAAAGATTATCACAATGGACAAGATGGAATTTTGTTGAGAGCAAAGCTCGAGACGAATAGAT
1 TGAAAAAGATTATCACAATGGACAAGATCAAATTTTATCGAGAGCAAAGCTCGAAACAAATAAAT
* *
614858 TAATCAAGATAGCATATTTTGCTAGAATACAAA
66 TAATCAAGATAGCAAATTTTGCTAAAATACAAA
614891 AATGATAATA
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
108 85 1.00
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (108 bp):
TGAAAAAGATTATCACAATGGACAAGATCAAATTTTATCGAGAGCAAAGCTCGAAACAAATAAAT
TAATCAAGATAGCAAATTTTGCTAAAATACAAAGTGAATAAGA
Found at i:628200 original size:23 final size:23
Alignment explanation
Indices: 628169--628213 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
628159 TACAATCAAT
628169 ATTACACATATC-AACAAGCCATA
1 ATTACACAT-TCAAACAAGCCATA
*
628192 ATTAGACATTCAAAACAAGCCA
1 ATTACACATTC-AAACAAGCCA
628214 AAATAAGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.11
23 8 0.42
24 9 0.47
ACGTcount: A:0.49, C:0.24, G:0.07, T:0.20
Consensus pattern (23 bp):
ATTACACATTCAAACAAGCCATA
Found at i:634747 original size:33 final size:33
Alignment explanation
Indices: 634710--634852 Score: 101
Period size: 33 Copynumber: 4.3 Consensus size: 33
634700 TGGTCCAACC
634710 ATGGTCTTACGTTCATAGTGCCATAACCCAGTT
1 ATGGTCTTACGTTCATAGTGCCATAACCCAGTT
* * * *
634743 ATGGTCTTATC-ATCAGAATGCCATAGCCCA-TCT
1 ATGGTCTTA-CGTTCATAGTGCCATAACCCAGT-T
* * * * * *** ***
634776 ATGGTCTTACATATAAACACTGCCTTGGTCCAACC
1 ATGGTCTTACGT-T-CATAGTGCCATAACCCAGTT
634811 ATGGTCTTACGTTCATAGTGCCATAACCCAGTT
1 ATGGTCTTACGTTCATAGTGCCATAACCCAGTT
634844 ATGGTCTTA
1 ATGGTCTTA
634853 TCTGGCAATT
Statistics
Matches: 80, Mismatches: 24, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
32 2 0.03
33 53 0.66
34 3 0.04
35 22 0.28
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (33 bp):
ATGGTCTTACGTTCATAGTGCCATAACCCAGTT
Found at i:634805 original size:101 final size:101
Alignment explanation
Indices: 634615--634854 Score: 390
Period size: 101 Copynumber: 2.4 Consensus size: 101
634605 AATTCATCCT
* * * * *
634615 TTACATTCGTAGTGTCATAACCCAATTATGGTCTTGTCATCAGAATGCCATAGCCCAGCTACGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTACGGT
*
634680 CTTACATATAAATAATGCCATGGTCCAACCATGGTC
66 CTTACATATAAACAATGCCATGGTCCAACCATGGTC
* *
634716 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCATCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTACGGT
* *
634781 CTTACATATAAACACTGCCTTGGTCCAACCATGGTC
66 CTTACATATAAACAATGCCATGGTCCAACCATGGTC
634817 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
634855 TGGCAATTCA
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 129 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.31
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTACGGT
CTTACATATAAACAATGCCATGGTCCAACCATGGTC
Done.