Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1381
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: 20963
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Found at i:18924 original size:1 final size:1
Alignment explanation
Indices: 18918--19017 Score: 119
Period size: 1 Copynumber: 100.0 Consensus size: 1
18908 GGCGTCCTCC
* * * *
18918 AAAAAAAAAAAAAACAACAAAAAAAAAACAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
18983 AAACAAAAACAAAAAAAACAAACAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19018 GGGGGTCCGG
Statistics
Matches: 81, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 81 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:18942 original size:19 final size:18
Alignment explanation
Indices: 18918--19017 Score: 132
Period size: 19 Copynumber: 5.4 Consensus size: 18
18908 GGCGTCCTCC
18918 AAAAAAAAAAAAAACAACA
1 AAAAAAAAAAAAAACAA-A
18937 AAAAAAAAACAAAAA-AAA
1 AAAAAAAAA-AAAAACAAA
*
18955 AAAAAAAAAACAAA-AAA
1 AAAAAAAAAAAAAACAAA
18972 AAAAAAAAAAAAAACAAA
1 AAAAAAAAAAAAAACAAA
*
18990 AACAAAAAAAACAAACAAA
1 AA-AAAAAAAAAAAACAAA
19009 ACAAAAAAA
1 A-AAAAAAA
19018 GGGGGTCCGG
Statistics
Matches: 74, Mismatches: 3, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
17 20 0.27
18 15 0.20
19 33 0.45
20 6 0.08
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAACAAA
Found at i:18971 original size:40 final size:40
Alignment explanation
Indices: 18918--19017 Score: 148
Period size: 40 Copynumber: 2.5 Consensus size: 40
18908 GGCGTCCTCC
* *
18918 AAAAAAAA-AAAAAACAACAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAACAAAAAAAAAAAAAAAAAAAACAAAAAAAAAA
*
18957 AAAAAAAACAAAAAAAAAAAAAAAAAAAACAAAAACAAAA
1 AAAAAAAACAAAAAAAAAAAAAAAAAAAACAAAAAAAAAA
* *
18997 AAAACAAACAAAACAAAAAAA
1 AAAAAAAACAAAAAAAAAAAA
19018 GGGGGTCCGG
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 8 0.15
40 47 0.85
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (40 bp):
AAAAAAAACAAAAAAAAAAAAAAAAAAAACAAAAAAAAAA
Found at i:20492 original size:29 final size:28
Alignment explanation
Indices: 20453--20898 Score: 239
Period size: 27 Copynumber: 15.8 Consensus size: 28
20443 TCACCCTTCA
* *
20453 AAAGTCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-CTTTTTC
*
20482 AAAGCCCACAAGTCAGTGGCATTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTTTTTC
*
20510 GAAAGCCCACAAGTCAGTGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGC-ACTTTTTC
* *
20538 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA--CTTTTTC
* * * *
20568 GAAGCCCACAAGTCGGTGG-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACTTTTTC
* * *
20595 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA--CTTTTTC
* * * *
20625 TTTTGTAAGCTCACAACTC--TAAGCAC-TTTTC
1 -----AAAGCCCACAAGTCAGT-GGCACTTTTTC
* *
20656 --AGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCA-CTTTTTC
*
20683 AAAGCCCACAAGTCAGTGGCATATTTTTC
1 AAAGCCCACAAGTCAGTGGCA-CTTTTTC
* *
20712 AAAAGCCCACAAGT-AGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGC-ACTTTTTC
* * *
20740 AAAG-CCACAAGTTAGTGGCACCCTGTTC
1 AAAGCCCACAAGTCAGTGGCA-CTTTTTC
20768 AAAAGCCCACAAGTCAGTGGCA-TATTTTC
1 -AAAGCCCACAAGTCAGTGGCACT-TTTTC
* * *
20797 AAAAGCCCAC-ACTCA--GGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGC-ACTTTTTC
