Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold86
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: 313076
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
File 3 of 3
Found at i:289282 original size:42 final size:41
Alignment explanation
Indices: 289144--289390 Score: 171
Period size: 41 Copynumber: 5.8 Consensus size: 41
289134 CAGGACGCCT
* * *
289144 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTCA
1 TTTCCCTTTTTCCTTTGTCCTCAAAGAGCAGGACACA-TTTA
* * *
289186 TTTCCTTCTTTTCCCTTCTAGTTCTTAAAGAGCAGGACACACTTTA
1 TTTCC--CTTTTTCCTT-T-GTCCTCAAAGAGCAGGACACA-TTTA
*
289232 -TTCTCCTTTTTCCTTTGTCCTCAAAAAGCAGGACACATTTAA
1 TTTC-CCTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTT-A
* * * **
289274 TTTCCC-TTTTCCTTTGTCTTCAAAGGGCATGATGCATTTTA
1 TTTCCCTTTTTCCTTTGTCCTCAAAGAGCAGGACACA-TTTA
* ** * *
289315 TTTCCTTTTTTTCCTTAATCC-CTAAGGAGCAGGACCCATTTCA
1 TTTCC-CTTTTTCCTTTGTCCTC-AAAGAGCAGGACACATTT-A
**
289358 -TTCTCC-TTTTCCTTAATCCTCAAAGAGCAGGAC
1 TTTC-CCTTTTTCCTTTGTCCTCAAAGAGCAGGAC
289391 GTCCCCTTCC
Statistics
Matches: 164, Mismatches: 27, Indels: 29
0.75 0.12 0.13
Matches are distributed among these distances:
41 57 0.35
42 37 0.23
43 26 0.16
44 17 0.10
45 4 0.02
46 23 0.14
ACGTcount: A:0.21, C:0.27, G:0.12, T:0.40
Consensus pattern (41 bp):
TTTCCCTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTA
Found at i:290054 original size:50 final size:49
Alignment explanation
Indices: 289974--290105 Score: 158
Period size: 50 Copynumber: 2.7 Consensus size: 49
289964 TTTCACAATT
* *
289974 TGTATCGATACATTGTTCATCGTATTGATACATTCGGAGTTTTACCCAAA
1 TGTATCGATACATTGTTCATTGTATCGATACATTCGGAG-TTTACCCAAA
* * * * *
290024 TGTATCGATGCATTGTTCATTGTATCGATACATTCTGTGTTTACCTAGA
1 TGTATCGATACATTGTTCATTGTATCGATACATTCGGAGTTTACCCAAA
* * *
290073 TGTATCGATACATT-TGCAATGTATCAATACATT
1 TGTATCGATACATTGTTCATTGTATCGATACATT
290106 TAAGCATTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
48 16 0.23
49 21 0.30
50 34 0.48
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (49 bp):
TGTATCGATACATTGTTCATTGTATCGATACATTCGGAGTTTACCCAAA
Found at i:291956 original size:79 final size:79
Alignment explanation
Indices: 291864--292018 Score: 222
Period size: 79 Copynumber: 2.0 Consensus size: 79
291854 TCATTCATGT
* * *
291864 TTTTATTTCCAAAATACCAATTTTTTACAATCGAAGATACTCCAACCCCGTTATTT-TCGAGGGG
1 TTTTATTTCCAAAACACCAATTTTTCACAATCGAAGATACTCCAACCCCGTTATTTCT-AAGGGG
291928 ATACTCCAACCCCAA
65 ATACTCCAACCCCAA
* * **
291943 TTTTATTTTCAAAACACCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCTAAGGGGA
1 TTTTATTTCCAAAACACCAATTTTTCACAATCGAAGATACTCCAACCCCGTTATTTCTAAGGGGA
*
292008 TACTCTAACCC
66 TACTCCAACCC
292019 TGTTATTTTC
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
79 66 0.99
80 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (79 bp):
TTTTATTTCCAAAACACCAATTTTTCACAATCGAAGATACTCCAACCCCGTTATTTCTAAGGGGA
TACTCCAACCCCAA
Found at i:292007 original size:28 final size:28
Alignment explanation
Indices: 291975--292048 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 28
291965 TTTCATAATC
291975 GGGGATACTCCAACCCCGTTA-TTTCTAA
1 GGGGATACTCCAACCCCGTTATTTTC-AA
* * *
292003 GGGGATACTCTAACCCTGTTATTTTCGA
1 GGGGATACTCCAACCCCGTTATTTTCAA
292031 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
292049 ATTTTATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 36 0.90
29 4 0.10
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTTCAA
