Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold616
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: 18748
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1414 original size:33 final size:33
Alignment explanation
Indices: 1372--1434 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1362 TGAGACAATG
1372 TATCGATACAAT-TCCTCATGTATCGATACATTA
1 TATCGATACAATGTCC-CATGTATCGATACATTA
*
1405 TATCGATACAATGTGCCATGTATCGATACA
1 TATCGATACAATGTCCCATGTATCGATACA
1435 AACAATGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (33 bp):
TATCGATACAATGTCCCATGTATCGATACATTA
Found at i:3067 original size:161 final size:159
Alignment explanation
Indices: 2508--3086 Score: 671
Period size: 161 Copynumber: 3.6 Consensus size: 159
2498 AGGTCTAAAC
* * * * *
2508 TTTTTTAAATTCATCAAATATTATTATTTATTTCATATTAATCCAGTTTTCAAAAATTTATTCA-
1 TTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAATTTTTAAAAATTCATTCAT
* * * * * *
2572 TT-CATCAA-TTT-AAATTTTTCCTTGAAATTTTCTTTTTCAAAATACGAAG-TTTGTACTCCAT
66 TTCCATAAATTTTGAATTTTTTCCTTGAAATTTTCTTTTTC-GAATACGGAGTTTTCTACTCCGT
** *
2633 AAATTTTTTCGAAAGGATTTTTCTTTTTTTTA
130 AAATTTTTTCGGGAGAATTTTTC--TTTTTTA
* * * * * *
2665 TTTTTAAAATTCATCAAATCTTATTATTTATTTCATATTAATGCAGTTTCTAAGAATTTATTCAT
1 TTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAATTTTTAAAAATTCATTCAT
2730 TTCCATAAATTTTGAATTTTTTCCTTGAAATTCCTT-TTTTT-GAGATACGGAGTTTTCTACTCC
66 TTCCATAAATTTTGAATTTTTTCCTTGAAATT--TTCTTTTTCGA-ATACGGAGTTTTCTACTCC
*
2793 GTAAATTTTTTCAAGGA-AATTTTTCTTTTTT-
128 GTAAATTTTTTC-GGGAGAATTTTTCTTTTTTA
**** * *
2824 TAAAAAAAATTTATCAAATATTATTATTTA-TTCATAGTAATTC-ATTTTTGAAAAATTCATTCA
1 TTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAATTTTT-AAAAATTCATTCA
* *
2887 TTTCCATAAATTTTGAATTTGTTCCTTGAAATTTTCATTTTTCGAATATGGAGTTTTCTACTCCG
65 TTTCCATAAATTTTGAATTTTTTCCTTGAAATTTTC-TTTTTCGAATACGGAGTTTTCTACTCCG
2952 TAAA-TTTTTCGGGAGAATTTTTTCTAATTTTTA
129 TAAATTTTTTCGGGAGAA-TTTTTCT--TTTTTA
*
2985 TTTTTAAAATTCATTAAATATTATTATTTATTTCAT-TTAATTCAATTTTTAAAAATTCATTCAT
1 TTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAATTTTTAAAAATTCATTCAT
* *
3049 TTCCATGAATTTTGAATTTTTTCCTTGAAATCTTCTTT
66 TTCCATAAATTTTGAATTTTTTCCTTGAAATTTTCTTT
3087 ATCCAAAAAA
Statistics
Matches: 361, Mismatches: 41, Indels: 37
0.82 0.09 0.08
Matches are distributed among these distances:
156 5 0.01
157 70 0.19
158 91 0.25
159 31 0.09
160 18 0.05
161 100 0.28
162 43 0.12
163 3 0.01
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.51
Consensus pattern (159 bp):
TTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAATTTTTAAAAATTCATTCAT
TTCCATAAATTTTGAATTTTTTCCTTGAAATTTTCTTTTTCGAATACGGAGTTTTCTACTCCGTA
AATTTTTTCGGGAGAATTTTTCTTTTTTA
Found at i:3106 original size:320 final size:317
Alignment explanation
Indices: 2514--3139 Score: 796
Period size: 320 Copynumber: 2.0 Consensus size: 317
2504 AAACTTTTTT
* * *
2514 AAATTCATCAAATATTATTATTTATTTCATATTAATCCAGTTTTCAAAAATTTATTCATTCATCA
1 AAATTCATCAAATATTATTATTTATTTCATAGTAATCCAGTTTTCAAAAATTCATTCATTCATAA
*
2579 ATTTAAATTTTTCCTTGAAATTTTCTTTTTCAAAATACGAAGTTTGTACTCCATAAATTTTTTCG
66 ATTTAAATTTTTCCTTGAAATTTTCTTTTTCAAAATACGAAGTTTCTACTCCATAAATTTTTTCG
* ** *
2644 AAAGGATTTTTCTTTTTTTTATTTTTAAAATTCATCAAATCTTATTATTTATTTCATATTAATGC
131 AAAGAATTTTTCTAATTTTTATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATGC
* * * * *** *
2709 AGTTTCTAAGAATTTATTCATTTCCATAAATTTTGAATTTTTTCCTTGAAATTCCTTTTTTTGAG
196 AATTTCTAAAAATTCATTCATTTCCATAAATTTTGAATTTTTTCCTTGAAATTCCTTTATCCAAA
* * * *
2774 ATACGGAGTTTTCTACTCCGT-AAATTTTTTCAAG-GAAATTTTTCTTTTTTTAAAAA
261 AAACGAAGTTTTCTACACCATAAAATTTTTTCAAGAG-AATTTTTCTTTTTTTAAAAA
* * * *
