Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1225
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: 2333
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Found at i:534 original size:199 final size:199
Alignment explanation
Indices: 194--1556 Score: 2636
Period size: 199 Copynumber: 6.8 Consensus size: 199
184 ATGATTTCTC
194 ACACCGTTTTACGAAAACTGAGAACAGAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACC
1 ACACCGTTTTACGAAAACTGAGAACAGAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACC
259 ACCTTTAGCGGTGTTTTTCCCTTAGCGCCACAAAACCCATTAAATTCACAGCCAAAAACTGCACC
66 ACCTTTAGCGGTGTTTTTCCCTTAGCGCCACAAAACCCATTAAATTCACAGCCAAAAACTGCACC
324 GTTTTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGGCAA
131 GTTTTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGGCAA
389 AACG
196 AACG
393 ACACCGTTTTACGAAAACTGAGAACAGAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACC
1 ACACCGTTTTACGAAAACTGAGAACAGAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACC
458 ACCTTTAGCGGTGTTTTTCCCTTAGCGCCACAAAACCCATTAAATTCACAGCCAAAAACTGCACC
66 ACCTTTAGCGGTGTTTTTCCCTTAGCGCCACAAAACCCATTAAATTCACAGCCAAAAACTGCACC
523 GTTTTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGGCAA
131 GTTTTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGGCAA
588 AACG
196 AACG
592 ACACCGTTTTACGAAAACTGAGAACAGAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACC
1 ACACCGTTTTACGAAAACTGAGAACAGAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACC
657 ACCTTTAGCGGTGTTTTTCCCTTAGCGCCACAAAACCCATTAAATTCACAGCCAAAAACTGCACC
66 ACCTTTAGCGGTGTTTTTCCCTTAGCGCCACAAAACCCATTAAATTCACAGCCAAAAACTGCACC
722 GTTTTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGGCAA
131 GTTTTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGGCAA
787 AACG
196 AACG
791 ACACCGTTTTACGAAAACTGAGAACAGAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACC
1 ACACCGTTTTACGAAAACTGAGAACAGAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACC
856 ACCTTTAGCGGTGTTTTTCCCTTAGCGCCACAAAACCCATTAAATTCACAGCCAAAAACTGCACC
66 ACCTTTAGCGGTGTTTTTCCCTTAGCGCCACAAAACCCATTAAATTCACAGCCAAAAACTGCACC
921 GTTTTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGGCAA
131 GTTTTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGGCAA
986 AACG
196 AACG
990 ACACCGTTTTACGAAAACTGAGAACAGAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACC
1 ACACCGTTTTACGAAAACTGAGAACAGAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACC
1055 ACCTTTAGCGGTGTTTTTCCCTTAGCGCCACAAAACCCATTAAATTCACAGCCAAAAACTGCACC
66 ACCTTTAGCGGTGTTTTTCCCTTAGCGCCACAAAACCCATTAAATTCACAGCCAAAAACTGCACC
1120 GTTTTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGGCAA
131 GTTTTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGGCAA
1185 AACG
196 AACG
1189 ACACCGTTTTACGAAAACTGAGAACAGAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACC
1 ACACCGTTTTACGAAAACTGAGAACAGAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACC
*
1254 ACCTTTAGCGGCGTTTTTCCCTTAGCGCCACAAAACCCATTAAATTCACAGCCAAAAACTGCACC
66 ACCTTTAGCGGTGTTTTTCCCTTAGCGCCACAAAACCCATTAAATTCACAGCCAAAAACTGCACC
1319 GTTTTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGGCAA
131 GTTTTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGGCAA
1384 AACG
196 AACG
1388 ACACCGTTTTACGAAAACTGAGAACAGAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACC
1 ACACCGTTTTACGAAAACTGAGAACAGAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACC
* * * * * * *
1453 ACATTTAGCGGCGTTTTTACCGTAGCTCCGCAAAACCCATTAAATTCGCAGCCAAAAACTGCACC
66 ACCTTTAGCGGTGTTTTTCCCTTAGCGCCACAAAACCCATTAAATTCACAGCCAAAAACTGCACC
* *
1518 GTTTTGTCTTCATTATTAAGAATATTTTGTGGCGTTTTT
131 GTTTTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTT
1557 GTTCAAAACG
Statistics
Matches: 1155, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
199 1155 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (199 bp):