Found at i:292024 original size:107 final size:108
Alignment explanation
Indices: 291899--292094 Score: 342
Period size: 107 Copynumber: 1.8 Consensus size: 108
291889 TACAATCGAA
291899 GATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAATTTTATTT-TCAAAACACCAA
1 GATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAATTTTATTTCT-AAAACACCAA
291963 TTTTTCATAATC-GGGGATACTCCAACCCCGTTATTTCTAAGGG
65 TTTTTCATAATCAGGGGATACTCCAACCCCGTTATTTCTAAGGG
* * *
292006 GATACTCTAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAAT
1 GATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAATTTTATTTCTAAAACACCAAT
292071 TTTTCATAATCAGGGGATACTCCA
66 TTTTCATAATCAGGGGATACTCCA
292095 GCTCTGTCGT
Statistics
Matches: 84, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
107 71 0.85
108 13 0.15
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32
Consensus pattern (108 bp):
GATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAATTTTATTTCTAAAACACCAAT
TTTTCATAATCAGGGGATACTCCAACCCCGTTATTTCTAAGGG
Found at i:293175 original size:19 final size:20
Alignment explanation
Indices: 293151--293201 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
293141 TATAATTGTC
293151 CATGTATCGATACAATG-AT
1 CATGTATCGATACAATGCAT
293170 CATGTATCGATACAATGCAT
1 CATGTATCGATACAATGCAT
*
293190 AATGTATCGATA
1 CATGTATCGATA
293202 TATCTGGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATGCAT
Found at i:293915 original size:6 final size:6
Alignment explanation
Indices: 293906--293936 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
293896 AACTTTAAGT
293906 GGGAGG GGGAGG GGGA-G GGGAGG GGGAGG GG
1 GGGAGG GGGAGG GGGAGG GGGAGG GGGAGG GG
293937 AAGGAAGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.16, C:0.00, G:0.84, T:0.00
Consensus pattern (6 bp):
GGGAGG
Found at i:293927 original size:11 final size:11
Alignment explanation
Indices: 293906--293937 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
293896 AACTTTAAGT
293906 GGGAGGGGGAGG
1 GGGA-GGGGAGG
293918 GGGAGGGGAGG
1 GGGAGGGGAGG
293929 GGGAGGGGA
1 GGGAGGGGA
293938 AGGAAGAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.19, C:0.00, G:0.81, T:0.00
Consensus pattern (11 bp):
GGGAGGGGAGG
Found at i:300537 original size:27 final size:27
Alignment explanation
Indices: 300507--300558 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
300497 TTTTATGTGG
300507 AAAAAATAGTATTTTAGTAAATAGTAT
1 AAAAAATAGTATTTTAGTAAATAGTAT
* *
300534 AAAAAATAGTATTTTGGTAAGTAGT
1 AAAAAATAGTATTTTAGTAAATAGT
300559 TTAACTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (27 bp):
AAAAAATAGTATTTTAGTAAATAGTAT
Found at i:303341 original size:17 final size:17
Alignment explanation
Indices: 303295--303343 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
303285 TACTTATTCG
*
303295 TATCTTAAATAAATATT
1 TATCTTAAATAAATATA
*
303312 TA-CTCAAATTAAATATA
1 TATCTTAAA-TAAATATA
303329 TATCTTAAATAAATA
1 TATCTTAAATAAATA
303344 ATAAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 5 0.19
17 17 0.63
18 5 0.19
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (17 bp):
TATCTTAAATAAATATA
Found at i:307025 original size:20 final size:19
Alignment explanation
Indices: 306997--307091 Score: 57
Period size: 20 Copynumber: 4.8 Consensus size: 19
306987 CAAAAACTCA
*
306997 AAATATATCGATACAAAGC
1 AAATGTATCGATACAAAGC
* *
307016 AAATTGTATCGATA-ATTATGG
1 AAA-TGTATCGATACA--AAGC
* * *
307037 GAATATATCGATATAAAGC
