Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2768
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: 32810
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Found at i:9454 original size:20 final size:19
Alignment explanation
Indices: 9431--9567 Score: 78
Period size: 20 Copynumber: 6.9 Consensus size: 19
9421 ATGCACATTA
9431 GTGCCCCTGTTTGCACTTT
1 GTGCCCCTGTTTGCACTTT
* ***
9450 GGTGCCCTTAAATGCACATTT
1 -GTGCCCCTGTTTGCAC-TTT
* ****
9471 GTGCCACTGAACACACATTT
1 GTGCCCCTGTTTGCAC-TTT
*
9491 GTGCCCCTGTTCGCACTTT
1 GTGCCCCTGTTTGCACTTT
* * *
9510 GGTACCCCTGTATACACTTT
1 -GTGCCCCTGTTTGCACTTT
9530 AGTGTCCCC-GTTTGCACGTTT
1 -GTG-CCCCTGTTTGCAC-TTT
*
9551 GTGCCCCTGTTCGCACT
1 GTGCCCCTGTTTGCACT
9568 ACGATGCCCT
Statistics
Matches: 90, Mismatches: 22, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
19 8 0.09
20 72 0.80
21 10 0.11
ACGTcount: A:0.15, C:0.31, G:0.20, T:0.34
Consensus pattern (19 bp):
GTGCCCCTGTTTGCACTTT
Found at i:9552 original size:60 final size:60
Alignment explanation
Indices: 9488--9637 Score: 212
Period size: 60 Copynumber: 2.5 Consensus size: 60
9478 TGAACACACA
* * * *
9488 TTTGTGCCCCTGTTCGCACTTTGGTACCCCTGTATACACTTTAGTGTCCCCGTTTGCACG
1 TTTGTGCCCCTGTTCGCACTTTGGTGCCCCTGTAAACAATTCAGTGTCCCCGTTTGCACG
** * *
9548 TTTGTGCCCCTGTTCGCACTACGATGCCCTTGTAAACAATTCAGTGTCCCCGTTTGCACG
1 TTTGTGCCCCTGTTCGCACTTTGGTGCCCCTGTAAACAATTCAGTGTCCCCGTTTGCACG
*
9608 TTTGTG-CCCTGTTCGCACTTTAGTGCCCCT
1 TTTGTGCCCCTGTTCGCACTTTGGTGCCCCT
9638 ATTCTGTATA
Statistics
Matches: 77, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 19 0.25
60 58 0.75
ACGTcount: A:0.13, C:0.32, G:0.20, T:0.35
Consensus pattern (60 bp):
TTTGTGCCCCTGTTCGCACTTTGGTGCCCCTGTAAACAATTCAGTGTCCCCGTTTGCACG
Found at i:11709 original size:42 final size:43
Alignment explanation
Indices: 11658--11760 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 43
11648 TTGAGATTTG
*
11658 CATGTAAGACCATGTCTGAGACATTAGCATC-ATATATGATTA
1 CATGTAAGACCATGTCTGAGACAGTAGCATCGATATATGATTA
* * * * * * *
11700 CATGTAAGACCCTGTTTGGGACAGTGGCATCGTTGTTTGATTA
1 CATGTAAGACCATGTCTGAGACAGTAGCATCGATATATGATTA
* *
11743 CTTGTAAGACCACGTCTG
1 CATGTAAGACCATGTCTG
11761 GGACGTTGGC
Statistics
Matches: 48, Mismatches: 12, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
42 26 0.54
43 22 0.46
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.32
Consensus pattern (43 bp):
CATGTAAGACCATGTCTGAGACAGTAGCATCGATATATGATTA
Found at i:17775 original size:8 final size:8
Alignment explanation
Indices: 17762--17786 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
17752 TTTTTAATGA
17762 TATTTTAT
1 TATTTTAT
17770 TATTTTAT
1 TATTTTAT
17778 TATTTTAT
1 TATTTTAT
17786 T
1 T
17787 TAGCATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:23670 original size:44 final size:44
Alignment explanation
Indices: 23599--23740 Score: 214
Period size: 44 Copynumber: 3.2 Consensus size: 44
23589 TATGTGATAT
* * *
23599 CGTGTAAGACCACGTCTAGGACATTGGCATC-ATATTGAAATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-ATTGAGATTTA
* *
23643 CGTGTAAGATCACGTCTGGGACGTTGGCATCGAATTTAGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGAGATTTA
23687 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGAGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGAGATTTA
*
23731 TGTGTAAGAC
1 CGTGTAAGAC
23741 TCTGTCTGGG
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 88 0.99
45 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (44 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGAGATTTA
Found at i:26194 original size:98 final size:98
Alignment explanation
Indices: 26050--26334 Score: 313
Period size: 101 Copynumber: 2.8 Consensus size: 98
26040 ACAACCAAGG
* * **
26050 TGGTGGAGCCATTCTTTATGGCTCCACCAAAATAAAATATCA-TTTTTAAAATTTTGGATTGAAA
1 TGGTGGCGCCATTCTTTATGGCTCCACC-AAATAAAATATTATTTTTTAAAATTTTAAATTGAAA
*
26114 AACAACACATTTAAAAAAAATCCATAC-AGTACAC
65 AAAAACACATTTAAAAAAAAT-CATACAAGTACAC
* * * * * *
26148 TGGTGGCGTCATTCTTTATAGCTCCACCAAATAAAAAATTATTTTTTTAAATTTTAAAATAAAAA
1 TGGTGGCGCCATTCTTTATGGCTCCACCAAATAAAATATTATTTTTTAAAATTTTAAATTGAAAA
* * * * *
26213 AATAATAGATTTAAAAATATATTATACATAGTATAC
66 AA-AACACATTTAAAAA-AAATCATACA-AGTACAC
* * *
26249 TGGTGGCGCCATTCTATATGGATCTACCAAATAAAATATTATTTTTTAAAATTTTTAAATTTGAA
1 TGGTGGCGCCATTCTTTATGGCTCCACCAAATAAAATATTATTTTTTAAAA-TTTTAAA-TTGAA
26314 AAAAAACCACATTTAAAAAAA
64 AAAAAA-CACATTTAAAAAAA
26335 CCTTAGTAAT
Statistics
Matches: 151, Mismatches: 28, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
97 11 0.07
98 44 0.29
99 16 0.11
100 3 0.02
101 50 0.33
102 10 0.07
103 17 0.11
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (98 bp):
TGGTGGCGCCATTCTTTATGGCTCCACCAAATAAAATATTATTTTTTAAAATTTTAAATTGAAAA
AAAACACATTTAAAAAAAATCATACAAGTACAC
Found at i:29160 original size:62 final size:62
Alignment explanation
Indices: 29084--29210 Score: 227
Period size: 62 Copynumber: 2.0 Consensus size: 62
29074 TATTCTAAAT
29084 TTTAATTACTATCTTATCTATGATGTTTCATACAAAGTTCAAAATTATGGGGTATGGGTCGA
1 TTTAATTACTATCTTATCTATGATGTTTCATACAAAGTTCAAAATTATGGGGTATGGGTCGA
* * *
29146 TTTAATTATTATCTTATCTATGATGTTTCCTACGAAGTTCAAAATTATGGGGTATGGGTCGA
1 TTTAATTACTATCTTATCTATGATGTTTCATACAAAGTTCAAAATTATGGGGTATGGGTCGA
29208 TTT
1 TTT
29211 CACTTCACAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (62 bp):
TTTAATTACTATCTTATCTATGATGTTTCATACAAAGTTCAAAATTATGGGGTATGGGTCGA
Found at i:29807 original size:14 final size:13
Alignment explanation
Indices: 29788--29824 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
29778 TCTGCGGTAG
29788 GGTTTAGGGTTATT
1 GGTTTAGGGTTA-T
29802 GGTTTAGGGTTAT
1 GGTTTAGGGTTAT
29815 GG-TTAGGGTT
1 GGTTTAGGGTT
29825 TTAGTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 8 0.35
13 3 0.13
14 12 0.52
ACGTcount: A:0.14, C:0.00, G:0.41, T:0.46
Consensus pattern (13 bp):
GGTTTAGGGTTAT
Found at i:30128 original size:93 final size:92
Alignment explanation
Indices: 29968--30245 Score: 366
Period size: 93 Copynumber: 3.0 Consensus size: 92
29958 AATTAATTAA
29968 TACTTGAGTAATTTAATTAAAAAATTTTAAAATCAGATTAGGATTTAGAGTTAAGGGTTTTTAAG
1 TACTTGAGTAATTTAATT-AAAAA-TTTAAAATCAGATTAGGATTTAGAGTTAAGGGTTTTTAAG
*
30033 AAAAAATCTAATAAACTAGGGTTTGAGGT
64 AAAAAATCTAATAAATTAGGGTTTGAGGT
*
30062 TACTTGAGTAATTTAATTAAAAATTTAAAAATCAGATTAGGATTTAGAGTTAAGGGTTTTTCAGA
1 TACTTGAGTAATTTAATTAAAAATTT-AAAATCAGATTAGGATTTAGAGTTAAGGGTTTTTAAGA
* *
30127 AAAAATCAAATAAATTAGGG-TTCAGGGT
65 AAAAATCTAATAAATTAGGGTTTGA-GGT