ACACCGTTTTACGAAAACTGAGAACAGAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACC
ACCTTTAGCGGTGTTTTTCCCTTAGCGCCACAAAACCCATTAAATTCACAGCCAAAAACTGCACC
GTTTTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGGCAA
AACG
Found at i:1736 original size:47 final size:48
Alignment explanation
Indices: 1673--1771 Score: 146
Period size: 47 Copynumber: 2.1 Consensus size: 48
1663 CATAGTTTTG
* * **
1673 TTTAGGTAATATTTATAAAAATTAGATAAAATTATCAATTTTAGT-TT
1 TTTAAGTAATATTTATAAAAATTAGATAAAAATAAAAATTTTAGTGTT
*
1720 TTTAAGTAATATTTATAAAAATTAGGTAAAAATAAAAATTTTAGTGTT
1 TTTAAGTAATATTTATAAAAATTAGATAAAAATAAAAATTTTAGTGTT
1768 TTTA
1 TTTA
1772 TTTCTTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
47 40 0.87
48 6 0.13
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.45
Consensus pattern (48 bp):
TTTAAGTAATATTTATAAAAATTAGATAAAAATAAAAATTTTAGTGTT
Found at i:1809 original size:9 final size:9
Alignment explanation
Indices: 1795--1843 Score: 73
Period size: 9 Copynumber: 5.4 Consensus size: 9
1785 TTTCTTTTAT
*
1795 TTTTTATAA
1 TTTTTACAA
1804 TTTTTACAA
1 TTTTTACAA
1813 TTTTTTACAA
1 -TTTTTACAA
1823 -TTTTACAA
1 TTTTTACAA
1831 TTTTTACAA
1 TTTTTACAA
1840 TTTT
1 TTTT
1844 AAATTATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
8 8 0.22
9 20 0.54
10 9 0.24
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTTTACAA
Found at i:1815 original size:19 final size:18
Alignment explanation
Indices: 1793--1848 Score: 80
Period size: 17 Copynumber: 3.2 Consensus size: 18
1783 TTTTTCTTTT
*
1793 ATTTTTTATAATTTTTACA
1 ATTTTTTACAA-TTTTACA
1812 ATTTTTTACAATTTTACA
1 ATTTTTTACAATTTTACA
1830 A-TTTTTACAATTTTA-A
1 ATTTTTTACAATTTTACA
1846 ATT
1 ATT
1849 ATTATATTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
16 2 0.06
17 15 0.43
18 8 0.23
19 10 0.29
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTTTACAATTTTACA
Found at i:1816 original size:8 final size:8
Alignment explanation
Indices: 1805--1848 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
1795 TTTTTATAAT
1805 TTTTACAA
1 TTTTACAA
1813 TTTTTTACAA
1 --TTTTACAA
1823 TTTTACAA
1 TTTTACAA
1831 TTTTTACAA
1 -TTTTACAA
1840 TTTTA-AA
1 TTTTACAA
1847 TT
1 TT
1849 ATTATATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 4 0.12
8 13 0.39
9 8 0.24
10 8 0.24
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (8 bp):
TTTTACAA
Found at i:1862 original size:21 final size:20
Alignment explanation
Indices: 1837--1891 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 20
1827 ACAATTTTTA
1837 CAATTTTAAATTATT-ATATT
1 CAATTTTAAATTATTCATA-T
*
1857 CAAATTATTATA-TATTGCATAT
1 C-AATT-TTAAATTATT-CATAT
1879 CAATTTTAAATTA
1 CAATTTTAAATTA
1892 ATAATCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
20 5 0.18
21 14 0.50
22 6 0.21
23 3 0.11
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (20 bp):
CAATTTTAAATTATTCATAT
Found at i:2117 original size:89 final size:89
Alignment explanation
Indices: 1940--2166 Score: 273
Period size: 89 Copynumber: 2.6 Consensus size: 89
1930 TATAAAGAAC
* * * * * *
1940 TTATTTAATATATCAATTAAAAAGTACTAATTAATCCAAATCTTAAACCCTAACTCGACCCCAAA
1 TTATTTAATATATAAATTAAAAAGTACTAATTAATCTAAAACCTAAACCCAAACTCGAACCCAAA
*
2005 TCCCTAACCCCTAACCCCTAAACT
66 TCCCGAACCCCTAACCCCTAAACT
* *
2029 TTATTTAATATAT-AATTAAAAAGCACTAATTAATCTAAACCCTAAACCCAAAAC-CTGAAACCC
1 TTATTTAATATATAAATTAAAAAGTACTAATTAATCTAAAACCTAAACCC-AAACTC-G-AACCC
* *
2092 -GA-CCACGAATCCCTAACCCCTAAACT
63 AAATCC-CGAACCCCTAACCCCTAAACT
* *
2118 TTATTTAATATATAAATTAAAAAATAATAATTAATCTAAAACCTAAACC
1 TTATTTAATATATAAATTAAAAAGTACTAATTAATCTAAAACCTAAACC
2167 ATATCCCAAT
Statistics
Matches: 120, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
88 35 0.29
89 50 0.42
90 35 0.29
ACGTcount: A:0.45, C:0.25, G:0.03, T:0.28
Consensus pattern (89 bp):
TTATTTAATATATAAATTAAAAAGTACTAATTAATCTAAAACCTAAACCCAAACTCGAACCCAAA
TCCCGAACCCCTAACCCCTAAACT
Done.