1 AAATGTATCGATACAAAGC
* *
307056 AAATTGTATCAATACAAATGG
1 AAA-TGTATCGATACAAA-GC
*
307077 GAATGTATCGATACA
1 AAATGTATCGATACA
307092 TTTACTTATA
Statistics
Matches: 56, Mismatches: 14, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
19 8 0.14
20 40 0.71
21 8 0.14
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.28
Consensus pattern (19 bp):
AAATGTATCGATACAAAGC
Found at i:307043 original size:40 final size:40
Alignment explanation
Indices: 306998--307091 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
306988 AAAAACTCAA
* *
306998 AATATATCGATACAAAGCAAATTGTATCGATA-ATTATGGG
1 AATATATCGATACAAAGCAAATTGTATCAATACA-AATGGG
*
307038 AATATATCGATATAAAGCAAATTGTATCAATACAAATGGG
1 AATATATCGATACAAAGCAAATTGTATCAATACAAATGGG
*
307078 AATGTATCGATACA
1 AATATATCGATACA
307092 TTTACTTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 47 0.98
41 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.29
Consensus pattern (40 bp):
AATATATCGATACAAAGCAAATTGTATCAATACAAATGGG
Found at i:307223 original size:21 final size:20
Alignment explanation
Indices: 307172--307225 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
307162 CATTTGAGAC
*
307172 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTA
*
307192 ATGTATCGATACATTCAGTA
1 ATGTATCGATACATTCACTA
*
307212 ATTGTATTGATACA
1 A-TGTATCGATACA
307226 AATTGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:311452 original size:28 final size:29
Alignment explanation
Indices: 311408--311475 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 29
311398 TAATTTATTT
311408 TTAAAATTTATTC-AA-ATAAATTAAAAA
1 TTAAAATTTATTCAAATATAAATTAAAAA
*
311435 TTAAAAATTTATTTAAATATAAATTAAAAA
1 TT-AAAATTTATTCAAATATAAATTAAAAA
*
311465 TTATAATTTAT
1 TTAAAATTTAT
311476 AATTTATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 10 0.28
29 10 0.28
30 14 0.39
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (29 bp):
TTAAAATTTATTCAAATATAAATTAAAAA
Found at i:311510 original size:36 final size:36
Alignment explanation
Indices: 311440--311511 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
311430 AAAAATTAAA
* *
311440 AATTTATTTAAATATAAATTAAAAATTATAATTTAT
1 AATTTATTTAAATATAAATTAAAAATAAGAATTTAT
* *
311476 AATTTATTTAAGTGA-AAATTAAAAATAAGCATTTAT
1 AATTTATTTAAAT-ATAAATTAAAAATAAGAATTTAT
311512 TTAATACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (36 bp):
AATTTATTTAAATATAAATTAAAAATAAGAATTTAT
Found at i:312823 original size:27 final size:27
Alignment explanation
Indices: 312789--312849 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
312779 TTTTTATATA
312789 ATAAAATTTACATA-ATA-TATATAAAAT
1 ATAAAATTTA-ATATATATTATAT-AAAT
*
312816 ATAAAA-TTAATATATATTATATAATT
1 ATAAAATTTAATATATATTATATAAAT
312842 ATAAAATT
1 ATAAAATT
312850 GCAAGGTCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 3 0.10
26 15 0.50
27 12 0.40
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
ATAAAATTTAATATATATTATATAAAT
Found at i:312921 original size:19 final size:20
Alignment explanation
Indices: 312892--312941 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
312882 CCAAAGATTA
312892 TCTTA-TTTTTTAA-ATAAG
1 TCTTATTTTTTTAACATAAG
* *
312910 TCTTATTTTTTTAACTTAAT
1 TCTTATTTTTTTAACATAAG
312930 TC-TATTTTTTTA
1 TCTTATTTTTTTA
312942 GCTTAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 5 0.18
19 18 0.64
20 5 0.18
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (20 bp):
TCTTATTTTTTTAACATAAG
Done.