2830 AAATTTATCAAATATTATTATTTA-TTCATAGTAATTCATTTTTGAAAAATTCATTCATTTCCAT
1 AAATTCATCAAATATTATTATTTATTTCATAGTAATCCAGTTTTCAAAAATTCATTCA-TT-CAT
* * * * *
2894 AAATTTTGAATTTGTTCCTTGAAATTTTCATTTTTC-GAATATGGAGTTTTCTACTCCGTAAA-T
64 AAA-TTTAAATTT-TTCCTTGAAATTTTC-TTTTTCAAAATACGAAG-TTTCTACTCCATAAATT
** *
2957 TTTTCGGGAGAATTTTTTCTAATTTTTATTTTTAAAATTCATTAAATATTATTATTTATTTCAT-
125 TTTTCGAAAGAA-TTTTTCTAATTTTTATTTTTAAAATTCATCAAATATTATTATTTATTTCATA
* * * *
3021 TTAATTCAATTTTTAAAAATTCATTCATTTCCATGAATTTTGAATTTTTTCCTTGAAATCTTCTT
189 TTAATGCAATTTCTAAAAATTCATTCATTTCCATAAATTTTGAATTTTTTCCTTGAAAT-TCCTT
*
3086 TATCCAAAAAACTAAGTTTTCTACACCATAAAATTTTTTCAAGAGAATTTTTCT
253 TATCCAAAAAACGAAGTTTTCTACACCATAAAATTTTTTCAAGAGAATTTTTCT
3140 CGATTTAAAA
Statistics
Matches: 263, Mismatches: 37, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
315 28 0.11
316 25 0.10
317 5 0.02
318 8 0.03
319 85 0.32
320 89 0.34
321 22 0.08
322 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.50
Consensus pattern (317 bp):
AAATTCATCAAATATTATTATTTATTTCATAGTAATCCAGTTTTCAAAAATTCATTCATTCATAA
ATTTAAATTTTTCCTTGAAATTTTCTTTTTCAAAATACGAAGTTTCTACTCCATAAATTTTTTCG
AAAGAATTTTTCTAATTTTTATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATGC
AATTTCTAAAAATTCATTCATTTCCATAAATTTTGAATTTTTTCCTTGAAATTCCTTTATCCAAA
AAACGAAGTTTTCTACACCATAAAATTTTTTCAAGAGAATTTTTCTTTTTTTAAAAA
Found at i:3313 original size:2 final size:2
Alignment explanation
Indices: 3306--3330 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3296 ACCAAATATT
3306 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3331 TAGAAACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4860 original size:160 final size:162
Alignment explanation
Indices: 4647--4948 Score: 430
Period size: 160 Copynumber: 1.9 Consensus size: 162
4637 GTAAATTAAA
* * **
4647 TAATATTTATTTTTTCTAATATTTTATATTCCTATGGGCATCTGTTAGGGTATAAAAAATTTCAA
1 TAATATTTATTTTTTCGAATATTTTATATTCCTATGGCCATCTCATAGGGTATAAAAAATTTCAA
* *
4712 AAACCTTTCATATTCTTTCGGGCTTCAATTAGGGTACAAAATGATATTTT-TAAATTAAATAAAA
66 AAACCTTTCATATTCTTTCGGGCTTCAATTAAGGTACAAAATGATATTTTCAAAATTAAATAAAA
4776 TTAAATTAAATTGGTATTATTGGGATAAATTC
131 TTAAATTAAATTGGTATTATTGGGATAAATTC
* ** *
4808 TAATATTTA-TTTTTCGAATCTTTTATATTTTTATGGCCATC-CATAGGGGTATAAAAGATTTCA
1 TAATATTTATTTTTTCGAATATTTTATATTCCTATGGCCATCTCATA-GGGTATAAAAAATTTCA
* * * * *
4871 AAAACCTTTCGTATTTTTTCGGGCTTCCATTAAGGTACGAAATGGTATTTTCAAAATTAAATAAA
65 AAAACCTTTCATATTCTTTCGGGCTTCAATTAAGGTACAAAATGATATTTTCAAAATTAAATAAA
*
4936 ATTAAATTGAATT
130 ATTAAATTAAATT
4949 AATACTTTCC
Statistics
Matches: 123, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
159 2 0.02
160 88 0.72
161 33 0.27
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (162 bp):
TAATATTTATTTTTTCGAATATTTTATATTCCTATGGCCATCTCATAGGGTATAAAAAATTTCAA
AAACCTTTCATATTCTTTCGGGCTTCAATTAAGGTACAAAATGATATTTTCAAAATTAAATAAAA
TTAAATTAAATTGGTATTATTGGGATAAATTC
Found at i:6969 original size:13 final size:13
Alignment explanation
Indices: 6951--6976 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6941 TACACAAAGT
6951 ATGTATCGATACA
1 ATGTATCGATACA
6964 ATGTATCGATACA
1 ATGTATCGATACA
6977 CCAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:6994 original size:34 final size:32
Alignment explanation
Indices: 6935--6997 Score: 90
Period size: 34 Copynumber: 1.9 Consensus size: 32
6925 GCCAAACTTA
**
6935 TATCGATACACAAAGTATGTATCGATACAATG
1 TATCGATACACAAAAAATGTATCGATACAATG
6967 TATCGATACACCAAAAAAATGTATCGATACA
1 TATCGATACA-C-AAAAAATGTATCGATACA
6998 TTAGCTTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 10 0.37
33 1 0.04
34 16 0.59
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (32 bp):
TATCGATACACAAAAAATGTATCGATACAATG
Done.