*
20823 AAAGCCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGC-ACTTTTTC
* **
20850 AAAGCCCACAAATCAGTGGCACCCTTT-
1 AAAGCCCACAAGTCAGTGGCACTTTTTC
* *
20877 AAAGCCCA-AAATCGGTGGCACT
1 AAAGCCCACAAGTCAGTGGCACT
20899 CCATCTTAAC
Statistics
Matches: 334, Mismatches: 47, Indels: 75
0.73 0.10 0.16
Matches are distributed among these distances:
24 9 0.03
25 12 0.04
26 36 0.11
27 87 0.26
28 28 0.08
29 87 0.26
30 54 0.16
31 5 0.01
32 1 0.00
33 1 0.00
34 3 0.01
35 11 0.03
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCACTTTTTC
Found at i:20553 original size:27 final size:27
Alignment explanation
Indices: 20447--20586 Score: 109
Period size: 29 Copynumber: 4.9 Consensus size: 27
20437 CATTCCTCAC
* *
20447 CCTTCAAAAGTCCACAAGTCAGTGGCATTT
1 CCTTC-AAAGCCCACAAGTCAGTGGCA--A
** *
20477 TTTTCAAAGCCCACAAGTCAGTGGCATT
1 CCTTCAAAGCCCACAAGTCAGTGGCA-A
**
20505 TTTTCGAAAGCCCACAAGTCAGTGGCAA
1 CCTTC-AAAGCCCACAAGTCAGTGGCAA
* *
20533 CCTTCAAAGCCCACAAATCAGTGGCAC
1 CCTTCAAAGCCCACAAGTCAGTGGCAA
* *
20560 CCTTTTCCGAAGCCCACAAGTCGGTGG
1 CC--TT-CAAAGCCCACAAGTCAGTGG
20587 TCTTTTCCAA
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.23
28 10 0.11
29 43 0.45
30 20 0.21
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (27 bp):
CCTTCAAAGCCCACAAGTCAGTGGCAA
Found at i:20598 original size:57 final size:56
Alignment explanation
Indices: 20453--20622 Score: 148
Period size: 57 Copynumber: 2.9 Consensus size: 56
20443 TCACCCTTCA
* * * * *
20453 AAAGTCCACAAGTCAGTGGCATTTTTTTCAAAGCCCACAAGTCAGTGGCA-TTTTTTCG
1 AAAGCCCACAAGTCAGTGG---TCTTTTCAAAGCCCACAAATCAGTGGCACCTTTTCCG
**
20511 AAAGCCCACAAGTCAGTGG-CAACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCG
1 AAAGCCCACAAGTCAGTGGTC--TTTTCAAAGCCCACAAATCAGTGGCA-CCTTTTCCG
* * * *
20569 -AAGCCCACAAGTCGGTGGTCTTTTCCAAAGTCCACAACTCCGTGGCACTCTTTT
1 AAAGCCCACAAGTCAGTGGTCTTTT-CAAAGCCCACAAATCAGTGGCAC-CTTTT
20623 TCTTTTGTAA
Statistics
Matches: 92, Mismatches: 13, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
56 26 0.28
57 41 0.45
58 25 0.27
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.25
Consensus pattern (56 bp):
AAAGCCCACAAGTCAGTGGTCTTTTCAAAGCCCACAAATCAGTGGCACCTTTTCCG
Found at i:20760 original size:85 final size:82
Alignment explanation
Indices: 20656--20870 Score: 310
Period size: 85 Copynumber: 2.6 Consensus size: 82
20646 AGCACTTTTC
20656 AGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCA
1 AGCCCACAAGTTAGTGGCACCC-TTTCAAAGCCCACAAGTCAGTGGCATA-TTTTCAAAAGCCCA
*
20721 CAAGT-AGTGGCAACCTTTAAA
64 C-ACTCA--GGCAACCTTTAAA
20742 AG-CCACAAGTTAGTGGCACCCTGTTCAAAAGCCCACAAGTCAGTGGCATATTTTCAAAAGCCCA
1 AGCCCACAAGTTAGTGGCACCCT-TTC-AAAGCCCACAAGTCAGTGGCATATTTTCAAAAGCCCA
20806 CACTCAGGCAACCTTTAAA
64 CACTCAGGCAACCTTTAAA
* * *
20825 AGCCCACAAGTCAGTGGCAACC-TTCAAAGCCCACAAATCAGTGGCA
1 AGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
20871 CCCTTTAAAG
Statistics
Matches: 121, Mismatches: 4, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
81 20 0.17
82 3 0.02
83 15 0.12
84 20 0.17
85 38 0.31
86 25 0.21
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (82 bp):
AGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATATTTTCAAAAGCCCACA
CTCAGGCAACCTTTAAA
Done.