* * * * * * *
30155 TACTTGAGTAAATTAATTATAAATTTATAAT-AAATTA-G-TTTAGGGTTTAGGGTTTTTAAGTA
1 TACTTGAGTAATTTAATTAAAAATTTAAAATCAGATTAGGATTTAGAGTTAAGGGTTTTTAAGAA
* *
30217 AAAACCTAAATAAATTAGGGTTTGGGGT
66 AAAATCT-AATAAATTAGGGTTTGAGGT
30245 T
1 T
30246 TACGGTTACT
Statistics
Matches: 164, Mismatches: 16, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
89 25 0.15
90 17 0.10
91 7 0.04
92 10 0.06
93 87 0.53
94 18 0.11
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.37
Consensus pattern (92 bp):
TACTTGAGTAATTTAATTAAAAATTTAAAATCAGATTAGGATTTAGAGTTAAGGGTTTTTAAGAA
AAAATCTAATAAATTAGGGTTTGAGGT
Found at i:30130 original size:46 final size:46
Alignment explanation
Indices: 29987--30130 Score: 111
Period size: 46 Copynumber: 3.1 Consensus size: 46
29977 AATTTAATTA
*
29987 AAAAATTTTAAAATCAGATTAGGATTTAGAGTTAAGGGTTTTTAAG
1 AAAAATTTAAAAATCAGATTAGGATTTAGAGTTAAGGGTTTTTAAG
* * * * * *
30033 AAAAAATCTAATAAA-C----TAGGGTTT-GAGGTTACTTGAGTAATTTAATT
1 -AAAAATTTAA-AAATCAGATTAGGATTTAGA-GTTA--AGGGT-TTTTAA-G
*
30080 AAAAATTTAAAAATCAGATTAGGATTTAGAGTTAAGGGTTTTTCAG
1 AAAAATTTAAAAATCAGATTAGGATTTAGAGTTAAGGGTTTTTAAG
30126 AAAAA
1 AAAAA
30131 ATCAAATAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 25
0.65 0.13 0.23
Matches are distributed among these distances:
42 2 0.03
43 11 0.15
45 6 0.08
46 20 0.28
47 13 0.18
48 6 0.08
50 11 0.15
51 2 0.03
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.35
Consensus pattern (46 bp):
AAAAATTTAAAAATCAGATTAGGATTTAGAGTTAAGGGTTTTTAAG
Found at i:30507 original size:126 final size:126
Alignment explanation
Indices: 30282--30567 Score: 464
Period size: 126 Copynumber: 2.3 Consensus size: 126
30272 TAATTTAAAG
* * * * *
30282 AAGCTCCGACGTGGACGCGCTTTTACTACAGTGGCTCCTGAGAAAGTAATTTCGAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
*
30347 CTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
66 CTGAGCAAACAATGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
* * *
30408 AAGCTCCCACGTGGACACGCTTTTGTTACAGTAGCTCCTGAAAAAATAATTTTGAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
30473 CTGAGCAAACAATGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
66 CTGAGCAAACAATGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
* * *
30534 ATGCTTCCACGTGGACGTGCTTTTGCTACAGTAG
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAG
30568 TTGAACGTTA
Statistics
Matches: 146, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 146 1.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (126 bp):
AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
CTGAGCAAACAATGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
Found at i:30793 original size:34 final size:35
Alignment explanation
Indices: 30738--30810 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 35
30728 TTATATTAAA
* *
30738 AATGTAAAAGTAAATTTCTATTTTAGTACATGAAAT
1 AATGTAAAAG-AAATTTCTATTTCAGTACATCAAAT
*
30774 AATGTAAAAG-AATTTCTATTTCATTACATCAAAT
1 AATGTAAAAGAAATTTCTATTTCAGTACATCAAAT
30808 AAT
1 AAT
30811 ATCAAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 24 0.71
36 10 0.29
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.38
Consensus pattern (35 bp):
AATGTAAAAGAAATTTCTATTTCAGTACATCAAAT
Done.