Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold564
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: 28822
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:6718 original size:20 final size:20
Alignment explanation
Indices: 6695--6748 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
6685 AACTAAGAAG
6695 GAGCTGAATGAGCTAAGGA-T
1 GAGCTGAATGAGCT-AGGATT
* *
6715 GAGCTCAATGAGCTATGATT
1 GAGCTGAATGAGCTAGGATT
6735 GAGCTGAATGAGCT
1 GAGCTGAATGAGCT
6749 TGAAGTAGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.24
Consensus pattern (20 bp):
GAGCTGAATGAGCTAGGATT
Found at i:19271 original size:19 final size:19
Alignment explanation
Indices: 19249--19286 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19239 AACTAGCCAA
19249 GGACAACTCAAGAGTCATT
1 GGACAACTCAAGAGTCATT
19268 GGACAACTCAAGAGTCATT
1 GGACAACTCAAGAGTCATT
19287 TTCTAAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
GGACAACTCAAGAGTCATT
Found at i:21728 original size:24 final size:24
Alignment explanation
Indices: 21704--21750 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
21694 AAACTACTTC
21704 TAAAGAAAACTCAAGAGAGAATTCT
1 TAAAGAAAACTCAA-AGAGAATTCT
*
21729 TAGAGAAAACTCAAAGAGAATT
1 TAAAGAAAACTCAAAGAGAATT
21751 TTCACTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (24 bp):
TAAAGAAAACTCAAAGAGAATTCT
Found at i:26867 original size:27 final size:28
Alignment explanation
Indices: 26837--26900 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 28
26827 ATAATAAAGT
*
26837 ATGTATATAATATGTA-TATATATTAAA
1 ATGTATATAATATATAGTATATATTAAA
* * *
26864 ATGTTTAAAATATATATGTATATATTAAC
1 ATGTATATAATATATA-GTATATATTAAA
*
26893 ATGCATAT
1 ATGTATAT
26901 GCGCACATAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
27 13 0.46
29 15 0.54
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (28 bp):
ATGTATATAATATATAGTATATATTAAA
Found at i:26938 original size:15 final size:13
Alignment explanation
Indices: 26918--26955 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
26908 TATATGTAGG
26918 TATAATAATATATAA
1 TATAATAATA-A-AA
26933 TATAATAATAAAA
1 TATAATAATAAAA
26946 -ATAATAATAA
1 TATAATAATAA
26956 CAAAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
13 2 0.09
14 1 0.04
15 10 0.43
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TATAATAATAAAA
Found at i:26960 original size:15 final size:15
Alignment explanation
Indices: 26934--26967 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
26924 AATATATAAT
*
26934 ATAATAATAAAAATA
1 ATAATAACAAAAATA
*
26949 ATAATAACAAAATTA
1 ATAATAACAAAAATA
26964 ATAA
1 ATAA
26968 AATAGACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAATAACAAAAATA
Found at i:27437 original size:21 final size:21
Alignment explanation
Indices: 27412--27487 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
27402 CATATCTTCT
27412 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
**
27433 TCTAAGATTACATATATCATA
1 TCTAAGATTGTATATATCATA
* *
27454 TCTAGGATTG--CATATCATA
1 TCTAAGATTGTATATATCATA
27473 TCTAAGATTGTATAT
1 TCTAAGATTGTATAT
27488 CCTCGAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 17 0.37
21 29 0.63
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.41
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:27470 original size:19 final size:19
Alignment explanation
Indices: 27425--27488 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
27415 AAGATTGTAT
*
27425 ATATCATATCTAAGATTAC
1 ATATCATATCTAAGATTGC
*
27444 ATATATCATATCTAGGATTGC
1 --ATATCATATCTAAGATTGC
*
27465 ATATCATATCTAAGATTGT
1 ATATCATATCTAAGATTGC
27484 ATATC
1 ATATC
27489 CTCGAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 22 0.56
21 17 0.44
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:27957 original size:132 final size:131
Alignment explanation
Indices: 27780--28300 Score: 889
Period size: 132 Copynumber: 4.0 Consensus size: 131
27770 AGACTTGCTG
* * *
27780 GCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCCCTACT
1 GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACT
*
27845 GCTTAGGGATATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGG
66 GCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGG
27910 T
131 T
* *
27911 GCCTTAAATCTGCTTCCCACTATCTTCGAAAGATAAGATTTTCCGTCTTTGATCTGCTCCACTAC
1 G-CTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTAC
* *
27976 TGCTTAGGGATATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGACACAAGGCTTG
65 TGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTG
28041 GTT
130 G-T
*
28044 GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTCCACTACT
1 GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACT
* *
28109 GCTTAGGGAGATAAGATCTACAATCTTCAACCTAATCCGCTGCTGCTCATGGAGACAAGGCTTGG
66 GCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGG
28174 T
131 T
* *
28175 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGTTTCACTAC
1 -GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTAC
*
28240 TGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTACTCAGGGAGACAAGG
65 TGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGG
28301 TGATGTGACC
Statistics
Matches: 368, Mismatches: 19, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
131 2 0.01
132 364 0.99
133 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (131 bp):
GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACT
GCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGG
T
Found at i:28121 original size:44 final size:44
Alignment explanation
Indices: 27809--28257 Score: 115
Period size: 44 Copynumber: 10.2 Consensus size: 44
27799 TATCTTGGAA
* ** *
27809 AGATAAGATTTGCCGTCTTCGATCTGCTCCCCTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * * * * *
27853 ATATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* ** **** * * **
27897 AGACAAGGCTTGGTGCCTTAAATCTGCTTCCCACTA-T-CTTCGAA
1 AGATAAGATTTGCCATCTTTAATCTGC-T-CCACTACTGCTTAGGG
* * *
27941 AGATAAGATTTTCCGTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * * * * *
27985 ATATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * ** ** * *
28029 ACACAAGGCTTG-GTTGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCAT-CTTTAATCTGC-T-CCACTACTGCTTAGG-G
*
28073 AGATAAGATTTGCCATCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * ** * * * *
28117 AGATAAGATCTACAATCTTCAACCTAATCCGCTGCTGCTCATGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* ** **** * *
28161 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCATCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* * * *
28205 AGATAAGATTTGCCGTCTTTGATCTGTTTCACTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
28249 AGATAAGAT
1 AGATAAGAT
28258 CTACAATCTT
Statistics
Matches: 268, Mismatches: 119, Indels: 36
0.63 0.28 0.09
Matches are distributed among these distances:
42 17 0.06
43 10 0.04
44 218 0.81
45 11 0.04
46 12 0.04
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (44 bp):
AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
Done.